available online at www.studiesinmycology.org doi:10.3114/sim.2011.70.01 Studies in Mycology 70: 1–51. 2011. Phylogeny of Penicillium and the segregation of Trichocomaceae into three families J. Houbraken1,2 and R.A. Samson1 1 CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; 2Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands. *Correspondence: Jos Houbraken, j.houbraken@cbs.knaw.nl Abstract: Species of Trichocomaceae occur commonly and are important to both industry and medicine. They are associated with food spoilage and mycotoxin production and can occur in the indoor environment, causing health hazards by the formation of β-glucans, mycotoxins and surface proteins. Some species are opportunistic pathogens, while others are exploited in biotechnology for the production of enzymes, antibiotics and other products. Penicillium belongs phylogenetically to Trichocomaceae and more than 250 species are currently accepted in this genus. In this study, we investigated the relationship of Penicillium to other genera of Trichocomaceae and studied in detail the phylogeny of the genus itself. In order to study these relationships, partial RPB1, RPB2 (RNA polymerase II genes), Tsr1 (putative ribosome biogenesis protein) and Cct8 (putative chaperonin complex component TCP-1) gene sequences were obtained. The Trichocomaceae are divided in three separate families: Aspergillaceae, Thermoascaceae and Trichocomaceae. The Aspergillaceae are characterised by the formation flask-shaped or cylindrical phialides, asci produced inside cleistothecia or surrounded by Hülle cells and mainly ascospores with a furrow or slit, while the Trichocomaceae are defined by the formation of lanceolate phialides, asci borne within a tuft or layer of loose hyphae and ascospores lacking a slit. Thermoascus and Paecilomyces, both members of Thermoascaceae, also form ascospores lacking a furrow or slit, but are differentiated from Trichocomaceae by the production of asci from croziers and their thermotolerant or thermophilic nature. Phylogenetic analysis shows that Penicillium is polyphyletic. The genus is re-defined and a monophyletic genus for both anamorphs and teleomorphs is created (Penicillium sensu stricto). The genera Thysanophora, Eupenicillium, Chromocleista, Hemicarpenteles and Torulomyces belong in Penicillium s. str. and new combinations for the species belonging to these genera are proposed. Analysis of Penicillium below genus rank revealed the presence of 25 clades. A new classification system including both anamorph and teleomorph species is proposed and these 25 clades are treated here as sections. An overview of species belonging to each section is presented. Key words: Aspergillus, Eupenicillium, nomenclature, Penicillium, Talaromyces, taxonomy. Taxonomic novelties: New sections, all in Penicillium: sect. Sclerotiora Houbraken & Samson, sect. Charlesia Houbraken & Samson, sect. Thysanophora Houbraken & Samson, sect. Ochrosalmonea Houbraken & Samson, sect. Cinnamopurpurea Houbraken & Samson, Fracta Houbraken & Samson, sect. Stolkia Houbraken & Samson, sect. Gracilenta Houbraken & Samson, sect. Citrina Houbraken & Samson, sect. Turbata Houbraken & Samson, sect. Paradoxa Houbraken & Samson, sect. Canescentia Houbraken & Samson. New combinations: Penicillium asymmetricum (Subramanian & Sudha) Houbraken & Samson, P. bovifimosum (Tuthill & Frisvad) Houbraken & Samson, P. glaucoalbidum (Desmazières) Houbraken & Samson, P. laeve (K. Ando & Manoch) Houbraken & Samson, P. longisporum (Kendrick) Houbraken & Samson, P. malachiteum (Yaguchi & Udagawa) Houbraken & Samson, P. ovatum (K. Ando & Nawawi) Houbraken & Samson, P. parviverrucosum (K. Ando & Pitt) Houbraken & Samson, P. saturniforme (Wang & Zhuang) Houbraken & Samson, P. taiwanense (Matsushima) Houbraken & Samson. New names: Penicillium coniferophilum Houbraken & Samson, P. hennebertii Houbraken & Samson, P. melanostipe Houbraken & Samson, P. porphyreum Houbraken & Samson. Introduction The Trichocomaceae comprise a relatively large family of fungi well-known for their impact, both positive and negative, on human activities. The most well-known species of this family belong to the genera Aspergillus, Penicillium and Paecilomyces. Species belonging to Trichocomaceae are predominantly saprobic and represent some of the most catabolically and anabolically diverse microorganisms known. Some species are capable of growing at extremely low water activities (i.e. xerotolerant and/ or osmotolerant), low temperatures (psychrotolerant) and high temperatures (thermotolerant). Members of Trichocomaceae secrete secondary metabolites (extrolites) that are known as mycotoxins (e.g. aflatoxins, ochratoxins, patulin), while other extrolites are used as pharmaceuticals, including antibiotics such as penicillin and the cholesterol-lowering agent lovastatin. Furthermore, members of Trichocomaceae are also known for their production of organic acids and diverse enzymes that degrade a wide variety of complex biomolecules (Geiser et al. 2006, Pitt & Hocking 2009, Samson et al. 2010). The taxon Trichocomaceae was introduced by Fischer (1897) and the classification of this family was studied extensively using phenotypic characters (Malloch & Cain 1972, Subramanian 1972, Malloch 1985a, b, von Arx 1986). These studies include only teleomorph genera because Trichocomaceae is based on Trichocoma, a teleomorph genus, and thus not applicable for anamorph genera (Malloch 1985b). However, it is noted that anamorph genera with phialidic structures are linked to Trichocomaceae (Malloch & Cain 1972). Currently, only the phylogenetic relationships within certain genera of Trichocomaceae, e.g. Aspergillus, Penicillium and Paecilomyces, are elucidated (Peterson 2000a, b, Samson et al. 2004, Peterson 2008, Samson et al. 2009), but the relationships among the genera are still poorly studied. Penicillium is an anamorph genus and belongs phylogenetically to Trichocomaceae (Berbee 1995, Peterson 2000a). The name Penicillium is derived from penicillus, which means “little brush” and was introduced by Link in 1809. Many new species were described in the 19th century, and Dierckx (1901) was the first researcher who introduced a subgeneric classification system for the genus. Copyright 2011 CBS-KNAW Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD Utrecht, The Netherlands. You are free to share - to copy, distribute and transmit the work, under the following conditions: Attribution: You must attribute the work in the manner specified by the author or licensor (but not in any way that suggests that they endorse you or your use of the work). Non-commercial: You may not use this work for commercial purposes. No derivative works: You may not alter, transform, or build upon this work. For any reuse or distribution, you must make clear to others the license terms of this work, which can be found at http://creativecommons.org/licenses/by-nc-nd/3.0/legalcode. Any of the above conditions can be waived if you get permission from the copyright holder. Nothing in this license impairs or restricts the author’s moral rights. 1 Houbraken & Samson He proposed the subgenera Aspergilloides, Biverticillium and Eupenicillium and Biourge (1923) followed Dierckx’s classification system and expanded it with two sections, four series and six subsections. Thom (1930: 155–159) did not accept Dierckx’s and Biourge’s subgeneric classification system and introduced a new system with four divisions (subgenera), 12 sections and 18 subsections (series). His system was mainly based on colony characteristics and conidiophore branching and the monographs of Raper & Thom (1949) and Ramírez (1982) are in line with that of Thom (1930). Pitt (1980) did not follow Thom’s concept and, based on conidiophore characters, phialide shapes and growth characteristics, divided Penicillium into four subgenera, 10 sections and 21 series. In addition, he treated Eupenicillium separately from Penicillium and subdivided the former genus into eight series. In 1985, Stolk & Samson proposed another taxonomic scheme for Penicillium anamorphs and this classification was primary based on phialide shape and conidiophore branching. They divided Penicillium in 10 sections and 18 series and this taxonomic scheme treated strict anamorphs, as well as anamorphs of sexual Penicillium species. More recently, Frisvad & Samson (2004) studied subgenus Penicillium and five sections and 17 series were recognised. The first attempt to make a subgeneric classification of Eupenicillium was undertaken by Pitt (1980) and eight series were introduced. This classification was based on a combination of various characters, such as growth rates in standard conditions, colony morphology and microscopical characters of both teleomorphic and anamorphic states. In the monograph of Stolk & Samson (1983), four sections were introduced for the classification of Eupenicillium, and Pitt’s concept of using series of species was abandoned. To date, only a limited number of studies have investigated the phylogenetic relationship of Penicillium at genus level. Berbee (1995), based of 18S rDNA sequences, demonstrated that Penicillium is polyphyletic. The genus splits up in two clades: one clade includes Talaromyces species and members of the subgenus Biverticillium and the other clade includes Eupenicillium species and Penicillium species accommodated in the subgenera Penicillium, Furcatum and Aspergilloides (LoBuglio & Taylor 1993, LoBuglio et al. 1993, Berbee et al. 1995, Ogawa et al. 1997, Wang & Zhuang 2007). Peterson (2000a) studied the phylogeny of Eupenicillium and members of the subgenera Penicillium, Furcatum and Aspergilloides in more detail. He subsequently divided the studied species in six groups and showed that many subgeneric taxa in Penicillium are polyphyletic. Furthermore, his data indicated that the current classification systems based on conidiophore branching is not congruent with the phylogeny and a new subgeneric classification system is needed. Pleomorphism in fungi was first demonstrated by Tulasne (1851). Together with his discovery, he was already aware of the problem raised by the nomenclature of composite species and he stated that the imperfect forms must someday be submerged in the Ascomycota. He thus established a first principle of pleomorphic nomenclature and suggested the precedence of the perfect state name over imperfect names (Hennebert 1971). In 1910, “dual nomenclature” was introduced and this was established in the International Code of Botanical Nomenclature (ICBN). The problem of naming fungi that exhibit pleomorphic life cycles was addressed in previous versions of article 59 of the ICBN and implied that more than one name for a single taxon can be used (Cline 2005). Recently, the proposal to revise article 59 was accepted at the 2011 IBC Nomenclature Section 2 at Melbourne and the principle of "one fungus : one name" was established (Norvell et al. 2011). In the present study, the phylogenetic relationships between Penicillium and other members of the family Trichocomaceae are studied using a combined analysis of four loci (RPB1, RPB2, Tsr1 and Cct8). In this study, the principle "one fungus - one name" is applied and priority is given to the oldest family, genus and section names using the single-name nomenclature (Hawksworth et al. 2011, Norvell 2011). Penicillium is delimited, various genera are placed in synonymy, and new combinations in Penicillium are made for the species belonging to the genera Thysanophora, Eupenicillium, Chromocleista, Hemicarpenteles and Torulomyces. Subsequently, the phylogeny of Penicillium is studied and a new sectional classification system is proposed. In addition, an overview of species in each section is presented. Material and methods Strains The first part of this study treats the phylogenetic relationships of the Penicillium species among Trichocomaceae. A selection of strains is made in order to study these relationships and in most cases the types of the genera were selected. The second part deals with the phylogeny of Penicillium. For this study, the type species of the various subgenera and sections in Penicillium and Eupenicillium were selected, and this selection is supplemented with other related species. An overview of strains used in the study of the phylogeny of Trichocomaceae and Penicillium presented in Table 1. In the third part of this study, a new sectional classification system for Penicillium is proposed and lists of species in each section are compiled. For the preparation of these lists, mostly type strains were selected of accepted Penicillium and Eupenicillium species. This selection is based on the overview of “accepted species and their synonyms in the Trichocomaceae” by Pitt et al. (2000) and supplemented with species described after 2000. An overview of these strains is shown in Table S1 (Supplementary Information - online only) and partly in Table 1 (species names indicated with two asterisks). All strains are maintained in the CBS-KNAW culture collection and additional strains were obtained from IBT (culture collection of Center for Microbial Biotechnology (CMB) at Department of Systems Biology, Technical University of Denmark), NRRL (ARS Culture Collection, U.S. Department of Agriculture, Peoria, Illinois, USA), ATCC (American Type Culture Collection, Manassas, VA, USA) and IMI (CABI Genetic Resources Collection, Surrey, UK). DNA extraction, amplification and sequencing Genomic DNA was extracted using the Ultraclean Microbial DNA isolation kit (MoBio Laboratories, Carlsbad, CA, USA), according to the manufacturer’s instructions. Parts of the following loci were amplified and sequenced for the species listed in Table 1: 1. RPB1, RNA polymerase II largest subunit (regions E and F; according Matheny et al. 2002), 2. RPB2, RNA polymerase II second largest subunit (regions 5–7), 3. Cct8, subunit of the cytosolic chaperonin Cct ring complex, related to Tcp1p and required for the assembly of actin and tubulins in vivo (Stoldt et al. 1996, Kim et al. 1994), 4. Tsr1, protein required for processing of 20S pre-rRNA in the cytoplasm Phylogeny of Penicillium and Trichocomaceae Table 1. Strains used in phylogenetic analysis of Trichocomaceae and other families. CBS no. Name Other collections Origin RPB1 RPB2 Tsr1 Cct8 CBS 267.72NT Aphanoascus cinnabarinus* ATCC 26215 Soil, Japan JN121625 JN121477 JN121783 JN121903 CBS 172.66 Aspergillus aculeatus* ATCC 16872 = IMI 211388 Tropical soil JN121590 JN121448 JN121755 JN121895 CBS 600.67T Aspergillus amylovorus* ATCC 18351 = IMI 129961 = MUCL 15648 Wheat starch, Kharkiv, Ukraine JN121705 JN121538 JN121844 JN121931 CBS 463.65NT Aspergillus arenarius* ATCC 16830 = IMI 055632 = IMI 055632ii Soil, Mysore, Karnataka, India JN121684 JN121520 JN121825 JN121917 CBS 653.74T Aspergillus aureofulgens* Natural truffle soil, Provence, France JN121712 JN121545 JN121851 JN121936 CBS 109.46NT Aspergillus avenaceus* ATCC 16861 = IMI 016140 = NRRL 517 Seed of Pisum sativum (pea), England, UK JN121565 JN121424 JN121731 JN121878 CBS 468.65NT Aspergillus biplanus* ATCC 16858 = IMI 235602 Soil, Tilaran, Costa Rica JN121685 JN121520 JN121826 JN121917 CBS 707.71T Aspergillus bisporus* ATCC 22527 = NRRL 3693 Soil injected into mouse, Clarksburg, Maryland, USA JN121715 JN121548 JN121854 JN121939 CBS 127.61NT Aspergillus brunneouniseriatus* ATCC 16916 = IMI 227677 Soil under Dalbergia sissoo, India JN121583 JN121442 JN121749 JN121889 CBS 121611 Aspergillus calidoustus* Patient (case 4), man with allogeneic HSCT, probably lung infection, man, Washington, USA JN121579 JN121438 JN121745 JN121887 CBS 566.65NT Aspergillus candidus* ATCC 1002 = IMI 091889 = NRRL 303 Unknown source JN121702 JN121535 JN121841 JN121929 CBS 196.64NT Aspergillus cervinus* ATCC 15508 = IMI 107684 Soil, West Malaysia, Malaysia JN121595 JN121452 JN121759 JN121896 CBS 473.65NT Aspergillus clavatoflavus* ATCC 16866 = IMI 124937 Rain forest soil,Tulley, Queensland, Australia JN121686 JN121521 JN121827 JN121918 Aspergillus clavatus1* NRRL 1 (= ATCC 1007 = CBS 513.65 = IMI 15949) Unknown source Fedorova et al. (2008) CBS 476.65NT Aspergillus conjunctus* ATCC 16796 = IMI 135421 Forest soil, Palmar, Province of Puntarenas, Costa Rica JN121688 JN121523 JN121829 JN121920 CBS 553.77T Aspergillus coremiiformis* ATCC 38576 = 223069 Soil, Ivory Coast JN121700 JN12153 JN121839 JN121926 CBS 656.73NT Aspergillus egyptiacus* IMI 141415 Sandy soil, under Olea europaea (olive tree), Mediterranean Coast, Ras-el-Hikma, Egypt JN121713 JN121546 JN121852 JN121937 CBS 128202 Aspergillus flavus1* NRRL 3357 (= ATCC 200026) Peanut cotyledons, USA Unpublished Aspergillus fumigatus1* Af293 Patient with invasive aspergillosis Nierman et al. (2005) CBS 116.56NT Aspergillus funiculosus* ATCC 16846 = IMI 054397 = IMI 054397ii Soil, Ibadan, Nigeria JN121572 JN121431 JN121738 JN121883 CBS 118.45T Aspergillus janus* ATCC 16835 = IMI 016065 = IMI 016065ii = MUCL 31307 = NRRL 1787 Soil, Panama JN121576 JN121435 JN121742 JN121885 CBS 538.65NT Aspergillus kanagawaensis* ATCC 16143 = IMI 126690 Forest soil under Pinus banksiana, Wisconsin, USA JN121698 JN121531 JN121837 JN121925 CBS 151.66T Aspergillus leporis* ATCC 16490 Dung of Lepus townsendii (white-tailed Jackrabbit ), near Saratoga, Wyoming, USA JN121589 JN121446 JN121753 JN121893 CBS 513.88 Aspergillus niger1* Derived from NRRL 3122 and currently used as enzyme production strain. Pel et al. (2007) T www.studiesinmycology.org GenBank accession or reference1 3 Houbraken & Samson Table 1. (Continued). CBS no. Name Other collections Origin GenBank accession or reference1 RPB1 RPB2 Tsr1 Cct8 CBS 101887 Aspergillus ochraceoroseus* ATCC 42001 = IBT 14580 Soil, Tai National Forest, Ivory Coast JN121557 JN121416 JN121723 JN121871 CBS 108.08NT Aspergillus ochraceus* ATCC 1008 = CBS 547.65 = IMI 016247 = IMI 016247iii = IMI 016247iv = NRRL 1642 = NRRL 398 Unknown source JN121562 JN121421 JN121728 JN121875 CBS 622.67T Aspergillus penicilliformis* ATCC 18328 = IMI 129968 = IMI 132431 Soil under Nicotiana tabacum, Moldavia, Romania JN121708 JN121542 JN121848 JN121934 CBS 130294 Aspergillus penicillioides* DTO 11C3 Indoor environment, Germany JN121578 JN121437 JN121744 JN121886 CBS 578.65NT Aspergillus pulvinus* ATCC 16842 = IMI 139628 Forest soil, Liberia, Province of Guanacaste, Costa Rica JN121703 JN121536 JN121842 JN121930 CBS 117.33NT Aspergillus restrictus* ATCC 16912 = CBS 541.65 = IMI 016267 = MUCL 31313 = NRRL 154 = NRRL 4155 Cloth, UK JN121574 JN121432 JN121740 JN121884 CBS 649.93T Aspergillus robustus* CBS 428.77 = IBT 14305 Surface soil from thornforest, near Mombasa, Kenya JN121711 JN121544 JN121850 JN121935 CBS 139.61NT Aspergillus sparsus* ATCC 16851 = IMI 019394 = IMI 019394ii = MUCL 31314 = NRRL 1933 Soil, Costa Rica JN121586 JN121444 JN121751 JN121891 CBS 112812T Aspergillus steynii* IBT 23096 Dried arabica green coffee bean, on parchment, internal infection, Chamumdeshuran Estata, Karnataka, district Giris, India JN121569 JN121428 JN121735 JN121880 CBS 264.81 Aspergillus sydowii* Grains and milling fractions, Triticum aestivum, India JN121624 JN121476 JN121782 JN121902 Aspergillus terreus1* NIH 2624 Clinical isolate Unpublished CBS 272.89 Aspergillus togoensis* NRRL 13550 Seed, near La Maboké, Central African Republic JN121627 JN121480 JN121785 JN121904 CBS 245.65 Aspergillus versicolor* ATCC 11730 = ATCC 16020 = IMI 045554 = IMI 045554ii = IMI 045554iii = IMI 045554iv = MUCL 19008 Cellophane, Indiana, USA JN121614 JN121468 JN121775 JN121899 CBS 104.07NT Aspergillus wentii* ATCC 1023 = IMI 017295 = IMI 017295ii = NRRL 1269 = NRRL 375 Soybeans, Java, Indonesia JN121559 JN121418 JN121725 JN121873 CBS 506.65NT Aspergillus zonatus* ATCC 16867 = IMI 124936 Forest soil, Province of Linon, Fortuna, Costa Rica JN121691 JN121526 JN121832 JN121921 CBS 380.74T Basipetospora halophilica* IFO 9650 Undaria pinnatifida (Wakame), Osaka, Japan JN121666 JN121509 JN121815 JN121910 CBS 100.11NT Byssochlamys nivea* ATCC 22260 Unknown source JN121511 JF417414 JF417381 JF417514 CBS 101075 Byssochlamys spectabilis* ATCC 90900 = FRR 5219 Heat processed fruit beverage; Tokyo Japan JN121554 JF417446 JF417412 JF417546 CBS 605.74T Byssochlamys verrucosa* ATCC 34163 Nesting material of Leipoa ocellata (Malleefowl), Pulletop Nature Reserve, New South Wales, Australia JN680311 JN121540 JN121746 JN121932 T 4 Phylogeny of Penicillium and Trichocomaceae Table 1. (Continued). CBS no. Name Other collections Origin GenBank accession or reference1 RPB1 RPB2 Tsr1 Cct8 CBS 132.31T Chrysosporium inops* IMI 096729 = UAMH 802 Skin man, Italy JN121584 JN121443 JN121750 JN121890 Coccidioides immitis1* Strain “RS” Vaccine strain - origin unknown Sharpton et al. (2009) CBS 525.83T Cristaspora arxii* ATCC 52744 = FMR 416 Soil, Tarragona, Spain JN121695 JN121529 JN121835 JN121924 CBS 157.66NT Dichotomomyces cejpii* Orchard soil, near Tiraspol, Moldova JN121589 JN121447 JN121754 JN121894 Emericella nidulans1* FGSC A4 (= ATCC 38163 = CBS 112.46) Unknown source Galagan et al. (2005) CBS 229.60T Eupenicillium hirayamae* ATCC 18312 = IMI 078255 = IMI 078255ii = NRRL 143 Milled rice, Thailand JN121604 JN121459 JN121766 JN121946 CBS 518.65NT Eurotium amstelodami* ATCC 16464 = IMI 229971 = NRRL 90 Unknown substrate JN121694 JN121528 JN121834 JN121923 CBS 516.65NT Eurotium herbariorum* ATCC 16469 = IMI 211383 = NRRL 116 Unpainted board, Washington, USA JN121693 JN121527 JN121833 JN121922 CBS 260.73T Fennellia flavipes* ATCC 24484 = IMI 171883 = NRRL 5504 Cellulose material buried in forest soil, Pak Thong Chai, Thailand JN121623 JN121475 JN121781 JN121901 CBS 252.87T Geosmithia viridis* IMI 288716 Soil; bank of creek flowing into Little River; New South Wales; Australia JN121620 JF417422 JF417389 JF417522 CBS 295.48IsoT Hamigera avellanea* ATCC 10414 = IMI 040230 = NRRL 1938 Soil; San Antonio, Texas, USA JN121632 JF417424 JF417391 JF417524 CBS 377.48NT Hamigera striata* ATCC 10501 IMI 039741 = NRRL 717 Canned blueberries, USA JN121665 JN121508 JN121814 JN121909 CBS 527.65T Hemicarpenteles paradoxus* ATCC 16918 = IMI 061446 = NRRL 2162 Dung of Opossum, Wellington, New Zealand JN121696 JN121530 JN121836 JN121989 CBS 607.74T Leiothecium ellipsoideum* ATCC 32453 Soil, between rocks, Mystras, Peloponnesos, Greece JN121707 JN121541 JN121847 JN121933 CBS 109402T Monascus argentinensis* FMR 7393 Soil sample, El Infiernillo, Tafi del Valle, Tucumán province, Argentina JN121564 JN121423 JN121730 JN121877 CBS 113675 Monascus lunisporas* FMR 6679 Soil sample, Corcovado Mountain, Tijuca National Park, Rio de Janeiro, Brazil JN121570 JN121429 JN121736 JN121881 CBS 109.07T Monascus purpureus* ATCC 16365 = ATCC 16426 = IMI 210765 = NRRL 1596 Fermented rice grain, ‘ang-quac’ (purple coloured rice), KagokTegal, imported from China, Prov. Quouantoung, Java, Indonesia JN121563 JN121422 JN121729 JN121876 CBS 558.71T Neocarpenteles acanthosporum* ATCC 22931 = IMI 164621 Soil, Bougainville Island, Solomon Islands JN121701 JN121534 JN121840 JN121928 Neosartorya fischeri* NRRL 181 Canned fruit CBS 350.66 Paecilomyces aerugineus* IMI 105412 Debris of Glyceria maxima, Attenborough, Notts., UK JN121657 JN121502 JN121808 JN121907 CBS 761.68 Penicilliopsis clavariiformis* CSIR 1135 Unknown source, Pretoria, South Africa JN121716 JN121549 JN121855 JN121940 CBS 246.67HT Penicillium abidjanum** ATCC 18385 = FRR 1156 = IMI 136244 Savannah soil, near Abidjan, Ivory Coast JN121615 JN121469 JN121777 JN121954 CBS 209.28LT Penicillium adametzii* ATCC 10407 = IMI 039751 = MUCL 29106 = NRRL 737 Soil under conifers, Poznan, Poland JN121598 JN121455 JN121762 JN121944 T www.studiesinmycology.org 5 Houbraken & Samson Table 1. (Continued). CBS no. Name Other collections Origin RPB1 RPB2 Tsr1 Cct8 CBS 317.67HT Penicillium alutaceum** ATCC 18542 = FRR 1158 = IFO 31728 = IMI 136243 Soil, near Pretoria, South Africa JN121641 JN121489 JN121795 JN121968 CBS 220.66IsoT Penicillium arenicola* ATCC 18321 = ATCC 18330 = IMI 117658 = NRRL 3392 Soil from pine forest, Kiev, Ukraine JN121601 JN121457 JN121764 JN121897 CBS 241.56NT Penicillium atrovenetum** ATCC 13352 = FRR 2571 = IFO 8138 = IMI 061837 Soil, Sussex Downs, England JN121614 JN121467 JN121774 JN121953 CBS 299.48AUT Penicillium camemberti** ATCC 1105 = ATCC 4845 = FRR 878 = IBT 21508 = IMI 027831 = IMI 092200 = MUCL 29790 = NRRL 877 = NRRL 878 French Camembert cheese, Connecticut, USA JN121635 JN121484 JN121790 JN121963 CBS 300.48NT Penicillium canescens* ATCC 10419 = IMI 028260 = MUCL 29169 = NRRL 910 Soil, England JN121636 JN121485 JN121791 JN121964 CBS 233.81 Penicillium caperatum FRR 71 = IMI 216895 Neotype of E. brefeldianum; soil, Murrumbidgee Irrigation Area, N.S.W., Australia JN121610 JN121465 JN121772 JN121952 CBS 352.67HT Penicillium catenatum* ATCC 18543 = IMI 136241 Desert soil, Upington, Cape Province, South Africa JN121659 JN121504 JN121810 JN121980 CBS 304.48T Penicillium charlesii* ATCC 8730 = CBS 342.51 = IMI 040232 = NRRL 1887 = NRRL 778 Unknown source, UK JN121637 JN121486 JN121792 JN121965 CBS 306.48NT Penicillium chrysogenum** ATCC 10106 = FRR 807 = IBT 5233 = IMI 024314 = IMI 092208 = MUCL 29079 = MUCL 29145 = NRRL 807 = NRRL 810 Cheese, Storrs, Connecticut JN121638 JN121487 JN121793 JN121966 Penicillium chrysogenum1* Wisconsin 54-1255 Moldy cantaloupe Peoria, Illinois, USA van den Berg et al.(2008) CBS 490.66 Penicillium cinnamopurpureum* ATCC 18337 = IMI 114483 Type of E. cinnamopurpureum; cultivated soil, South Africa JN121690 JN121525 JN121831 JN121988 CBS 258.29NT Penicillium citreonigrum* ATCC 48736 = 092209 Rotting stem, Belgium = MUCL 28648 = MUCL 29062 = MUCL 29116 = NRRL 761 JN121622 JN121474 JN121780 JN121957 CBS 139.45NT Penicillium citrinum* ATCC 1109 = IMI 091961 = MUCL 29781 = NRRL 1841 Unknown JN121585 JF417416 JF417383 JF417516 CBS 232.38 Penicillium citrinum** Thom 4733.73 Type of P. implicatum; unknown source, Belgium JN121608 JN121463 JN121770 JN121950 CBS 119387T Penicillium coffeae* IBT 27866 = NRRL 35363 Peduncle, Coffea arabica, Oahu, Aiea, Hawaii, USA JN121577 JN121436 JN121743 JN121862 CBS 231.38 Penicillium corylophilum** ATCC 10452 = IFO 7726 = IMI 039817 = NRRL 872 Type of P. humuli; Humus lupulus (hops), Weihenstephan, Germany JN121606 JN121461 JN121768 JN121948 CBS 271.89HT Penicillium cryptum* ATCC 60138 = IMI 296794 = NRRL 13460 Soil from QuercusBetula forest, Hempstead Lake State Park, Long Island, New York JN121626 JN121478 JN121784 JN121958 6 GenBank accession or reference1 Phylogeny of Penicillium and Trichocomaceae Table 1. (Continued). CBS no. Name Other collections Origin RPB1 RPB2 Tsr1 Cct8 CBS 660.80T Penicillium dendriticum* IMI 216897 Leaf litter of Eucalyptus pauciflora, Kosciusko National Park, New South Wales, Australia JN121714 JN121547 JN121853 JN121938 CBS 112082epiT Penicillium digitatum** IBT 13068 Citrus limon, Italy JN121567 JN121426 JN121733 JN121858 CBS 456.70T Penicillium dimorphosporum* ATCC 22783 = ATCC 52501 = FRR 1120 = IMI 149680 Mangrove swamp soil, below high tide level, Tooraddin, Westernport Bay, Sawtell’s Inlet, Victoria, Australia JN121683 JN121517 JN121823 JN121985 CBS 322.48AUT Penicillium duclauxii* ATCC 10439 = IMI Canvas, France 040044 = MUCL 28672 = MUCL 29094 = MUCL 29212 = NRRL 1030 JN121643 JN121491 JN121797 JN121905 CBS 112493T Penicillium ellipsoideosporum** AS 3.5688 Banyan seeds, Pingxiang, Guanbxi Province, China (data after Wang et al. 2007) JN121568 JN121427 JN121734 JN121859 CBS 318.67HT Penicillium erubescens** ATCC 18544 = FRR 814 = IFO 31734 = IMI 136204 Nursery soil, Pretoria, South Africa JN121642 JN121490 JN121796 JN121969 CBS 323.71NT Penicillium euglaucum* Soil, Argentina JN121644 JN121492 JN121798 JN121970 CBS 325.48 Penicillium expansum* ATCC 7861 = IBT 5101 = IMI 039761= MUCL 29192 = NRRL 976 Fruit of Malus sylvestris; USA JN121645 JF417427 JF417394 JF417527 CBS 229.81NT Penicillium fellutanum** ATCC 10443 = CBS 326.48 = FRR 746 = IFO 5761 = IMI 039734 = IMI 039734iii = NRRL 746 Unknown source, USA JN121605 JN121460 JN121767 JN121947 CBS 124.68T Penicillium fractum* ATCC 18567 = FRR 3448 = IMI 136701 = NRRL 3448 Soil, Univ. Shinshu, Ueda-shi, Nagano Pref, Japan JN121582 JN121441 JN121748 JN121864 CBS 295.62NT Penicillium fuscum** ATCC 14770 = IFO 7743 = IMI 094209 = MUCL 31196 = NRRL 3008 = WSF 15c Type of E. pinetorum and neotype of Citromyces fuscus; pine-birch forest soil, Vilas County, Wisconsin, USA JN121633 JN121483 JN121789 JN121962 CBS 125543NT Penicillium glabrum* IBT 22658 = IMI 91944 Unknown JN121717 JF417447 JF417413 JF417547 CBS 599.73T Penicillium gracilentum* ATCC 28047 = ATCC 48258 = IMI 216900 Soil, Brown River, Port Moresby, Central Dist., Papua New Guinea JN121704 JN121537 JN121843 JN121990 CBS 185.27NT Penicillium griseofulvum* ATCC 11885 = IBT 6740 = IMI 075832 = IMI 075832ii = MUCL 28643 = NRRL 2152 = NRRL 2300 Unknown source, Belgium JN121592 JN121449 JN121756 JN121865 CBS 277.58T Penicillium griseolum* ATCC 18239 = IMI 071626 = NRRL 2671 Acidic dune sand, Dorset, Stufland, England JN121629 JN121480 JN121786 JN121959 CBS 336.48NT Penicillium herquei** ATCC 10118 = FRR 1040 = IFO 31747 = IMI 028809 = MUCL 29213 = NRRL 1040 Leaf, France JN121647 JN121494 JN121800 JN121972 CBS 341.68T Penicillium idahoense* ATCC 22055 = IMI 148393 Soil, Latàh Co., Univ. of Idaho Plant Science Farm, Idaho, USA JN121652 JN121499 JN121805 JN121976 CBS 351.67T Penicillium inusitatum* ATCC 18622 = IMI 136214 Forest soil, Knysna Valley, Cape Province, South Africa JN121658 JN121503 JN121809 JN121979 www.studiesinmycology.org GenBank accession or reference1 7 Houbraken & Samson Table 1. (Continued). CBS no. Name Other collections Origin RPB1 RPB2 Tsr1 Cct8 CBS 247.56NT Penicillium isariiforme* ATCC 18425 = IMI 060371 = MUCL 31191 = MUCL 31323 = NRRL 2638 Woodland soil, Zaire JN121616 JN121470 JN121720 JN121993 CBS 338.48NT Penicillium islandicum* ATCC 10127 = IMI 040042 = MUCL 31324 = NRRL 1036 Unknown source, Cape Town, South Africa JN121648 JN121495 JN121801 JN121906 CBS 339.48NT Penicillium italicum** ATCC 10454 = FRR 983 = IBT 23029 = IMI 039760 = MUCL 15608 = NRRL 983 Fruit, Citrus Experiment Station, Riverside, California, USA JN121649 JN121496 JN121802 JN121973 CBS 340.48NT Penicillium janthinellum* ATCC 10455 = IMI 040238 = NRRL 2016 Soil, Nicaragua JN131650 JN121497 JN121803 JN121974 CBS 341.48T Penicillium javanicum* ATCC 9099 = FRR 707 = IMI 039733 = MUCL 29099 = NRRL 707 Type of P. javanicum, E. javanicum and P. indonesiae; root of Camellia sinensis (green tea), Buitenzorg, Java, Indonesia JN121651 JN121498 JN121804 JN121975 CBS 247.67T Penicillium katangense* ATCC 18388 = IMI 136206 = NRRL 5182 Soil, Katanga, Zaire JN121618 JN121471 JN121777 JN121955 CBS 344.61T Penicillium kewense* ATCC 18240 = IMI 086561= MUCL 2685 = NRRL 3332 Culture contaminant of mineral oil, Kew, Surrey, England, UK JN121654 JF417428 JF417395 JF417528 CBS 106.11NT Penicillium lanosum* ATCC 10458 = IMI 040224 = MUCL 29232 = NRRL 2009 Unknown source, Germany JN121561 JN121420 JN121727 JN121857 CBS 343.48T Penicillium lapidosum* ATCC 10462 = IMI 039743 = NRRL 718 Canned blueberry, Washington, USA JN121653 JN121500 JN121806 JN121977 CBS 277.70T Penicillium lassenii* ATCC 22054 = IMI 148395 Soil under conifers, Tehama Co., Lassen National Forest, 1300 m alt., California, USA JN121630 JN121481 JN121787 JN121960 CBS 116871T Penicillium macrosclerotiorum* AS 3.6581 Soil, Chongqing, Wushan County, Sichuang Province, China JN121573 JN121432 121739 JN121860 CBS 647.95HT Penicillium malachiteum* IBT 17515 Soil, Nihondaira Pref. Park, Shimizu-shi, Shimizu-ken, Japan JN121710 JN121543 JN121849 JN121991 Penicillium marneffei1* ATCC 18224 (CBS 334.59 = IMI 68794) Bamboo rat (Rhizomys sinensis); Vietnam Unpublished CBS 256.55NT Penicillium megasporum* ATCC 12322 = IMI 216904 = NRRL 2232 Heath soil,Suffolk, England JN121621 JN121473 JN121779 JN121900 CBS 642.68NT Penicillium minioluteum* IMI 089377 = MUCL 28666 Unknown JN121709 JF417443 JF417409 JF417543 CBS 353.48NT Penicillium namyslowskii* ATCC 11127 = IMI 040033 = MUCL 29226 = NRRL 1070 Soil under Pinus sp.; Puszcza Bialowieska, Poland JN121660 JF417430 JF417397 JF417530 CBS 203.84HT Penicillium nepalense** NHL 6482 Rice soil, Boudha, Kathmandu, Nepal JN121596 JN121453 JN121760 JN121868 CBS 489.66T Penicillium ochrosalmoneum* ATCC 18338 = IMI 116248ii Type of E. ochrosalmoneum; cornmeal, South Africa JN121689 JN121524 JN121830 JN121987 CBS 232.60NT Penicillium olsonii* IBT 23473 = IMI 192502 Root, Picea abies, alt. 1980 m., Pitztal, Austria JN121609 JN121464 JN121771 JN121952 CBS 190.68T Penicillium ornatum* ATCC 18608 = IMI 137977 = NRRL 3471 Soil, Moto-machi, Oshima Islands, Japan JN121594 JN121451 JN121758 JN121867 CBS 462.72HT Penicillium osmophilum** IBT 14679 Agricultural soil, Wageningen, the Netherlands JN121683 JN121518 JN121824 JN121986 8 GenBank accession or reference1 Phylogeny of Penicillium and Trichocomaceae Table 1. (Continued). CBS no. Name Other collections Origin RPB1 RPB2 Tsr1 Cct8 CBS 219.30NT Penicillium oxalicum** ATCC 1126 = FRR 787 = IMI 192332 = MUCL 29047 = NRRL 787 Soil, Connecticut JN121600 JN121456 JN131763 JN121944 CBS 251.56T Penicillium ramusculum* ATCC 12292 = IMI 063546 = NRRL 3459 Culture contaminant, Brazil JN121620 JN121472 JN121778 JN121956 CBS 367.48NT Penicillium restrictum** ATCC 11257 = FRR 1748 = IMI 040228 = NRRL 1748 Soil, Honduras JN121662 JN121506 JN121812 JN121981 CBS 231.61NT Penicillium sacculum (syn. Eladia saccula)* ATCC 18350 = IMI 051498 Soil, Madrid, Spain JN121607 JN121462 JN121769 JN121949 CBS 122276T Penicillium saturniforme** AS 3.6886 Soil, Jiling Province, China JN121580 JN121439 JN121746 JN121863 CBS 290.48T Penicillium shearii* ATCC 10410 = IMI 039739 = IMI 039739iv = NRRL 715 Soil, Tela, Honduras JN121631 JN121482 JN121788 JN121961 CBS 228.89T Penicillium shennangjianum** AS 3.4526 Mouldy pea, Hubei Province, Shennongjia, China JN121603 JN121458 JN121766 JN121945 CBS 372.48NT Penicillium simplicissimum* ATCC 10495 = IFO 5762 = IMI 039816 Flannel bag, Cape, South Africa JN121662 JN121507 JN121813 JN121981 CBS 315.67T Penicillium stolkiae* ATCC 18546 = IMI 136210 Peaty forest soil, Eastern Transvaal, South Africa JN121640 JN121488 JN121794 JN121967 CBS 117503T Penicillium thiersii* IBT 27050 = NRRL 28162 Old, black stroma, encrusting the surface of dead Acer saccharum log, alt. 300 m., New Glarus Woods State Park, Wisconsin, USA JN121575 JN121434 JN121741 JN121861 CBS 347.59 Penicillium thomii** IFO 6031 = IMI 068221 Type of P. thomii var. flavescens; soil, Japan JN121655 JN121501 JN121807 JN121978 CBS 430.69T Penicillium tularense* ATCC 22056 = IMI 148394 Soil, under Pinus ponderosa and Quercus kelloggii, Tulare Co., Pine Flat, California JN121681 JN121516 JN121822 JN121984 CBS 603.74NT Penicillium verrucosum** ATCC 48957 = FRR 965 = IBT 12809 = IBT 4733 = IMI 200310 = IMI 200310ii = MUCL 28674 = MUCL 29089 = MUCL 29186 = NRRL 965 Unknown source, Belgium JN121706 JN121539 JN121845 JN121991 CBS 390.48NT Penicillium viridicatum** ATCC 10515= IBT 23041 = IMI 039758 = IMI 039758ii = NRRL 963 Air, District of Columbia, Washington D.C., USA JN121668 JN121511 JN121817 JN121983 CBS 430.64IsoT Phialomyces macrosporus* ATCC 16661 = IMI 110130 = MUCL 9776 Soil, near Rotorua, New Zealand JN121680 JN121515 JN121821 JN121915 CBS 128032T Phialosimplex caninus* UAMH 10337 Bone marrow aspirate ex dog, San Antonio, Texas, USA JN121587 JN121445 JN121752 JN121892 CBS 109945T Phialosimplex chlamydosporus* FMR 7371 = IMI 387422 Disseminated infection in a dog JN121566 JN121425 JN121732 JN121879 CBS 366.77T Phialosimplex sclerotialis* IAM 14794 Fodder of ray-grass and lucerne, France JN121661 JN121505 JN121811 JN121908 CBS 384.61T Polypaecilum insolitum* ATCC 18164 = IMI 075202 = MUCL 3078 Ear of human, Leeds, Yorkshire, England, UK JN121667 JN121510 JN121816 JN121911 CBS 101166 Polypaecilum pisci* Yeast extract, Netherlands JN121555 JN121415 JN121722 JN121870 CBS 101.69T Rasamsonia argillacea* Mine tip with a very high surface temperature; Staffordshire, UK JN121556 JF417415 JF417382 JF417515 www.studiesinmycology.org DTO 97E4 = IMI 156096 = IBT 31199 GenBank accession or reference1 9 Houbraken & Samson Table 1. (Continued). CBS no. Name Other collections Origin RPB1 RPB2 Tsr1 Cct8 CBS 413.71T Rasamsonia byssochlamydoides* DTO 149D6 = IBT 11604 Dry soil under Douglas fir; Oregon, USA JN121675 JF417437 JF417403 JF417537 CBS 275.58NT Rasamsonia cylindrospora* DTO 138F8 = IBT 31202 = ATCC 18223 = IMI 071623 Culture contaminant; Berkshire, England, UK JN121628 JF417423 JF417390 JF417523 CBS 393.64T Rasamsonia emersonii* DTO 48I1 = IBT 21695 = ATCC 16479 = IMI 116815 = IMI 116815ii Compost; Italy JN121670 JF417434 JF417401 JF417534 CBS 114.72IsoT Sagenoma viride* ATCC 22467 = NRRL 5575 Soil, Australia JN121571 JN121430 JN121737 JN121882 CBS 545.86T Sagenomella bohemica* CCF 2330 = IAM 14789 Peloids for balneological purposes, Frantiskovy Lázne Spa, West Bohemia, Czech Republic JN121699 JN121532 JN121838 JN121927 CBS 398.69 Sagenomella diversispora* Forest soil under Populus tremuloides; Petawawa, Ontario, Canada JN121673 JF417435 JF417402 JF417536 CBS 399.69 Sagenomella diversispora* MUCL 15012 Forest soil under Thuja occidentalis, Aberfoyle, Ontario, Canada JN121674 JN121513 JN121819 JN121913 CBS 426.67 Sagenomella griseoviridis* ATCC 18505 = IMI 113160 Unknown source JN121677 JF417438 JF417404 JF417538 CBS 427.67IsoT Sagenomella humicola* ATCC 18506 = IMI 113166 Forest soil under Thuja occidentalis; Ontario, Canada JN121678 JF417439 JF417405 JF417539 CBS 429.67IsoT Sagenomella striatispora* ATCC 18510 = IMI 113163 Soil; Guelph, Ontario, Canada JN121679 JF417440 JF417406 JF417540 CBS 414.78T Sagenomella verticillata* IAM 14697 Conifer forest soil, Sweden JN121676 JN121514 JN121820 JN121914 CBS 124.53NT Sclerocleista ornata* ATCC 16921 = IMI 055295 = MUCL 15643 = NRRL 2256 Soil in oak forest, Dane Co., Madison, Wisconsin, USA JN121581 JN121440 JN121747 JN121888 CBS 105.25 Sclerocleista thaxteri* IMI 055296 = NRRL 2292 Dung of caterpillar, USA JN121560 JN121419 JN121726 JN121874 CBS 296.48T Talaromyces bacillisporus* ATCC 10126 = IMI 040045 = NRRL 1025 Begonia leaf; New York City, New York, USA JN121634 JF417425 JF417392 JF417525 CBS 100537T Talaromyces convolutus* IBT 14989 Soil, Kathmandu, Nepal JN121553 JN121414 JN121721 JN121869 CBS 100536 Talaromyces emodensis* IBT 14990 Soil; Kathmandu, Nepal JN121552 JF417445 JF417411 JF417545 CBS 310.38NT Talaromyces flavus* IMI 197477 = NRRL 2098 Unknown substrate; New Zealand JN121639 JF417426 JF417393 JF417526 CBS 398.68T Talaromyces leycettanus* ATCC 22469 = IMI 178525 Coal spoil tip soil; Leycett, Staffordshire, England, UK JN121672 JF417435 JF417402 JF417535 CBS 348.51NT Talaromyces luteus* IMI 089305 Soil, UK JN121656 JF417429 JF417396 JF417529 CBS 475.71 Talaromyces purpureus* ATCC 24069 = ATCC 52513 = FRR 1731 = IMI 181546 Soil, near Esterel, France JN121687 JN121522 JN121828 JN121919 Talaromyces stipitatus1* ATCC 10500 (= NRRL 1006 = CBS 375.48 = IMI 39805) Rotting wood; Louisiana, USA Unpublished CBS 236.58T Talaromyces thermophilus* ATCC 10518 = IMI 048593 = NRRL 2155 Parthenium argentatum, decaying plant; California, USA JN121611 JF417420 JF417387 JF417520 CBS 373.48T Talaromyces trachyspermus* ATCC 10497 = IMI 040043 = NRRL 1028 Unknown source, USA JN121664 JF417432 JF417399 JF4174532 CBS 391.48NT Talaromyces wortmanii* ATCC 10517 = IMI 040047 = NRRL 1017 Unknown source JN121669 JF417433 JF417400 JF417533 CBS 891.70 Thermoascus aurantiacus* IMI 173037 Wood; Firenze, Italy JN121719 JF417444 JF417410 JF417544 T IsoT 10 GenBank accession or reference1 Phylogeny of Penicillium and Trichocomaceae Table 1. (Continued). CBS no. Name Other collections Origin GenBank accession or reference1 RPB1 RPB2 Tsr1 Cct8 CBS 396.78 Thermoascus aurantiacus* JCM 12816 Sawdust, in lumber yard, Toronto, Ontario, Canada JN121671 JN121512 JN121818 JN121912 CBS 181.67T Thermoascus crustaceus* ATCC 16462 = IMI 126333 Parthenium argentatum, decaying plant; Salinas, California, USA JN121591 JF417417 JF417384 JF417517 CBS 528.71NT Thermoascus thermophilus* IMI 123298 = NRRL 5208 Wood and bark of Pinus; Sweden JN121697 JF417442 JF417408 JF417542 CBS 218.34 Thermomyces lanuginosus* MUCL 8338 Fruit shell of Theobroma cacao JN121599 JF417418 JF417385 JF417518 CBS 224.63 Thermomyces lanuginosus* MUCL 8337 Mushroom compost; Gossau-Zürich Switzerland JN121602 JF417419 JF417386 JF417519 CBS 334.68T Thysanophora canadensis* ATCC 18741 = IMI 137644 = MUCL 21216 Needle of Tsuga canadensis, Bell’s Corners, Ontario, Canada JN121647 JN121493 JN121799 JN121971 CBS 206.57T Thysanophora taxi* ATCC 18484 = MUCL 11402 Litter, Berlin, Germany JN121597 JN121454 JN121761 JN121942 CBS 185.65 Torulomyces lagena* MUCL 8221 Bog soil under Thuja plicata, Guelph, Ontario, Canada JN121593 JN121450 JN121757 JN121866 CBS 247.57 Trichocoma paradoxa* MUCL 39666 = IBT 31159 Unknown source; Hachijô, Japan JN121617 JF417421 JF417388 JF417521 CBS 103.73 Trichocoma paradoxa* Unknown source, Japan JN121558 JN121417 JN121724 JN121872 CBS 788.83 Trichocoma paradoxa* Rotting stump of cut down tree, Myojoji Temple near Hakui Noto Park, Ishikawa Pref., Japan JN121718 JN121550 JN121856 JN121941 CBS 512.65NT Warcupiella spinulosa* ATCC 16919 = IMI 075885 = NRRL 4376 Jungle soil; BerakasMuara, Brunei JN121692 JF417441 JF417407 JF417541 CBS 236.71T Xeromyces bisporus* IMI 063718 Mouldy stick of liquorice, JN121612 Homebush, New South Wales, Australia JN121466 JN121773 JN121898 1 Sequences derived from published full genome data. * Strains used in the study of Trichocomaceae (Fig. 1); ** Strains used in for the preparation of Figs 1 and 7. CBS, culture collection of the CBS-KNAW Fungal Biodiversity Centre, Utrecht, Netherlands (WDCM 133) http://www.cbs.knaw.nl/databases/index.htm; DTO, internal culture collection of CBS-KNAW Fungal Biodiversity Centre; IMI, CABI Genetic Resources Collection, Surrey, UK (WDCM 214) http://www.cabi.org/; IBT, culture collection of Center for Microbial Biotechnology (CMB) at Department of Systems Biology, Technical University of Denmark (WDCM 758) http://www.biocentrum.dtu.dk/; NRRL, ARS Culture Collection, U.S. Department of Agriculture, Peoria, Illinois, USA (WDCM 97) http://nrrl.ncaur.usda.gov/; ATCC, American Type Culture Collection, Manassas, VA, USA (WDCM 1) http://www.atcc.org/; MUCL, Mycotheque de l’Universite catholique de Louvain, Leuven, Belgium (WDCM 308). (Gelperin et al. 2001, Léger-Silvestre et al. 2004). Partial RPB2 data was obtained for the majority of species listed in Table S1. Exceptions are strains used in the study of Houbraken et al. (2011c); in that case, published partial β-tubulin sequences were used. The RPB1 fragment was amplified using the primer pair RPB1-F1843 and R3096, and RPB1-R2623 was occasionally used as an internal primer for sequencing. A part of the RPB2 locus was amplified using the primer pair RPB2-5F and RPB2-7CR (Liu et al. 1999) or the primer pair RPB2-5F_Eur and RPB2-7CR_Eur. The internal sequencing primers RPB2-F311 and RPB2-R310 were occasionally used when poor results were obtained with the regular forward and reverse primers. Amplification of a part of the Cct8 gene was performed using the primer pair Cct8-F660 and Cct8-R1595. No amplicons could be obtained in the case of 5–10 % of the analysed strains. In those cases, amplicons were generated using the primer pair Cct8-R1595 and Cct8-F94. A part www.studiesinmycology.org of the Tsr1 gene was amplified using the forward primers Tsr1F1526Pc or Tsr1-F1526 in combination with Tsr1-R2434. Annealing temperatures and primers used for amplification and sequencing are shown in Table 2. The PCR reactions were performed in 25 μL reaction mixtures containing 1 μL genomic DNA 2.5 μL PCR buffer, 0.75 µL MgCl2 (50 mM), 16.55 μL demineralised sterile water, 1.85 μL dNTP (1 mM), 0.50 μL of each primer (100 mM) and 0.1 μL Taq polymerase (5 U/ μL, BioTaq, Bioline). The PCR program typically was: 5 cycles of 30 s denaturation at 94 °C, followed by primer annealing for 30 s at 51 °C, and extension for 1 min at 72 °C; followed by 5 cycles with an annealing temperature at 49 °C and 30 cycles at 47 °C, finalised with an extension for final 10 min at 72 °C. Excess primers and dNTP’s were removed from the PCR product using the QIAQuick PCR purification kit (Qiagen). Purified PCR fragments were resuspended in 30–50 μL of water. PCR products were sequenced directly in both directions with the same primers and DYEnamic 11 Houbraken & Samson Table 2. Primers used in this study for amplification and sequencing. Locus Primer Sequence (5’–3’) Annealing ( °C) Fragment size (bp) References Cct8 F94 (Fwd) CGCAAC AAGATYGTBATYAACCA 50–52 F94-R1595: 1400–1450 Houbraken et al. 2011d F660 (Fwd) GIGTKGTBAAGATCATGGGWGG F660-R1595: 850–890 Houbraken et al. 2011d ca. 1000 This study RPB1 RPB2 Tsr1 R1595 (Rev) RTCMACRCCNGTIGTCCAGTA F1843 (Fwd) ATTTYGAYGGTGAYGARATGAAC R3096 (Rev) GRACRGTDCCRTCATAYTTRACC This study R2623 GCRTTGTTSARATCCTTMARRCTC This study 5F GAYGAYMGWGATCAYTTYGG 7CR CCCATRGCTTGYTTRCCCAT Liu et al. 1999 5F_Eur (Fwd) GAYGAYCGKGAYCAYTTCGG Houbraken et al. 2011d 48–51 ca. 1220 Liu et al. 1999 7CR_Eur (Rev) CCCATRGCYTGYTTRCCCAT Houbraken et al. 2011d F311 CATGATYCARCGIAAYATGGA This study R310 CCATRTTICGYTGRATCATGAA F1526Pc (Fwd) GARTAYCCBCARTCNGAGATGT F1626 (Fwd) GARTAYCCBCARTCNGAIATGT This study R2434 (Rev) ASAGYTGVARDGCCTTRAACCA Houbraken et al. 2011d ET Terminator Cycle Sequencing Kit (Amersham Bioscience, Roosendaal, The Netherlands). The cycle sequencing reaction mixture had a total reaction volume of 10 μL, and contained 1 μL of template DNA, 0.85 µL BigDye reagent, 3 μL buffer, 4.75 µL demineralised water and 0.4 μL primer (10 mM). Sequencing products were purified according to the manufacturers’ recommendations with Sephadex G-50 superfine columns (Amersham Bioscience, Roosendaal, The Netherlands) in a multiscreen HV plate (Millipore, Amsterdam, The Netherlands) and with MicroAmp Optical 96-well reaction plate (AB Applied Biosystems, Nieuwerkerk a/d Yssel, The Netherlands). Contigs were assembled using the forward and reverse sequences with the programme SeqMan from the LaserGene package (DNAStar Inc., Madison, WI). Phylogenetic analysis The protein coding nucleotide sequences were translated into amino acid data prior to alignment and subsequently aligned using the Muscle software in the MEGA5 package. After aligning, the amino acid data were translated into nucleotide data and used in the phylogenetic analysis. Combined sequence data sets were used in the study on the phylogeny of Trichocomaceae and Penicillium. Before combining the data sets, each data set was analysed using RAxML (Stamatakis et al. 2008). The number of bootstrap runs was set to 100. The program compat.py (from http://www.lutzonilab.net) was used to detect major topological incongruences among single gene data sets (Kauff & Lutzoni 2002). Conflicts were considered significant when a sequence was differentially resolved between two gene trees with greater than 70 % bootstrap support. If no conflicts were detected, then the data sets were combined. Statistical support was measured by Maximum Likelihood (ML) analysis using the RAxML (randomised axelerated maximum likelihood) software (Stamakis et al. 2008). The robustness of trees in the ML analyses was evaluated by 1000 bootstrap replications. A second measure for statistical support was performed by Bayesian tree inference (BI) analysis using MrBayes v. 3.1.2 (Ronquist & Huelsenbeck 2003). Prior to analysis, the most suitable substitution model was determined using MrModeltest v. 2.3 (Nylander 2004), utilising the Akaike Information Criterion (AIC). The Bayesian 12 Houbraken et al. 2011d 48–53 This study 48–50 ca. 820 Houbraken et al. 2011d analysis was performed with two sets of four chains (one cold and three heated) and the stoprule option, stopping the analysis at an average standard deviation of split frequencies of 0.01. The sample frequency was set to 100; the first 25 percent of trees were removed as burnin. The phylograms obtained with the RAxML analysis were used for presenting the data. Bootstrap values lower than 70 % were considered unreliable because their wide range of error and Bayesian posterior probabilities are considered unreliable below 0.95 (Murphy et al. 2001, Wilcox et al. 2002, Alfaro & Holder 2006). Therefore, only posterior probability (pp) values higher than 0.95 and bootstrap (bs) values higher than 70 % were plotted on those phylograms. Coccidioides immitis (strain RS), a member of Onygenales, was chosen to root the phylogram used in the study on the relationships of Penicillium species among Trichocomaceae. Penicillium (= Talaromyces) marneffei ATCC 18227T was selected as an outgroup for the analysis of the phylogeny of Penicillium. Various phylograms were prepared for assignment of species to sections. All data sets were based on partial RPB2 sequences and rooted with Talaromyces flavus CBS 310.38NT, with exception of the phylogram of sections Lanata-divaricata and Stolkia, which is based on partial β-tubulin data. Penicillium glabrum CBS 125543T was used as an outgroup. RESULTS Phylogeny of Trichocomaceae A phylogenetic study using four combined loci (RPB1, RPB2, Cct8 and Tsr1) was conducted to determine the relationship among members of Trichocomaceae. A total of 157 species were included in the analysis and the total length of the alignment was 3 111 characters, 1 939 of those characters were variable. The length of the Cct8, Tsr1, RPB1 and RPB2 partitions were 714, 669, 768, 960 base pairs long, respectively. The GTR+I+G model was optimal for all four partitions. The result of the analysis is shown in Fig. 1 and indicates that Trichocomaceae can be divided into three lineages. Lineage 1 is divided into seven clades (clades 1–7) and these clades are on a well-supported branch (100 % bs, 1.00 pp). The type species Phylogeny of Penicillium and Trichocomaceae Table 3. Details of each analysis of the data sets used for generating Figs 8, 10–13. Figure Clades, acc. Fig. 7 Locus No. isolates Length alignment Best-fit model 8 1, 2, 3 RPB2 50 916 SYM+I+G 10 6, 7, 10 and 13 RPB2 69 916 GTR+I+G 11 11, 12 β-tubulin 45 528 HKY+I+G 12 5, 14 RPB2 44 849 SYM+I+G 13 15–25 RPB2 86 916 GTR+I+G of the genera Chromocleista (C. malachitea), Eladia (E. saccula), Eupenicillium (E. crustaceum), Hemicarpenteles (H. paradoxus), Penicillium (P. expansum), Thysanophora (T. penicillioides) and Torulomyces (T. lagena) belong to clade 1. This clade is named Penicillium sensu stricto and is divided into two subclades: clade 1A and 1B. The types of subgenera Aspergilloides and Furcatum are accommodated in clade 1A and the type of subgenus Penicillium belongs to clade 1B. Clade 2 is moderately supported (< 70 % bs, 1.00 pp) and contains the type species of the genera Aspergillus (A. glaucus), Cristaspora (C. arxii), Phialosimplex (P. caninus), Polypaecilum (P. insolitum) and the teleomorphs of Aspergillus (Fennellia, Eurotium, Emericella, Neocarpenteles, Dichotomyces, Neosartorya, Sclerocleista). Not all teleomorph genera of Aspergillus are represented in our analysis; however, previous data has shown the genera Chaetosartorya, Neopetromyces and Petromyces also belong to this lineage (Peterson 2008). This clade is subdivided into six groups. Four of the six groups represent the Aspergillus subgenera as defined by Peterson (2008). In addition, also Aspergillus section Cremei and a clade with Phialosimplex and Polypaecilum are present. Clade 3 comprises the type species of Hamigera (H. avellanea), Warcupiella (W. spinosa) and Raperia (R. spinulosa) but this clade is poorly supported (< 70 % bs, < 0.95 pp). Clade 4 contains P. clavariiformis, the type species Penicilliopsis. The type species of the genera Basipetospora (B. rubra), Fraseriella (F. bisporus), Leiothecium (L. ellipsoideum), Monascus (M. ruber), Xeromyces (X. bisporus) cluster together in clade 5. Phialomyces (P. macrosporus) and Sclerocleista (S. ornata) belong to clade 6 and 7, respectively. Lineage 2 is subdivided into two clades: the type species of Thermoascus, Coonemeria and Dactylomyces belong to clade 8, and the types of the genera Byssochlamys (B. nivea) and Paecilomyces (P. variotii) belong to clade 9. The posterior probability value indicates a strong relationship between these two clades (0.99); however, the maximum likelihood analysis resulted in a bootstrap value lower than 70 % (67 %). The posterior probability and bootstrap values are also contradictory regarding the relationship between lineages 1 and 2 (< 70 % bs, 1.00 pp). Lineage 3 is subdivided into five clades (clades 10–14) and these clades are on a strongly supported branch (100 % bs, 1.00 pp). Clade 10 is centered on the type species of Talaromyces, T. flavus, and the type species of Sagenoma (S. viride) also belongs in this clade. The type species of Thermomyces (T. lanuginosus), Sagenomella (S. diversispora), Rasamsonia (R. emersonii) and Trichocoma (T. paradoxa) belong in clades 11–14, respectively. Phylogeny of Penicillium sensu stricto The phylogenetic relationship among members of Penicillium s. str. was studied using the same four combined loci (RPB1, RPB2, Cct8 and Tsr1). In total, 72 strains were included in the analysis and the total length of the alignment was 3 393 characters, and 1 805 of them were variable. Penicillium (= Talaromyces) marneffei was www.studiesinmycology.org used as an outgroup. The length of the Cct8, Tsr1, RPB1 and RPB2 partitions were 723, 759, 955, 957 base pairs, respectively. The best-fit model GTR+I+G was optimal for all four partitions. The result of the analysis is shown in Fig. 7 and confirms the result above that Penicillium s. str. can be divided into two distinct lineages. Similarly, the type species of subgenus Aspergilloides, P. aurantiobrunneum (= P. glabrum) and Furcatum (P. citrinum), belong to lineage 1 and the type of subgenus Penicillium belongs to lineage 2. Lineage 1 is subdivided in 14 clades (Fig. 7). These clades (1–14) were in most cases supported with a bootstrap value higher than 95 % and a posterior probability of 1.00. Lineage 2 is subdivided into 11 clades (15–25). Clades 20–25 are on well-supported branches; however, the overall bootstrap and posterior probability values of clades 15–19 are low. The numbering of the clades is therefore based on the analysis of the partial β-tubulin data in Samson et al. (2004), because well-supported clades (sections) were present in that phylogenetic treatment. Five separate phylograms (Figs 8, 10–13) were prepared in order to determine which species belong to which clade (section). Details of these analyses are summarised in Table 3. Discussion Part One: Phylogenetic analysis of Trichocomaceae Choice of genes Parts of the RPB1, RPB2, Tsr1 and Cct8 genes were only used for the construction of the phylogenetic relationships among members of Trichocomaceae and Penicillium species, and the ability of these genes for species recognition remains largely unexplored. The regions E and F (according Matheny et al. 2002) of the RPB1 gene were analysed. No additional sequence data of Trichocomaceae were published on this part of the RPB1 gene and comparison with other studies is therefore difficult. The regions 5–7 of the RPB2 gene are commonly used in taxonomic studies of Penicillium and Aspergillus and proved to be a good marker for species recognition (e.g. Peterson 2008, Serra et al. 2008, Peterson & Horn 2009, Peterson et al. 2010, Barreto et al. 2011). However, RPB1 and RPB2, as well as TEF1α, β-tubulin, and γ-actin, were not found among the best performing genes for fungal systematics (Aguileta et al. 2008). Aguileta et al. (2008) studied, using a bioinformatics approach, the performance of single-copy protein-coding genes for fungal phylogenetics. Their analyses of 30 published fungal genomes revealed that MCM7 (= MS456), Tsr1 (= MS277) and Cct8 (= FG610) were among the best single-copy genes in phylogenetic utility. MCM7, the best gene for recovering a largerscale phylogeny across fungal groups, was excluded in the current study since it was not variable enough within the genus Penicillium (Marthey et al. 2008). Tsr1 and Cct8 were also used in other (phylogenetic) studies of groups belonging to Trichocomaceae 13 Houbraken & Samson CBS 209.28LT Penicillium adametzii CBS 229.60T Eupenicillium hirayamae */* CBS 647.95HT Chromocleista malachita CBS 117503HT Penicillium thiersii */92 */62 CBS 125543NT Penicillium glabrum */* */55 CBS 119387HT Penicillium coffeae CBS 304.48T Penicillium charlesii CBS 277.58T Penicillium griseolum */* CBS 334.68T Thysanophora canadensis 0.98/53 CBS 206.57 206 57T Thysanophora taxi 0.97/*/* CBS 489.66T Eupenicillium ochrosalmoneum 0.95/CBS 247.56T Penicillium isariiforme */* CBS 251.56T Penicillium ramusculum CBS 190.68T Eupenicillium ornatum */* CBS 341.68T Eupenicillium idahoense CBS 490.66T Eupenicillium cinnamopurpureum */* CBS 353.48T Geosmithia namyslowskii -/*/* CBS 343.48T Eupenicillium lapidosum CBS 247.67T Eupenicillium katangense */92 -/88 CBS 258.29NT Penicillium citreonigrum g */* CBS 352.67T Eupenicillium catenatum T 0.97/68 CBS 456.70 Penicillium dimorphosporum */88 CBS 340.48NT Penicillium janthinellum -/*/* CBS 341.48T Eupenicillium javanicum */* CBS 372.48NT Penicillium simplicissimum CBS 315.67T Eupenicillium stolkiae */78 */* CBS 116871T Penicillium macrosclerotiorum */95 CBS 599.73T Eupenicillium gracilentum */* CBS 351.67T Eupenicillium inusitatum CBS 124.68T Eupenicillium fractum */* / CBS 139.45 139 45T Penicillium citrinum */81 */* CBS 290.48T Eupenicillium shearii CBS 323.71NT Eupenicillium euglaucum */86 CBS 271.89T Eupenicillium cryptum CBS 185.65 Torulomyces lagena CBS 277.70T Eupenicillium lassenii Penicillium s. str. */88 */* */* Wisconsin 54-1255 Penicillium chrysogenum -/CBS 344.61T Eupenicillium crustaceum */* CBS 185.27NT Penicillium griseofulvum */* CBS 325.48NT Penicillium expansum CBS 527.65T Hemicarpenteles paradoxus */* */* CBS 232.60NT Penicillium olsonii */* */* CBS 430.69T Eupenicillium tularense CBS 106.11T Penicillium lanosum */99 CBS 231.61NTEladia saccula (=Penicillium sacculum) CBS 300.48NT Penicillium canescens */* CBS 272.89 Aspergillus togoensis */* CBS 553.77T Aspergillus coremiiformis */99 NRRL 3357 Aspergillus flavus */* CBS 151.66T Aspergillus leporis CBS 109.46NT Aspergillus avenaceus 0.96/*/* / CBS 108.08 108 08NT Aspergillus ochraceus CBS 112812T Aspergillus steynii */99 CBS 649.93T Aspergillus robustus 0.94/*/* CBS 260.73T Fennellia flavipes 1.00/CBS 653.74T Aspergillus aureofulgens Incl. sections Circumdati, Flavi, 1.00/93 NIH 2624 Aspergillus terreus Candidi, Flavipedes, Nigri, 0.96/T CBS 118.45 Aspergillus janus */99 Terrei CBS 566.65NT Aspergillus candidus CBS 463.65NT Aspergillus arenarius */77 T -/- */* CBS 172.66 Aspergillus aculeatus CBS 513.88 Aspergillus niger */ */*/* CBS 245.65 Aspergillus versicolor */99 CBS 264.81 Aspergillus sydowii 0.98/51 FGSC A4 Emericella nidulans CBS 600.67T Aspergillus amylovorus */* CBS 656.73NT Aspergillus egyptiacus */98 */96 Incl. sections Nidulantes, Usti, CBS 121611 Aspergillus calidoustus */82 Ochraceorosei, Sparsi, (Aeni) CBS 707.71T Aspergillus bisporus */96 CBS 101887 Aspergillus ochraceoroseus */59 */* CBS 116.56T Aspergillus funiculosus */90 CBS 139.61NT Aspergillus sparsus CBS 468.65 468 65NT Aspergillus biplanus */85 CBS 476.65NT Aspergillus conjunctus */* NRRL 1NT Aspergillus clavatus */90 CBS 558.71T Neocarpenteles acanthosporus */* CBS 157.66NT Dichotomomyces cejpii */* NRRL 181NT Neosartorya fischeri Incl. sections Fumigati, Clavati */96 Af293 Aspergillus fumigatus and Cervini NT */* */51 CBS 538.65 Aspergillus kanagawaensis CBS 196.64NT Aspergillus cervinus Aspergillus s. str. -/53 */95 Clade 1 Penicillium s. str. Clade 1A: subgenus Aspergilloides Clade 1B: subgenus P i illi Penicillium Clade 2 Aspergillus s. str. subgenus Circumdati subgenus Nidulantes subgenus Fumigati Fig. 1. Best-scoring Maximum Likelihood tree using RAxML based on combined data set of partial Cct8, Tsr1, RPB1 and RPB2 sequences showing the relationship among members of Trichocomaceae. The BI posterior probabilities (pp) values and bootstrap (bs) percentages of the maximum likelihood (ML) analysis are presented at the nodes (pp/bs). Values less than 50 % supported in the ML or less than 0.90 in the Bayesian analysis are indicated with a hyphen, whereas asterisks indicate full support (100 % bs or 1.00 pp). The branches with more than 95 % bootstrap support and 1.00 posterior probability values are thickened. The bar indicates the number of substitutions per site. The tree is rooted with Coccidioides immitis (strain RS). 14 Phylogeny of Penicillium and Trichocomaceae */* Clade 2, ctd Aspergillus s. str. CBS 109945T Phialosimplex chlamydosporus CBS 128032T Phialosimplex canicus CBS 380.74T Basipetospora halophilica */* */* CBS 384.61T Polypaecilum insolitum */* CBS 101166 Polypaecilum yp p pisci -/CBS 366.77T Phialosimplex sclerotialis NT */89 CBS 578.65 Aspergillus pulvinus */94 CBS 525.83T Cristaspora arxii */97 CBS 104.07NT Aspergillus wentii CBS 127.61NT Aspergillus brunneo-uniseriatus */64 */* CBS 516.65NT Eurotium herbariorum */77 CBS 518.65NT Eurotium amstelodami */* CBS 117.33NT Aspergillus restrictus Lineage 1 Incl. sections DTO 11C3 Aspergillus penicillioides Aspergillaceae */* CBS 622.67T Aspergillus penicilliformis -/*/* / 295 48IsoT Hamigera avellanea CBS 295.48 -/CBS 256.55NT Penicillium megasporum -/CBS 512.65NT Warcupiella spinulosa */94 CBS 377.48NT Hamigera striata 0.92/CBS 398.68T Talaromyces leycettanus */* CBS 761.68 Penicilliopsis clavariiformis CBS 506.65NT Aspergillus zonatus */* CBS 113675 Monascus lunisporas */99 CBS 109402T Monascus argentinensis */85 0.98/68 CBS 109.07T Monascus purpureus */* CBS 236.71T Xeromyces bisporus */* */57 CBS 132.31T Chrysosporium inops CBS 607.74T Leiothecium ellipsoideum -/CBS 473.65NT Aspergillus clavatoflavus */* CBS 430.64IsoT Phialomyces macrosporus */95 CBS 220.66IsoT Penicillium arenicola */* CBS 124.53NT Sclerocleista ornata CBS 105.25 Sclerocleista thaxteri */97 CBS 181.67T Thermoascus crustaceus */91 CBS 528.71NT Thermoascus thermophilus */* CBS 605.74T Byssochlamys verrucosa */* CBS 396.78 396 78 Thermoascus aurantiacus CBS 891.70 Thermoascus aurantiacus */* CBS 101075T Byssochlamys spectabilis (=Paecilomyces variotii) 0.99/67 CBS 100.11NT Byssochlamys nivea */* ATCC 18224T Penicillium marneffei */97 CBS 322.48AUT Penicillium duclauxii Lineage 2 */90 CBS 310.38NT Talaromyces flavus */85 Thermoascaceae CBS 414.78T Sagenomella verticillata */89 CBS 252.87T Geosmithia viridis 0.93/77 CBS 114.72IsoT Sagenoma viride */* ATCC 10500IsoT Talaromyces stipitatus */* CBS 545.86 545 86T Sagenomella S ll b bohemica h i */* CBS 350.66T Paecilomyces aerugineus NT */* CBS 267.72 “Aphanoascus cinnabarinus” */* CBS 642.68NT Penicillium mineoluteum */* CBS 373.48T Talaromyces trachyspermus */94 CBS 100537T Talaromyces convolutus */* */* CBS 475.71IsoT Talaromyces purpureus CBS 660.80T Penicillium dendriticum */99 CBS 100536T Talaromyces emodensis */88 CBS 296.48T Talaromyces bacillisporus */75 */* CBS 338.48NT Penicillium islandicum CBS 391.48NT Talaromyces wortmanii */* CBS 218.34 Thermomyces lanuginosus */* CBS 224.63 Thermomyces lanuginosus */99 CBS 236.58T Talaromyces thermophilus 0.98/72 CBS 348.51 Talaromyces luteus */* CBS 399.69 Sagenomella diversispora */93 CBS 398.69 Sagenomella diversispora */* CBS 426.67 Sagenomella griseoviride */* */* CBS 429.67IsoT Sagenomella striatispora CBS 427.67IsoT Sagenomella humicola */99 CBS 393.64 393 64T Rasamsonia emersonii Lineage 3 0.92/76 CBS 413.71T Rasamsonia byssochlamydoides Trichocomaceae */* CBS 101.69T Rasamsonia argillacea */97 CBS 275.58NT Rasamsonia cylindrospora CBS 247.57 Trichocoma paradoxa */* CBS 788.83 Trichocoma paradoxa CBS 103.73 Trichocoma paradoxa Strain “RS” Coccidioides immitis 0.99/- */* Phialosimplex & Polypaecilum Aspergillus section Cremei subgenus Aspergillus Restricti, Aspergillus Clade 3: Hamigera, Warcupiella Clade 4: Penicilliopsis Clade 5: Monascus, Xeromyces Leiothecium Clade 6: Phialomyces Clade 7: Sclerocleista Clade 8: Thermoascus Clade 9: Byssochlamys/Paecilomyces Clade 10:Talaromyces s. str. Clade 11: Thermomyces Clade 12: Sagenomella Clade 13: Rasamsonia Clade 14: Trichocoma 0.1 Fig. 1. (Continued). (López-Villavicencio et al. 2010, Peterson et al. 2010). Analysis of the Tsr1 gene generated the best resolved trees, when compared with Cct8, MCM7 and ITS (López-Villavicencio et al. 2010). The sequenced parts of the RPB1, RPB2, Tsr1 and Cct8 genes mainly contain exons, and the alignment of these loci is therefore www.studiesinmycology.org unambiguous. This is the main advantage over ITS regions where alignment above genus can be difficult. Furthermore, the ITS region is generally considered unreliable as a phylogenetic marker, especially above genus rank. β-tubulin and calmodulin sequences are often used in taxonomical studies of Penicillium, Paecilomyces 15 Houbraken & Samson and Aspergillus (e.g. Samson et al. 2004, Houbraken et al. 2007, Samson et al. 2009, Varga et al. 2011). However, a large part of these genes consists of intron data and these regions cannot be aligned above genus level, resulting in loss of information in these data sets. In addition, there is evidence that β-tubulins are present in the genome in multiple copies and thus have the potential of being phylogenetically misleading (Landvik et al. 2001, Peterson 2008). Phylogenetic analysis of Trichocomaceae Three lineages are recognised in Trichocomaceae (Fig. 1) and we propose to treat these three lineages as distinct families: Trichocomaceae, Aspergillaceae and Thermoascaceae. Lineage 1 corresponds with Aspergillaceae and this name is the oldest available family name within the analysed group of related genera. Malloch & Cain (1972) did not accept this family name since it was based on the asexual (anamorph) form-genus Aspergillus and therefore not applicable for ascomycete perfect (sexual) states. Because we are applying a single-name system and give priority to the oldest name, the family name Aspergillaceae is re-instated. Phylogenetically, Monascaceae belong to Aspergillaceae and this is in agreement with other studies that show that Monascus (type genus of Monascaceae) is related to Penicillium and/or Aspergillus (Berbee et al. 1995, Ogawa et al. 1997, Ogawa & Sugiyama 2000, Peterson 2008, Pettersson et al. 2011). In contrast, Stchigel et al. (2004), who used ITS sequence data to determine the molecular relationships of Monascaceae taxa, concluded that Monascus and Xeromyces form a well-supported, monophyletic clade (81 % bs), separate from Eurotiales (Stchigel & Guarro 2007). These contradictory results can be explained by a deeper taxon sampling in this study combined with a phylogeny based on sequences of four protein-coding genes instead of ITS sequences alone. The Thermoascaceae (= lineage 2) were introduced by Apinis (1967) and typified by Thermoascus. Lineage 3 corresponds to Trichocomaceae and this family was introduced by Fischer (1897) (as Trichocomataceae) and is typified by Trichocoma. The Eurotiaceae were placed in synonymy with this family because the name Trichocomaceae predates Eurotiaceae (Malloch & Cain 1972). The current analysis shows that Eurotiaceae (type genus Eurotium) should be placed in synonymy with Aspergillaceae. The family names Hemicarpenteleaceae, Penicilliopsidaceae, Phialomycetaeae, Warcupiellaceae, Xeromycetaceae and Talaromycetaceae were introduced by Locquin (1972, 1984) but all lack a Latin description and are invalidly published. Phenotypic classification and delimitation of Aspergillaceae, Trichocomaceae and Thermoascaceae Several studies on the classification of Trichocomaceae and Eurotiales based on phenotypic characters were published (Malloch & Cain 1972, Fennell 1973, Benny & Kimbrough 1980, Malloch 1985a, b, von Arx 1987) and an overview of selected studies is shown in Table 4. Some of these classifications differ significantly from each other. We compared the results of these studies with the current proposed phylogenetic classification and this showed that our phylogenetic classification largely corresponds with the phenotypic classification described by Malloch (1985a, b). Malloch (1985a, b) divided Trichocomaceae into two subfamilies, Trichomoideae and Dichlaenoideae, based on phenotypic characters including cleistothecial initials, peridium, ascus structure and ascospore morphology. Malloch’s list of genera belonging to Dichlaenoideae largely corresponds with the genera 16 we place in Aspergillaceae and his definition of Trichomoideae is comparable with our phylogenetically defined Trichocomaceae. There are two main differences: a) Monascus is treated here in Aspergillaceae and b) the genera Byssochlamys and Thermoascus are accommodated in Thermoascaceae; these were treated by Malloch (1985a, b) in Trichomoideae and Dichlaenoideae, respectively. Using the characters proposed by Malloch in his classification, Aspergillaceae are characterised by the production of asci inside cleistothecia, stromata, or are surrounded by Hülle cells and mainly have oblate to ellipsoidal ascospores with a furrow or slit. The conidia are mostly formed on flask shaped or cylindrical phialides. The Trichocomaceae are defined by having asci borne within a tuft or layer of loose hyphae, and ascospores are lacking slits or furrows. The phialides of species belonging to this family are mostly lanceolate or cylindrical. Apinis (1967) introduced Thermoascaceae and noted that the common essential character of genera of this family is the production of firm, somewhat sclerotioid, pseudoparenchymatous cleistothecia. The inclusion of Byssochlamys in this family does not fit in that description because it produces almost naked ascomata. Based on the relative branch length in Fig. 1, another possibility would be to delimit the Thermoascus clade (clade 8) and the Byssochlamys/ Paecilomyces clade (clade 9) as separate families. However, there are characters shared by Thermoascus and Byssochlamys including the production of asci in croziers and the formation of smooth or finely roughened ascospores lacking a furrow or slit. The relationship between these two genera is also illustrated by Byssochlamys verrucosa and Thermoascus crustaceus. Byssochlamys verrucosa phenotypically belongs to Byssochlamys, but is positioned phylogenetically in Thermoascus (Fig. 1) and Therm. crustaceus shares a Paecilomyces anamorph with members of the Byssochlamys/Paecilomyces clade. In addition, most members of both genera are thermotolerant or thermophilic. The genera Chaetosartorya, Cristaspora, Dichlaena, Dichotomomyces, Eupenicillium, Edyuillia, Emericella, Eurotium, Hamigera, Hemicarpenteles, Hemisartorya, Neosartorya, Penicilliopsis, Petromyces, Sclerocleista, Thermoascus and Warcupiella were placed by Malloch (1985 a, b) in Aspergillaceae (as subfamily Dichlaenoideae). The majority of these genera are also included in our classification, and exceptions are Edyuilla, which is synonymised with Eurotium (von Arx 1974) and Thermoascus, which is classified in Thermoascaceae. The main difference is the placement of Monascaceae is Aspergillaceae. Benny & Kimbrough (1980) placed the genera Ascorhiza, Leiothecium, Monascus and Xeromyces in Monascaceae and suggested a relationship with Ascosphaerales. Later, several authors included this family in Pezizales (Malloch 1981, Hawksworth & Pitt 1983). Von Arx (1987), in his revision of Eurotiales, included Monascus in Onygenaceae, and reduced Monascaceae to synonymy. More recently, Monascaceae was placed in Eurotiales (LoBuglio et al. 1993, Hawksworth et al. 1995). Fennell (1973) noted that species of both Monascaceae and Eurotiaceae, which approximates our definition Aspergillaceae, form a distinct cleistothecial wall. Nevertheless, Fennell (1973) separated these families based on the formation of aleurioconidia by members of Monascaceae, but our results show that this feature is insufficient for family delimitation. Anamorph genera were not treated by Malloch (1985a, b) and Fig. 1 shows that the genera Aspergillus, Basipetospora, Eladia, Fraseriella, Penicillium, Phialomyces, Phialosimplex, Polypaecilum, Thysanophora and Torulomyces are classified in Aspergillaceae. The teleomorph genera Chromocleista, Fennellia, Neocarpenteles and Neopetromyces, Phylogeny of Penicillium and Trichocomaceae Table 4. Overview of the classifications of the Trichocomaceae and Eurotiaceae by Benny & Kimbrough (1980), Malloch (1985b), von Arx (1987) and the current study. Benny & Kimbrough (1980) von Arx (1987) Malloch (1985b) Current study Trichocomaceae: Eurotiaceae: Trichomoideae: Aspergillaceae: Aphanoascus Chaetosartorya Byssochlamys Aspergillus (incl. teleomorphs, syn. Stilbothamnium) Byssochlamys Cristaspora Dendrosphaera Hamigera (incl. Merimbla) Chaetosartorya Dichlaena Sagenoma Leiothecium Dichotomomyces Talaromyces Monascus (incl. Basipetospora) Dichleana Emericella Trichocoma Penicilliopsis Edyuillia Eupenicillium Dichlaenoideae: Penicillium (syn. Chromocleista, Eladia, Eupenicillium, Hemicarpenteles, Thysanophora, Torulomyces) Emericella Eurotium Chaetosartorya Phialomyces Eupenicillium Fennellia Cristaspora Phialosimplex Eurotium Hemicarpenteles Dichlaena Polypaecilum Fennellia Mallochia2 Dichotomomyces Sclerocleista Hamigera Neosartorya Eupenicillium Warcupiella (incl. Raperia) Hemicarpenteles Saitoa Edyuillia (=Eurotium) Xeromyces Hemisartorya Emericella Thermoascaceae: Neosartorya Eurotium Paecilomyces (incl. Byssochlamys) Penicilliopsis Fennellia Thermoascus (syn. Coonemeria, Dactylomyces) Petromyces Hamigera Trichocomaceae: Roumegueriella1 Hemicarpenteles Dendrosphaera (tentatively, fide Malloch 1985b) Sagenoma Hemisartorya Rasamsonia Sclerocleista Neosartorya Sagenomella Talaromyces Penicilliopsis Talaromyces (syn. Sagenoma, Erythrogymnotheca) Trichocoma Petromyces Thermomyces Warcupiella Sclerocleista Trichocoma Monascaceae: Thermoascus Unknown status: Ascorhiza Warcupiella Ascorhiza (no strains available/studied) 3 Leiothecium Pseudocordyceps Monascus Sarophorum Xeromyces Dichleana Benny & Kimbrough (1980) accommodated Roumegueriella in the Trichocomaceae; however, Sung et al. (2007) showed that this genus belongs to the Bionectriaceae (Hypocreales) and is excluded in our study of the Trichocomaceae. 2The type species Mallochia, M. echinulata, has a close relationship with Amaurascopsis reticulata and both species belong to the Onygenales (Solé et al. 2002). 3Comparison of the ITS sequence of the type strain of the type of Hemisartorya, H. maritima (CBS 186.77), showed to have a 100 % homology with the type of A. versicolor CBS 583.65 (J. Houbraken, unpubl. data). 1 which were not treated in Malloch’s study (1985a, b), also belong to this family. The genera Byssochlamys, Dendrosphaera, Sagenoma, Talaromyces and Trichocoma were placed by Malloch (1985a, b) in Trichocomaceae (as subfamily Trichomoideae), and anamorphs in Paecilomyces or Penicillium were linked to it. The results of our phylogenetic analysis (Fig. 1) confirm the positioning of the genera Sagenoma, Talaromyces and Trichocoma in this family. In addition, the recently described genus Rasamsonia (Houbraken et al. 2011d), and the asexual genera Thermomyces and Sagenomella are classified in this family. Phylogenetic analysis shows that Byssochlamys is more closely related to Thermoascus. Fennell (1973) also observed the relationship between these two genera and stated that Byssochlamys is transitional between Thermoascaceae and Aspergillaceae (as Eurotiaceae). No strains of the genus Dendrosphaera were available and its position remains questionable. Kobayasi (1971) described an aleurioconidial state in Dendrosphaera eberhardtii and Benny & Kimbrough (1980) therefore suggested placing this species in Onygenales (which makes Dendrosphaeraceae a family of Onygenales). On the other www.studiesinmycology.org hand, Malloch (1985b) noted that D. eberhardtii and T. paradoxa produce similar brushes of soft hyphae bearing asci and ascospores suggesting the placement in Trichocomaceae. Following Malloch (1985b), we tentatively place this genus in Trichocomaceae, and consequently, Dendrosphaeraceae are synonymised with Trichocomaceae. Phylogeny of Aspergillaceae Seven clades (Fig. 1, clades 1–7) can be distinguished in Aspergillaceae. Each clade is discussed and phenotypic characters of the members belonging to those clades are compared with those of Penicillium. Clade 1: Penicillium sensu stricto Penicillium sensu lato is polyphyletic and species of this genus occur in the phylogenetically redefined families Aspergillaceae and Trichocomaceae (Fig. 1). The type species of Penicillium, Penicillium expansum, and the type species of Eupenicillium, E. crustaceum, form a clade within Aspergillaceae, defined here as Penicillium sensu stricto. The Penicillia not belonging to Penicillium 17 Houbraken & Samson s. str. are mainly classified in Trichocomaceae, in a clade together with the type species of Talaromyces, T. flavus (clade 10). The presence of two major clades in Penicillium is concordant with earlier studies using rDNA sequences (Berbee & Taylor 1995, Ogawa et al. 1997, Sugiyama 1998, Ogawa & Sugiyama 2000, Tamura et al. 2000). More recently, Wang & Zhuang (2007) used partial calmodulin sequences for the phylogenetic analysis of Penicillium and their data also supported the presence of two lineages in Trichocomaceae. However, their placement of Talaromyces trachyspermus on a single lineage is contradictory with our data. The Penicillium s. str. clade is most closely related to the Aspergillus clade (clade 2) and is phylogenetically more distant from genera with similar anamorphs such as Paecilomyces, Merimbla and the Penicillium species assigned to Trichocomaceae in this study. The phylogenetic study shows that various other genera belong to Penicillium s. str. The type species of the genera Chromocleista, Torulomyces, Thysanophora, Hemicarpenteles and Eladia are positioned in Penicillium s. str. These genera are considered here as synonyms of Penicillium, and the species are transferred as appropriate. Two well-supported subclades (Fig. 1A, B) can be distinguished within Penicillium s. str. Pitt (1980) classified Penicillium in four subgenera: Aspergilloides, Furcatum, Penicillium and Biverticillium. This system was mainly based on conidiophore branching and shape of the phialides. The type species of subgenus Penicillium (P. expansum) belongs to clade 1B and mainly comprises the species which are ter- and/or quarterverticillate. The type species of the subgenera Aspergilloides and Furcatum (P. aurantiobrunneum (= P. glabrum) and P. citrinum, respectively) are positioned in clade 1A, and monoverticillate and biverticillate species with flask shaped phialides more frequently occur in this clade. The type species of subgenus Biverticillium, Penicillium minioluteum, does not belong to Penicillium s. str. and is recombined as Talaromyces minioluteus elsewhere (Samson et al. 2011). Species with symmetrical biverticillate conidiophores and lanceolate phialdes belong to this clade. These observations confirm other studies that also showed that the current phenotype-based subgeneric classification, which is mainly based on the branching system of the Penicillium conidiophores, is incongruent with the molecular phylogeny (Peterson 2000a, Wang & Zhuang 2007). It is proposed here to abandon the current subgeneric classification and to synonymise subgenus Furcatum with Aspergilloides, because the latter is an older name. The subgenera Aspergilloides and Penicillium correspond to clades 1A and 1B, respectively. The phylogenetic structure within these clades is examined with more depth in Part 3 of the discussion. Clade 2: Aspergillus A limited number of Aspergillus species and related teleomorphs are included in this study. The majority of the studied Aspergillus strains form a clade with 51 % bootstrap and 1.00 posterior probability support and this clade is defined here as Aspergillus sensu stricto. Aspergillus s. str. is phylogenetically closely related to Penicillium s. str. (77 % bs, 1.00 pp). These genera are morphologically distinct. Aspergillus forms nonseptate stipes, which often terminate in a distinct inflated part (vesicle) and have a foot-cell (Raper & Fennell 1965). Furthermore, the phialides are produced synchronously from the vesicle in Aspergillus. The distinction between these two genera is largely supported by the phylogeny. However, there are a few exceptions. Aspergillus paradoxus, A. crystallinus and A. malodoratus phylogenetically belong to Penicillium (R.A. Samson, unpubl. data). However, Raper & Fennell (1965) also noted that A. 18 crystallinus and A. malodoratus produce triseriate structures that resemble Penicillium. In addition, there are also Aspergilli, which look similar to Penicillium. An example is Penicillium inflatum, which phylogenetically belongs to Aspergillus section Cremei and will be transferred from Penicillium to Aspergillus (R.A. Samson, unpubl. data). In addition, Aspergillus sydowii regularly produces small penicilli, and A. restrictus can produce diminutive vesiculate monoverticillate stipes, similar in appearance to those of some Penicillium species. The classification of the genus Aspergillus is traditionally based on morphological characters. Raper & Fennell (1965) divided the genus into 18 groups. More recently, Peterson (2008) studied the relationship among Aspergilli using a multigene phylogeny and accepted 5 subgenera (Aspergillus, Circumdati, Fumigati, Nidulantes and Ornati) and 16 sections. Our data largely corresponds with Peterson’s phylogeny, and four of the six subclades in Fig. 1 represent the Aspergillus subgenera as defined by Peterson (2008). However, there are some discrepancies. Sections Restricti and Aspergillus of the subgenus Aspergillus are on a well supported branch (100 % bs, 1.00 pp), confirming Peterson’s data. Peterson (2008) placed sections Clavati and Fumigati in a single subgenus and, because of lack of statistical support, tentatively placed section Cervini in this subgenus. The representatives of section Cervini (Aspergillus cervinus, A. kanagawaensis) used in our study show that this section is basal to sections Fumigati and Clavati and belongs in the subgenus Fumigati. This confirms the phenotypic data of Gams et al. (1985), who placed sections Fumigati and Cervini in subgenus Fumigati. Phylogenetically, the monophyletic subgenus Circumdati as proposed by Peterson (2008) contains sections Circumdati, Candidi, Flavi, Flavipedes, Nigri, Terrei and Cremei. The relationship between the former six sections is poorly supported in our analysis (30 % bs, 0.94 pp) and more studies on the phylogenetic structure of Aspergillus are needed. In contrast to previous published results (Peterson 1995, 2008), section Cremei appeared to be unrelated to the other sections of subgenus Circumdati. The studied members of section Cremei (A. pulvinus, A. wentii, A. brunneouniseriatus) formed a well supported clade with the type species of Cristaspora (C. arxii) and this clade is more closely related to members of the subgenus Aspergillus (64 % bs, 1.00 pp) than to subgenus Circumdati. The subgenus Nidulantes contains sections Nidulantes, Ochraceorosei, Usti, Sparsi and Aeni (Frisvad et al. 2005, Peterson 2008, Varga et al. 2010). These results were confirmed in our study, with exception of section Aeni, because no representatives were included in our study. Section Ornati in subgenus Ornati is not positioned in Aspergillus s. str. and species belonging to this section are placed in the clade 7. Peterson (2008) suggested that it would be possible to change the classification of Aspergillus by splitting the genus based on teleomorphic states associated with particular monophyletic groups. However, he advocated keeping Aspergillus as a monophyletic genus, since this would reflect the actual relationships of species displaying an aspergillum whereas dividing the form genus into several genera based on teleomorphs would de-emphasise the relationships for most biologists not intimately familiar with the genus. Teleomorph genera associated with Aspergillus anamorphs include Chaetosartorya, Dichotomomyces, Emericella, Eurotium, Fennellia, Neocarpenteles, Neopetromyces, Neosartorya and Petromyces. The type species of the genera Polypaecilum and Phialosimplex and the ex-type strain of Basipetospora halophilica form a strongly supported clade (100 % bs, 1.00 pp) within Aspergillus s. str. This clade is related to Aspergillus sections Cremei, Aspergillus Phylogeny of Penicillium and Trichocomaceae and Restricti (64 % bs, 1.00 pp). Recently, Phialosimplex was introduced for species with simple phialides borne laterally on vegetative hyphae. These phialides form chains of conidia and are mostly monophialidic, but a second opening can also be formed (polyphialides). Sagenomella chlamydosporus and S. sclerotialis were transferred to this genus and Phialosimplex canicus was described as a new species (Sigler et al. 2010). The transfer of S. sclerotialis to Phialosimplex created a paraphyletic genus with Polypaecilum embedded in it. The type species of Polypaecilum, P. insolitum, produces its conidia on polyphialides and this feature is shared with members of Phialosimplex (Smith 1961a). The formation of chlamydospores and the occurrence in patient material are also shared features of both genera. This indicates that these genera could be congeneric and more research is needed to clarify their taxonomic status. Basipetospora halophilica also belongs to this diverse clade. The production of short solitary conidiophores or conidiogeneous cells by this species is a shared character with members of Phialosimplex, Polypaecilum and many other genera; however, formation of polyphialides by this species was not described (Pitt & Hocking 1985). Furthermore, Polypaecilum morphs related to Thermoascus and Dichotomyces are not part of this clade and this genus is polyphyletic. Clade 3: Hamigera Hamigera, Warcupiella and the related anamorphs Merimbla and Raperia are positioned in clade 3. The statistical support of this clade is low (< 70 % bs, < 0.90 pp) and the studied species might not be related. We decided to place the species Hamigera avellanea, Hamigera striata, Penicillium megasporum, Talaromyces leycettanus and Warcupiella spinosa in our taxon sampling based on data presented in previous studies, in which it was demonstrated that these species are related (Ogawa & Sugiyama 2000, Tamura et al. 2000, Peterson 2008, Peterson et al. 2010). Penicillium giganteum, Merimbla ingelheimensis, Hamigera paravellanea, H. insecticola, H. inflata, H. terricola, H. pallida, H. fusca were not included in our study, but are also members of this clade (Ogawa & Sugiyama 2000, Peterson et al. 2010). Hamigera striata and Talaromyces leycettanus are on a strongly supported branch (94 % bs, 1.00 pp). Ogawa & Sugiyama (2000) showed in their 18S rDNA analysis that both species are related (83 % bs), confirming our data. Peterson et al. (2010) did not accept H. striata in Hamigera because of lack of statistical support and followed Benjamin’s (1955) placement of this species in Talaromyces. Our results indicate that Talaromyces is phylogenetically distant and we therefore maintain H. striata in Hamigera. Talaromyces leycettanus also warrants further attention. Stolk & Samson (1972) noted that the anamorph of T. leycettanus, Paecilomyces leycettanus, seems to occupy an intermediate form between Penicillium and Paecilomyces. The complex conidiophore of T. leycettanus resembles Merimbla (= anamorph of Hamigera) (Peterson et al. 2010), supporting its placement in this diverse clade. Warcupiella is monotypic, represented by Warcupiella spinulosa (Subramanian 1972) and this species was originally described as Aspergillus spinulosus (Raper & Fennell 1965). Later, Raperia was introduced by Subramanian & Rajendran (1979) to accommodate the anamorph of W. spinulosa (von Arx 1986). Our results and others (Tamura et al. 2000, Peterson 2008) show that W. spinulosa does not belong to Penicillium or Aspergillus, and is more closely related to Hamigera avellanea. The relationship between Warcupiella/Raperia and Hamigera was also noted by von Arx (1986), and he transferred W. spinulosa to Hamigera. Penicillium megasporum, another member of this clade, has little affinity with www.studiesinmycology.org Penicillium s. str. as noted by Pitt (1980), who created Penicillium series Megaspora for this species and P. asperosporum. Peterson et al. (2010) described the penicillus structure of P. megasporum as similar as that of Merimbla, but that phylogenetic analysis did not support inclusion of P. megasporum in the Hamigera clade. Our analysis lacks high bootstrap support to confidentially place P. megasporum, W. spinulosa and T. leycettanus in Hamigera. More research is needed to elucidate the classification of this diverse clade. Clade 4: Penicilliopsis Clade 4 comprises Aspergillus zonatus and Penicilliopsis clavariiformis and these two species form a strongly supported clade. Penicilliopsis is typified by P. clavariiformis and characterised by seed-borne, stipitate stromata. The anamorph genera Pseudocordyceps, Sarophorum and Stilbodendron are phenotypically related (Samson & Seifert 1985, Hsieh & Ju 2002). The former two genera have conidiogenous structures similar to those of Penicillium and the latter has Aspergillus-like conidiogenous structures. The sclerotia of Stilbothamnium morphologically resemble ascomata of Penicilliopsis. However, phylogenetically, the type species of Stilbothamnium, Aspergillus togoensis, belongs to Aspergillus subgenus Circumdati section Flavi and is unrelated to Penicilliopsis (Fig. 1). More research is needed to clarify the relationship between Penicillium, Penicilliopsis and the associated anamorph genera Pseudocordyceps and Sarophorum. Clade 5: Monascus, Xeromyces and Leiothecium The teleomorph genera Monascus, Xeromyces and Leiothecium belong in clade 5, as do the anamorph genera Fraseriella and Basipetospora (Pettersson et al. 2011, our data). Benny & Kimbrough (1980) placed Monascus, Xeromyces and Leiothecium in Monascaceae and this family is transferred here to Aspergillaceae (see part 1, phylogeny of Aspergillaceae). These genera have similar phenotypic characters including the formation of stalked ascomata and the production of aleurioconidia from undifferentiated conidiogenous cells. These features clearly set these genera apart from Penicillium s. str. and Aspergillus. Our results confirm those of Pettersson et al. (2011) and we follow their opinion in retaining Xeromyces for xerophilic Monascus-like species and Monascus for the species that grow at higher water activities. In addition, Pettersson et al. (2011) suggested that Chrysosporium inops should be transferred to a new genus. However, Fig. 1 shows that this species is closely related to X. bisporus and the xerophilic nature of boths species indicates a close relationship (Pitt & Hocking 2009, Pettersson et al. 2011). Leiothecium is basal to Monascus and the connection between these two genera was also noted by Samson & Mouchacca (1975). Aspergillus clavatoflavus is basal to this clade, but the relationship lacks statistical support. The micromorphology is A. clavatoflavus differs from the members of clade 5 and therefore this species is placed outside this clade, awaiting more conclusive data. Clade 6: Phialomyces The type species of Phialomyces, Phial. macrosporus (Misra & Talbot 1968), is positioned in clade 6 and is closely related to Penicillium arenicola (100 % bs, 1.00 pp). Merimbla humicoloides (= Penicillium humicoloides sensu Peterson et al. 2010) also belongs to this clade (R.A. Samson, unpubl. data). All three species are phylogenetically distinct form Penicillium s. str. Pitt (1980) 19 Houbraken & Samson placed P. arenicola in a separate section and series and noted that this species may not be a true Penicillium. Phenotypically, Phial. macrosporus, M. humicoloides and P. arenicola form conidia in shades of gold-brown, a feature uncommon for Penicillium species. These species can produce terverticillate conidiophores, a character also present in subgenus Penicillium (clade 1B). Our results indicate that P. arenicola and M. humicoloides should be transferred to another genus. Clade 7: Sclerocleista Sclerocleista ornata and S. thaxteri are basal to Phial. macrosporus and P. arenicola (Fig. 1). Sclerocleista ornata was originally described as Aspergillus ornatus (Raper et al. 1953), and later transferred to Sclerocleista (Subramanian 1972). Sclerocleista thaxteri was originally described in Sclerocleista and later von Arx (1974) transferred this species to Hemicarpenteles. The two species are closely related, and phylogenetically distant from H. paradoxus, the type species of Hemicarpenteles (Fig. 1, Penicillium s. str.). Peterson (2008) placed Sclerocleista basal to the Aspergilli, suggesting a monophyletic Aspergillus clade; however, our data do not support this conclusion. Sclerocleista differs from Penicillium s. str. in having an Aspergillus-type anamorph and purple coloured cleistothecia filled with lenticular ascospores (Raper & Fennell 1965). Phylogeny of Thermoascaceae Figure 1 shows that two clades (clade 8 and 9) are present in Thermoascaceae (= lineage 2). The phylogeny of these two clades and the comparison of the species belonging to these two clades with Penicillium s. str. is discussed below. Clade 8: Thermoascus Thermoascus aurantiacus, T. crustaceus and T. thermophilus are together with Byssochlamys verrucosa in a separate clade. The taxonomy of Thermoascus is treated in various studies. Apinis (1967) split Thermoascus in two: Thermoascus was retained for its type species T. aurantiacus, and T. thermophilus and T. crustaceus were transferred to Dactylomyces. Later, Mouchacca (1997) divided Dactylomyces further in two, creating Coonemeria for T. crustaceus. Although these species have different anamorphs (Paecilomyces/Polypaecilum), our phylogenetic study (Fig. 1) shows that these three species are closely related and should be retained in Thermoascus. Samson et al. (2009) noted that Byssochlamys verrucosa is misidentified in Byssochlamys but related to Thermoascus, and this observation is confirmed here. Thermoascus has a similar type of sclerotioid cleistothecium as members of Penicillium s. str. (Stolk & Samson 1983). These two genera differ mainly in ascomatal development. Ascomata of Thermoascus are initiated by an ascogonial coil (Stolk 1965, Subramanian & Rajendran 1980), whereas in Penicillium s. str. the formation begins with sclerotium-like bodies inside which the ascogonia develop. Furthermore, the anamorphs of Thermoascus are not of the Penicillium type, but can be similar to Paecilomyces. Clade 9: Paecilomyces The types of Paecilomyces (P. variotii) and Byssochlamys (B. nivea) occur together on a branch with 100 % bootstrap support. Using a polyphasic approach, Samson et al. (2009) showed that the genera Byssochlamys and Paecilomyces s. str. are closely related and form a monophyletic group. Paecilomyces was introduced 20 by Bainier (1907) and has priority over Byssochlamys (Westling 1909). Phylogenetic analysis of the 18S rDNA demonstrated that Paecilomyces sensu Samson (1974) is polyphyletic across two subclasses, Sordariomycetidae and Eurotiomycetidae. The type species of this genus, Paecilomyces variotii, and its thermophilic relatives belong in the Eurotiales (Luangsa-ard et al. 2004). Figure 1 shows that Paecilomyces s. str. is also phylogenetically distinct from Penicillium. Morphological characters also support this conclusion. The conidia of Paecilomyces s. str. are olive-brown and formed in phialides that have a broad base and end in a long and slender neck, while the conidia of Penicillium species are green and formed in flask or cylindrical shaped phialides. In addition, the conidiophores of Paecilomyces s. str. are more irregularly branched than those of Penicillium. The teleomorphs are also different: those of Paecilomyces (formerly known as Byssochlamys) are almost naked while Penicillium s. str. produces cleistothecia with a distinct wall. Phylogeny of Trichocomaceae Five clades (clades 10–15) can be recognised in the more narrowly delimited Trichocomaceae. The species treated in these clades are phylogenetically distinct from Penicillium s. str., but some are phenotypically similar. Clade 10: Talaromyces The majority of Penicillium species assigned to the subgenus Biverticillium belong in clade 10 (incl. type of subgenus Biverticillium, P. minioluteum) together with the type species of the genera Talaromyces and Sagenoma. These species are phylogenetically distant from Penicillium s. str. and therefore these species are transferred to the genus Talaromyces (Samson et al. 2011, this study). Phenotypically, Talaromyces differs from Penicillium s. str. by the formation of symmetrically branched conidiophores with lanceolate phialides, and the production of soft ascomata without a well-defined, persistant wall. Members of the Talaromyces clade grow slower on the agar medium G25N than Penicillium s. str. members (Pitt 1980). Also differences in ubiquinones and extrolites patterns are observed between Penicillium sensu stricto and Talaromyces. The Q9 ubiquinone system was present in most Penicillium sensu stricto species, while nearly all Talaromyces have Q10(H2) (Paterson 1998). In addition, extrolites such as mitorubrins, certain bisanthraquinones (rugulosin, skyrin), duclauxin and glauconic acide were detected in Talaromyces, but never found in Penicillium sensu stricto (Frisvad et al. 1998). The taxonomic and phylogenetic structure of Talaromyces is considered further by Samson et al. (2011). The neotype strain of Aphanoascus cinnabarinus sensu Udagawa and Takada also belongs to this clade. Much taxonomic confusion followed after the proposal of Aphanoascus by Zukal (1890). Most authors follow Apinis (1968) and maintain Aphanoascus that is typified by A. fulvescens. In addition, the neotypification of A. cinnabarinus by Udagawa & Takada (1973) was incorrect, because their neotype strain had a Paecilomyces anamorph, while Zukal’s original description and illustrations showed structures of a Chrysosporium anamorph (Stolk & Samson 1983). Based on morphological characters, Stolk & Samson (1983) suggested that Chromocleista cinnabarina (as A. cinnabarinus sensu Udagawa & Takada) belongs to Eurotiales, and that this species occupies an intermediate position between the genera Thermoascus and Talaromyces. The result of our multigene phylogeny shows that C. cinnabarina belongs to Talaromyces s. str. Phylogeny of Penicillium and Trichocomaceae This data is in concordance with the 18S rDNA sequence data of Ogawa & Sugiyama (2000), which shows that C. cinnabarina forms a monophyletic group with T. macrosporus and T. bacillisporus. No specimens of Erythrogymnotheca were studied, but an ITS sequence of the type species of this genus (E. paucispora) is deposited GenBank (AB176603) and a BLAST search on GenBank and internal CBS databases shows that this sequence belongs to Talaromyces s. str. Excluded genera: Geosmithia, Phialotubus and Yunnania The genera Geosmithia, Phialotubus and Yunnania have sometimes been hypothesised to be related to Penicillium (Gams 1978, Pitt 1980, Kong 1998). Our data shows that these genera do not belong to the Eurotiales and details are provided below. Geosmithia Clade 12 is centered around the type species of Sagenomella, S. diversispora, and this genus is phylogenetically unrelated to Penicillium s. str. Sagenomella was described by Gams (1978) for Acremonium-like fungi and is characterised by connected conidial chains and sympodially proliferating, often centrally swollen phialides. These characters are not present in Penicillium s. str. Molecular data showed that Sagenomella sensu Gams is polyphyletic (Endo et al. 1998, Thanh et al. 1998, our results). Sigler et al. (2010) transferred S. chlamydospora and S. sclerotialis to the new genus Phialosimplex and Sagenomella bohemica belongs in Talaromyces (Samson et al. 2011). The close relationship of this genus with Talaromyces indicates that Sagenomella is a reduced form of Talaromyces. The genus Geosmithia is typified by G. lavendula (Pitt 1978) and is a polyphyletic morphogenus introduced to classify Penicillium species, which are characterised by: a) cylindroidal phialides and conidia, b) rugulose to rugose conidiophores walls, metulae and phialides and c) conidial colour other than green (with the exception of G. namyslowskii). Anamorphs of Geosmithia have affinities with hypocrealean (Hypocreales: Bionectriaceae) and eurotialean (Eurotiales: Trichocomaceae) fungi, and the type species of Geosmithia, G. lavendula, is related to Acremonium alternatum, the type species of Acremonium (Ogawa et al. 1997, Rossman et al. 2001, Summerbell et al. 2011). Currently, there are 16 described species (Pitt 1980, Yaguchi et al. 1993, 1994, Pitt et al. 2000, Kolařík et al. 2004, 2005, 2010), and eight of these species (G. fassatiae, G. flava, G. langdonii, G. lavendula, G. morbida, G. obscura, G. pallida, and G. putterillii) belong to the Hypocreales. Geosmithia argillacea (teleomorph Talaromyces eburneus sensu Yaguchi et al. 2005), G. eburnea (teleomorph Talaromyces eburneus sensu Yaguchi et al. 1994), G. emersonii (teleomorph Talaromyces emersonii) and G. cylindrospora are closely related to each other and were recently transferred to Rasamsonia (Houbraken et al. 2011d, see clade 13 above). Geosmithia swiftii (teleomorph Talaromyces bacillisporus) and G. viridis belong to Talaromyces s. str. and G. namyslowskii and G. malachiteum (described as the anamorph of Chromocleista malachitea) belong to Penicillium s. str. (Fig. 1). Zaleski (1927) originally described Geosmithia namyslowskii as Penicillium namyslowskii and the new combination of Penicillium malachiteum is made elsewhere in this article. Clade 13: Rasamsonia Phialotubus Clade 11: Thermomyces Talaromyces thermophilus belongs to the same clade as the type of Thermomyces, T. lanuginosus. Talaromyces thermophilus and Therm. lanuginosus share similar characters, including their ability to grow at high temperatures and the formation of thick-walled chlamydospores or chlamydospore-like conidia. These characters are not shared by members of Penicillium s. str. Talaromyces luteus is basal to this clade. This species is not thermophilic and phenotypically different from Thermomyces and Tal. thermophilus, and it is therefore excluded from clade 11. Clade 12: Sagenomella The thermophiles Talaromyces emersonii and T. byssochlamydoides were transferred to Rasamsonia (Houbraken et al. 2011d), leaving T. thermophilus as sole thermophile in Talaromyces. However, our phylogenetic analysis shows that this species belongs to Thermomyces and not to Talaromyces. The genus Rasamsonia was erected for thermotolerant or thermophilic species, which have cylindrical phialides usually gradually tapering towards the apices, conidiophores with distinctly rough walled stipes, olivebrown conidia and ascomata, if present, with a scanty covering. This clade contains the species R. argillacea, R. brevistipitata, R. byssochlamydoides, R. cylindrospora, R. eburnea and R. emersonii (Houbraken et al. 2011d). Clade 14: Trichocoma The monotypic genus Trichocoma is typified by Trichocoma paradoxa and is characterised by asci born in hyphal masses or tufts that can be up to 10–20 mm long (Kominami et al. 1952, Malloch 1985b). The anamorph of this species resembles an anamorph of Talaromyces. However, Trichocoma produces conidia in shades of brown. Rasamsonia is phylogenetically related to Trichocoma, and can be differentiated by the presence of scanty ascomatal coverings and its ability to grow at temperatures above 40 °C. www.studiesinmycology.org Phialotubus (Roy & Leelavathy 1966) is monotypic with Phialotubus microsporus as the type. This species is characterised by the formation of cylindrical phialides with long hyaline threadlike projections, which get prolonged into the hyaline tube-like projection when conidia are formed (Fig. 2). The conidia are fusiform in shape and produced in chains (Roy & Leelavathy 1966, Gams 1978, Arx 1981). These characters suggest a close connection with the Eurotiales, for example with Paecilomyces, Phialomyces, Sagenomella and Torulomyces. However, a BLAST search on GenBank with an ITS sequence of strain CBS 861.70isoT (GenBank no. JN831360) did not retrieve any high similarity matches with members of the Eurotiales. The overall similarity matches were low and this species probably belongs to the class Sordariomycetes. Yunnania Kong (1998) proposed the genus Yunnania and typified it with Y. penicillata. The truncated conidia and the black or brownish black colonies resemble those of Scopulariopsis. In addition, the conidia are produced by annelides (Fig. 3). Examination of the type strain of Y. penicillata (CBS 130296T) showed that this species is morphologically related to Scedosporium. A BLAST search on GenBank with an ITS sequence of this species (GenBank no. JN831361) did not retrieve a high similarity match, but showed that this species belongs to the order Microascales. 21 Houbraken & Samson Fig. 2. Phialotubus microsporus CBS 861.70isoT. A. Colonies grown for 7 d at 25 °C, from left to right: CYA, MEA, OA. B–D. Conidiophores and conidia. Scale bar = 10 µm. Taxonomic implications Aspergillaceae Link, Abh. dt. Akad. Wiss. Berlin 1824: 165. 1826. = Eurotiaceae Clements and Shear, Gen. Fung. 50. 1931. = Monascaceae J. Schröter, Nat. Pflanzenfamilien 1: 148. 1894. = Hemicarpenteleaceae Locquin, Tribune Méd. (Paris) 1. 1972. nom. inval. (Art. 36). = Penicilliaceae Vuillemin, Pl. Jungh. 10: 172. 1910. (as Penicilliacées nom. inval. Art. 32.1b). = Penicilliopsidaceae Locquin, Tribune Méd. (Paris) 1. 1972. nom. inval. (Art. 36). = Phialomycetaeae Locquin, Mycologie générale et structurale: 212. 1984. nom. inval. (Art. 36). = Warcupiellaceae Locquin, Mycologie générale et structurale: 167. 1984. nom. inval. (Art. 36). = Xeromycetaceae Locquin, Tribune Méd. (Paris) 1. 1972. nom. inval. (Art. 36). Type: Aspergillus Fr: Fr. Thermoascaceae Apinis, Trans. Br. Mycol. Soc 50: 581. 1967. Type: Thermoascus Miehe 22 Trichocomaceae E. Fischer, Nat. Pflanzenfam. 1: 310. 1897. (as Trichocomataceae) = Talaromycetaceae Locquin, Mycologie générale et structurale: 176. 1984. nom. inval. (Art. 36). = Dendrosphaeraceae Ciferri ex Benny & Kimbrough, Mycotaxon 12: 22. 1980. Type: Trichocoma Junghuhn Part Two: Delimitation of Penicillium Authority The generic name Penicillium is attributed to Link (1809). Link included three species within Penicillium, P. glaucum, P. candidum and P. expansum. He illustrated P. candidum, which clearly shows structures of a Penicillium species. Later, Penicillium expansum was selected by Thom (1910) and later (co-)authors as the lectotype of Penicillium. The generic name Penicillium was attributed by Fries (1832: 406) to Link (1809). Hawksworth et al. (1976) proposed to conserve the generic name Penicillium as Penicillium Link ex Grey over Penicillium Fries 1832 (proposal no. 420), and lectotypified Phylogeny of Penicillium and Trichocomaceae Fig. 3. Yunnania penicillata CBS 130296T. A. Colonies grown for 7 d at 25 °C, from left to right: MEA, OA, CYA. B–D. Conidiophores and conidia. the genus with Penicillium expansum Link ex Grey. This proposal was countered by Jørgensen & Gunnerbeck (1977) because Fries listed “Mucor crustaceus L.” as a typical species of Penicillium and not as the type species of this genus. The proposal of Hawksworth et al. (1976) was therefore rejected (Petersen 1980). The general starting point for fungal names is Linnaeus 1753, but there are a few exceptions and these are mentioned in the ICBN under art. 13e. One exception is that names used by E.M. Fries’ “Systema mycologicum” 1821–1832 have a protected status. These names are sanctioned and have priority over older synonyms and homonyms. The authority used here is therefore Penicillium Link : Fries. Hemicarpenteles. Details regarding the position of these genera in Penicillium are presented below. Another important difference between our and Raper & Thom’s (1949) concept is the exclusion of Talaromyces and related Penicillium species. In our concept, only teleomorphs producing pseudoparenchymatous and sclerotioid ascomata are included (“Eupenicillium-type”), and Talaromyces species, with soft ascomata without a well-defined, persistent wall, are excluded (Samson et al. 2011). Also the Penicillium species, which have lanceolate phialides and metulae with equal lengths as the phialides, are excluded. These species are also phylogenetically distinct (Fig. 1). Our emended generic diagnosis is derived from Raper & Thom (1949) and is presented here: Generic diagnosis Penicillium Link : Fries, Systema Mycologicum 3: 406. 1832. Vegetative mycelium abundant, entirely submerged or more or less effused, irregularly branching, septate, hyaline or brightly coloured and forming a dense and compact mycelia colony with well-defined margins. Conidiophores borne from undifferentiated subsurface, superficial or aerial hyphae, rarely subapically proliferation under terminal penicillus. Stipes relatively narrow and thin walled, 2–5 µm, The concept of Penicillium has been refined and restated often in mycological history. The concept of Raper & Thom (1949) is followed here; however, there are some emendations. In our concept, Penicillium includes species with pigmented stipes (Thysanophora species, P. stolkiae and related species), as well as species formerly ascribed to the genera Eladia, Torulomyces, Chromocleista and www.studiesinmycology.org 23 Houbraken & Samson and in some species apically swollen, hyaline, in some species brown. Conidial apparatus usually a well defined structure (brush or broom), named the Penicillus; penicilli comprised of phialides born directly on the stipe, or with one, two or rarely more verticils of metulae and rami as supporting cells. Conidiogenous cells phialides, borne in succession, i.e. not synchronouse, rarely exceeding 15 µm in length, ampulliform, rarely cylindrical. Conidia in unbranched chains, borne basipetally, single celled, commonly between 2–5 µm in diameter, rarely exceeding 6 µm, en masse coloured in shades of green, rarely white, olive or brown. Chlamydospores absent. Sclerotia occasionally produced, composed of thick-walled cells, usually hard. Cleistothecia, if produced, usually hard, globose to subglobse, pseudoparenchymatous or sclerochymatous, ripening from the center outward and often tardily; white, pale, yellow, orange or brown coloured, occasionally black or red. Asci ellipsoidal to globose, usually 8-spored, 5–15 µm. Ascospores lenticular, usually with equatorial ridges, 2–5 µm. Synonyms of Penicillium The re-definition of the genus Penicillium has several taxonomic implications. Based on the phylogenetic data presented in Fig. 1 in combination with a review of literature, we place the genera Chromocleista, Carpenteles, Citromyces, Eladia, Eupenicillium, Hemicarpenteles, Thysanophora and Torulomyces in synonymy with Penicillium. More genera are congeneric with Penicillium and a more extended list can be found in Seifert et al. (2011: 333). Each genus is discussed here and new combinations are proposed below for the species accommodated in these genera. Penicillium Link : Fries, Systema Mycologicum 3: 406. 1832. = Penicillium Link, Obs. Mycol 1: 16. 1809 (nom. inval., Art. 13e). = Coremium Link ex Gray, Nat. Arr. Br. Pl. 1: 563. 1821. = Eupenicillium Ludwig, Lehrb. Nied. Kryptog.: 263. 1892. = Citromyces Wehmer, Bleitr. Kennt. Pilze 1: 1. 1893. = Carpenteles Langeron, C.r. Séanc. Soc. Boil. Paris 87: 344. 1922. = Torulomyces Delitsch, Systematik der Schimmelpilze: 91. 1943. = Thysanophora Kendrick, Can. J. Bot. 39: 820. 1961. = Eladia Smith, Trans. Brit. Mycol. Soc. 44: 47. 1961. = Hemicarpenteles Sarbhoy & Elphick, Trans. Brit. Mycol. Soc. 51: 156. 1968. = Penicillium Link ex Gray sensu Pitt, The Genus Penicillium: 154. 1980 (nom. inval., art 13e). = Chromocleista Yaguchi & Udagawa, Trans. Mycol. Soc. Japan 34: 101. 1993. Subgenus Aspergilloides Dierckx, Annls. Soc. Scient. Brux. 25: 85. 1901. = Subgenus Monoverticillium Biourge, Cellule 33: 265. 1923. = Subgenus Furcatum Pitt, The Genus Penicillium: 233. 1980. Subgenus Penicillium = Subgenus Eupenicillium Dierckx, Annls Soc. Scient. Brux. 25: 85. 1901. Chromocleista The genus Chromocleista, defined by the type species C. malachitea, belongs to Penicillium and is related to P. herquei (see Figs 1, 7). This genus was created by Yaguchi et al. (1993) for species that form bright coloured sclerotioid cleistothecia with a Geosmithia anamorph (Fig. 4). The close relationship with Eupenicillium was noted in the original description, but the presence of the Geosmithia anamorph was, according to the authors, sufficient to create a new genus. Using 18S rDNA sequence data, Ogawa & Sugiyama (2000) showed that C. malachitea groups with Eupenicillium javanicum, E. crustaceum, P. chrysogenum and Geo. namyslowskii. Furthermore, they indicated that the Geosmithia-anamorph of Chromocleista malachitea resembles P. herquei and the former species could 24 be placed in synonymy. Comparison of the β-tubulin sequences and RPB2 sequences of the (neo)type cultures of P. herquei CBS 336.48NT and C. malachitea CBS 647.95T showed homologies of 92.8 % and 94.7 % respectively. Furthermore, a BLAST search with the ITS, RPB2 and β-tubulin sequence data of C. malachitea CBS 647.95T on GenBank and local databases did not retrieve any high similarity matches with other described species and therefore this species is combined with Penicillium below. Citromyces Citromyces was introduced by Wehmer (1893) for monoverticillate Penicillium species. Many authors have agreed that this genus is a synonym of Penicillium (Westling 1911, Biourge 1923, Thom 1930, Raper & Thom 1949, Pitt 1980). Citromyces largely encompasses subgenus Aspergilloides as defined by Pitt (1980). In our classification system, Citromyces corresponds with section Aspergilloides. Eladia Thom (1930) and Raper & Thom (1949) regarded Penicillium sacculum Dale as a Scopulariopsis, and Smith (1961b) introduced the genus Eladia to accommodate this species and typified it with E. saccula. Smith (1961b) did not indicate why this species should not be considered a Penicillium. Pitt (1980) accepted the positioning of E. saccula in a separate genus and he noted that this genus is closely related to Penicillium, but differing in three features (Fig. 4): a) the phialides are born irregularly on stipes, b) phialides have a short collula and distinct thickening of the wall; c) the conidial chains are very short. Stolk & Samson (1985) did not accept this genus and transferred E. saccula to Penicillium and this position was retained in the list of accepted species in Trichocomaceae (Pitt et al. 2000). Our molecular data support the positioning of Smith’s neotype of Eladia succula (CBS 231.61NT) in Penicillium (Figs 1 and 7). This species is most closely related to P. canescens and P. atrovenetum (Fig. 7, clades 24, 25). The relationship of P. sacculum with these species (and also with e.g. P. janczewskii) was also suggested by Stolk & Samson (1985), who emphasised that all these species have swollen phialides with an abruptly narrowed neck and often short conidial chains. Six species were described in Eladia: E. saccula, E. inflata, E. minima, E. striatispora, E. pachyphialis and E. tibetensis. The current name for Eladia saccula is Penicillium sacculum Dale (1926). Extype strains of E. inflata (CBS 127833) and E. minima (CBS 127834) were examined and comparison of the RPB2 region (Fig. 8) showed that E. inflata and P. fuscum (= E. pinetorum, CBS 295.62T) are closely related. Eladia minima is closely related to P. heteromorphum (CBS 226.89T) and P. philippinense (CBS 623.72T). Eladia minima is closely related to P. heteromorphum, P. restrictum, Eup. katangense and Eup. philippinense (data not shown). More research is needed to determine species boundaries in this group of phylogenetical related species. No living ex-type material could be obtained for Eladia striatispora. Drawings of E. striatispora show a clear resemblance with P. striatisporum, and therefore E. striatispora is regarded as a synonym of P. striatisporum (Stolk 1969, Matsushima 1971, Kobayasi 1971). No type material could be obtained from E. pachyphialis and E. tibetensis and their taxonomic position remains uncertain. Eupenicillium and Carpenteles The genus Eupenicillium was introduced by Ludwig (1892) for an ascomycete species that Brefeld (1874) described and Phylogeny of Penicillium and Trichocomaceae Fig. 4. A–F. Penicillium malachiteum CBS 647.95HT. A. Colonies grown for 7 d at 25 °C, from left to right: MEA, CYA, YES, DG18. B–D. Conidiophores. E. Immature cleistothecia. F. Conidia. G–K. Penicillium sacculum CBS 123567. G. Colonies grown for 7 d at 25 °C, from left to right: MEA, CYA, YES, DG18. H–J. Conidiophores. K. Conidia. Scale bar = 10 µm. www.studiesinmycology.org 25 Houbraken & Samson illustrated as P. crustaceum. Unaware of Ludwig’s publication, Langeron (1922) introduced the genus Carpenteles for ascusproducing Penicillium species. Because we include sexual and asexual species in our definition of Penicillium, Eupenicillium and Carpenteles are considered synonyms of Penicillium. In most cases a Penicillium anamorph name is already available for these Eupenicillium species; however, in the case of E. bovifimosum and E. saturniforme, only the teleomorph was described and no Penicillium names linked to these species exist (Tuthill & Frisvad 2002, Wang & Zhuang 2009). The new combinations Penicillium bovifimosum and Penicillium saturniforme are proposed below for these two species. Hemicarpenteles The genus Hemicarpenteles was created by Sarbhoy & Elphick (1968) and H. paradoxus was designated as type (IMI 117502T = CBS 793.68T). This species is characterised by the presence of an Aspergillus anamorph and sclerotioid ascomata (Fig. 5). This unique combination led to the proposition of a new genus. If only ascoma development and characteristics were considered, then H. paradoxus is most similar to Eupenicillium, because both genera form sclerotioid cleistothecia that ripen from the centre outwards (Sarbhoy & Elphick 1968, Pitt 1980, Stolk & Samson 1983). Figure 1 shows the phylogenetic positioning of H. paradoxus in the genus Penicillium. The placement of this species in Penicillium is remarkable, since this species has an Aspergillus anamorph. The positioning of H. paradoxus in Penicillium is also supported by analysis of the ITS and D1/D2 regions of the 28S rDNA and partial calmodulin and β-tubulin data (Peterson 2000a, 2008) and the name Penicillium paradoxum will therefore be proposed (R.A. Samson, unpubl. data). The placement of an Aspergillustype anamorph in the genus Penicillium might be confusing, when using solely phenotypic characters for identification. Three other species are described in Hemicarpenteles: H. acanthosporus, H. ornatus and H. thaxteri. The former species was transferred to Neocarpenteles acanthosporus (Udagawa & Uchiyama 2002) and phylogenetic studies showed that this species is related to Aspergillus section Clavati (Tamura et al. 2000, Varga et al. 2007, Peterson 2000b, 2008). Hemicarpenteles ornatus and H. thaxteri are currently classified in Sclerocleista (Fig. 1, clade 7) (Pitt et al. 2000). Thysanophora Thysanophora was proposed by Kendrick (1961), based on Haplographium penicillioides. Haplographium penicillioides was transferred to Thysanophora because this species produces conidia from phialides in a basipetal succession and in dry chains, while Haplographium species produce ameroconidia in slime. Roumeguère (1890) noted in his description of H. penicillioides that this species also forms Penicillium-like conidiophores (“l’appareil fructifère ressemble à celui d’un Penicillium”). Preuss’ description of three new Penicillium species (P. finitimum, P. flexuosum and P. fuscipes) in 1851 from pine needles might be the first report of members Thysanophora. The habitat and descriptions certainly indicate this placement, but unfortunately, no type specimens were maintained (Kendrick 1961). Thysanophora species produce dark coloured colonies, have dark and stout conidiophores and the majority of species have secondary growth of the stipe by means of the proliferation of an apical penicillius (Fig. 6). Based on the combined RPB1, RPB2, Tsr1 and Cct8 data, it is clear that members of the genus Thysanophora 26 belong to Penicillium. Members of this genus form a separate clade within this genus (Figs 1, 7), confirming earlier results using rDNA sequences (Iwamoto et al. 2002, Peterson & Sigler 2002). Although stipe pigmentation of Thysanophora species is brown, this feature is thus not a useful phylogenetic character for separating this genus from Penicillium (Iwamoto et al. 2002). Melanised conidiophores appear in two separated lineages in Penicillium, namely in Thysanophora, and in a second lineage centered on P. stolkiae (Peterson & Sigler 2002). Another characteristic of Thysanophora is the secondary growth of the stipes. This character is not present in any other Penicillium species and could be argued as a feature sufficient to keep Thysanophora as a separate genus. However, that would create a paraphyletic clade in Penicillium or the need for at least eight genera to restore monophyly. To avoid both scenarios it is chosen here to transfer this genus to Penicillium. Thysanophora comprises eight accepted species, namely T. longispora, T. canadensis, T. taxi, T. striatispora, T. asymmetrica, T. verrucosa, T. glaucoalbida and T. taiwanensis (Minter 2007). Thysanophora penicillioides is regarded as a synonym of T. glauco-albida, because following the ICBN, the latter epithet has priority (Morelet 1968, Minter 2007). No type material was present in the CBS culture collection of T. striatispora, T. asymmetrica, T. verrucosa, T. glaucoalbida and T. taiwanensis. Only the species descriptions were studied and the species delimitation of MercadoSierra (1998) is largely followed. With exception of T. taxi, which was originally described as Penicillium taxi (Schneider 1956), all accepted species of Thysanophora are transferred here to Penicillium and new combinations are proposed below. Torulomyces The genus Torulomyces was erected for two species (T. lagena and T. viscosus) which form dry connected chains in a basipetal manner (Delitsch 1943). Stolk & Samson (1983) transferred Torulomyces lagena, the type species, to Penicillium. This transfer was based on morphological similarities, such as the phialide shape and cultural appearances (Fig. 6). Later, Pitt & Samson (1993) did not accept this transfer to Penicillium, and Torulomyces was re-instated. Our phylogenetic data support Stolk & Samson’s (1983) proposal to transfer Torulomyces to Penicillium and other species described in Torulomyces need to be combined with Penicillium. Currently, eight species are described in Torulomyces: T. brunneus, T. indicus, T. laevis, T. lagena, T. macrosporus, T. ovatus, T. parviverrucosus and T. viscosus. Isolate CBS 185.65 was designated as the neotype of P. lagena, and Eupenicillium limoneum was considered to be the teleomorph of this species (Stolk & Samson 1983). Unfortunately, the ex-type culture of E. limoneum (CBS 650.82T) maintained in the CBS collection is dead. Stolk & Samson (1983) are followed here and E. limoneum is kept in synonymy with P. lagena. Delitsch’s species Torulomyces viscosus remains doubtful since no type material is available and the diagnosis lacks critical details (Stolk & Samson 1983, Ando et al. 1998). No ex-type material of Torulomyces macrosporus could be obtained; based on its protologue (Matsushima 1987), T. macrosporum may belong to Monocillium (Ando et al. 1998). Torulomyces laevis, T. ovatus and T. parviverrucosus were described by Ando et al. (1998) and in the same publication Monocillium humicola var. brunneum was combined with T. brunneus. The type strain of T. brunneus CBS 382.64T is closely related to Torulomyces lagena CBS 185.65NT; these isolates have identical ITS sequences, but differ in their partial β-tubulin, calmodulin and RPB2 sequences (ITS 100 %; calmodulin 98.3 % and β-tubulin 98.4 % and RPB2 Phylogeny of Penicillium and Trichocomaceae Fig. 5. A–G. Penicillium kewense CBS 344.61T. A. Colonies grown for 7 d at 25 °C, from left to right: MEA, CYA, YES, DG18. B–C. Cleistothecia. D-E. Conidiophores. F. Conidia. G. Ascospores. H–N. Aspergillus paradoxus (= P. paradoxum, R.A. Samson unpubl. results) CBS 130295. H. Colonies grown for 7 d at 25 °C, from left to right: MEA (14 d), CYA, YES, DG18. I. Detail of conidiophores. J. Cleistothecia. K–L. Conidiophores. M. Ascospores. N. Conidia. Scale bar = 10 µm. 98.3 %; unpubl. data). Ando et al. (1998) is followed here and this species is kept as separate. No type material of T. laevis, T. ovatus and T. parviverrucosus was available for analysis, but a detailed www.studiesinmycology.org study of the species descriptions suggests they warrant separate species status. New combinations in Penicillium are proposed below. Various isolates with similar morphology to P. lagena are 27 Houbraken & Samson Fig. 6. A–H. Penicillium glaucoalbidum CBS 292.60. A. Colonies grown for 7 d at 25 °C, from left to right: MEA, CYA, YES, DG18. B–D. Conidiophores. E. Conidia. F–J. Penicillium lagena CBS 337.97. F. Colonies grown for 7 d at 25 °C, from left to right: MEA, CYA, YES, DG18. G–I. Conidiophores. J. Conidia. Scale bar = 10 µm. maintained in the CBS collections (CBS 185.65, CBS 382.64, CBS 287.66, CBS 337.97, CBS 120415, CBS 110532, DTO 82A8, DTO 92D1), and preliminary sequencing results show a sequence 28 variation among these strains, suggesting the presence of multiple species (unpubl. data). A thorough taxonomic study should be preformed to elucidate the species diversity in this clade. Phylogeny of Penicillium and Trichocomaceae The genus Monocillium needs further attention. This genus was established for a single species, M. indicum (Saksena 1955). Based on conidium morphogenesis, Hashmi et al. (1972) placed Monocillium in synonymy with Torulomyces, and later Kendrick & Carmichael (1973) made the combination Torulomyces indicus. However, a BLAST search with the ITS sequence of the type strain of M. indicum (UAMH 1499, GenBank GQ169328) showed that the closest relatives are among Hypocreaceae (Sigler et al. 2010). This is in agreement with Gams (1971), who showed that Monocillium species are anamorphs related to Niesslia species. accepted Penicillium and Eupenicillium species mentioned in the list of “accepted species and their synonyms in Trichocomaceae” (Pitt et al. 2000) were used as a starting point for dividing the species among the various sections, updated species described after 2000. In various cases, the same Penicillium and Eupenicillium species share the same ex-type specimen. However, if the type material of the Penicillium morph differs from the Eupenicillium morph, then both ex-type strains were included in the study and additional comments are given in the text. Part Three: Sectional delimitation within Penicillium s. str. = Eupenicillium sect. Pinetorum (Pitt) Stolk & Samson, Stud. Mycol. 23: 88. 1983. Classification Dierckx (1901) proposed the first infrageneric classification of Penicillium and introduced the subgenera Aspergilloides, Biverticillium and Eupenicillium (Biourge 1923). Biourge (1923) expanded this subdivision and accepted two subgenera, two sections, four series and six subsections. The sections Bulliardium (Asymetrica) was introduced by Biourge (1923) and in this section Penicillium species with branched conidiophores were included. No type species was designated and species with terverticillate conidiophores belong to Biourge´s definition of his section Bulliardium (Asymetrica). We decided to synonymise this section with section Penicillium. The section Biverticillium belongs to Talaromyces s. str. and is not treated here (Fig. 1). In the classical work of Thom (1930: 155–159), Penicillium is divided in four subgenera (although not named as such), and 12 sections and 17 subsections. Raper & Thom (1949) introduced various new sections, subsections and series and Ramírez (1982) largely followed Raper and Thom’s classification. Neither provided Latin descriptions for their newly introduced sections (and series), and these names are therefore regarded as nomen invalidum are not considered further here. Pitt (1980) divided Penicillium into four subgenera, 10 sections and 21 series. Five years later, Stolk & Samson (1985) proposed another taxonomic scheme for Penicillium anamorphs. In the latter taxonomic scheme, both sexual and asexual species were treated. More recently, Samson & Frisvad (2004) revised subgenus Penicillium and five sections and 17 series were recognised. An overview of sections and their type species of the studies of Thom (1930), Pitt (1980), Stolk & Samson (1985) and Frisvad & Samson (2004) is shown in Table 5. The classification of Eupenicillium does not have such a long history: Pitt (1980) was the first, and introduced eight series. In the monograph of Stolk & Samson (1983), four sections were introduced for the grouping of the Eupenicillium species and Pitt’s infrageneric concept of classifying species in series was abandoned. Accepted species and their position in the sections of Penicillium The phylogenetic relationship among Penicillium s. str. was studied using combined sequence data of four loci. Based on these results (Fig. 7), Penicillium is subdivided into two subgenera and 25 sections. An overview of these sections is presented in Table 5, together with the type species of each section. In our study, a new sectional subdivision is proposed and older names at different ranks (e.g. subgeneric, subsection and series names) and invalid names (Raper & Thom 1949, Ramírez 1982) are not considered. Assignment of the species to the various sections was mainly based on the overviews presented in Figs 8 and 10–13 and other published molecular-based data. The www.studiesinmycology.org Clade 1: section Aspergilloides In: Penicillium subgenus Aspergilloides. Type: Penicillium aurantiobrunneum Dierckx Most members of this section grow quickly on agar media, form velvety colonies and are predominantly monoverticillate. This section corresponds to group 2 of Peterson (2000a). Two teleomorph species are positioned in this section: P. fuscum and P. saturniforme. Stolk (1968) found ascospores in an old culture of the type strain of P. pinetorum and described the ascosporic state as Eupenicillium pinetorum. Later, the anamorph of E. pinetorum was linked to P. fuscum (Stolk & Samson 1983); the latter name is older than P. pinetorum and therefore used here. The taxonomic position of P. lapidosum warrants further attention. Peterson (2000a) suggested that this species is conspecific with P. thomii. However, our results show that the type strain of this species (CBS 343.48T) is phylogenetically related to P. namyslowskii (Fig. 7, clade 10) and therefore unrelated to section Aspergilloides. Based on the data presented in Fig. 8 and literature (Peterson 2000a, Peterson & Horn 2009, Wang & Zhuang 2009, Barreto et al. 2011), we place the following species in section Aspergilloides: Penicillium ardesiacum Novobranova, Novosti Sist. Nizs. Rast. 11: 228. 1974. Penicillium asperosporum Smith, Trans. Br. Mycol. Soc. 48: 275. 1965. Penicillium crocicola Yamamoto, Scient. Rep. Hyogo Univ. Agric., Agric. Biol. Ser. 2, 2: 28. 1956. Penicillium fuscum (Sopp) Biourge, Cellule 33: 103. 1923 (Stolk & Samson 1983). Penicillium georgiense Peterson & Horn, Mycologia 101: 79. 2009. Penicillium glabrum (Wehmer) Westling, Ark. Bot. 11: 131. 1911 (syn. P. terlikowskii; Barreto et al. 2011). Penicillium kananaskense Seifert, Frisvad & McLean, Can. J. Bot. 72: 20. 1994 (unpubl. data, K.A. Seifert). Penicillium lapatayae Ramírez, Mycopathol. 91: 96. 1985 (Frisvad et al. 1990c). Penicillium lividum Westling, Ark. Bot. 11: 134. 1911. Penicillium montanense Christensen & Backus, Mycologia 54: 574. 1963. Penicillium odoratum Christensen & Backus, Mycologia 53: 459. 1962 (this study, Fig. 8). Penicillium palmense Ramírez & Martínez, Mycopathol. 66: 80. 1978. Penicillium patens Pitt & Hocking, Mycotaxon 22: 197. 1985. Penicillium quercetorum Baghdadi, Nov. Sist. Niz. Rast. 5: 110. 1968. 29 30 P. fractum P. gracilentum P. janthinellum P. ochrosalmoneum A. paradoxus P. expansum P. cyaneum P. lanosum P. roqueforti P. sclerotiorum P. stolkiae S. glauco-albidum P. lagena P. turbatum Fasciculata* Fracta Gracilenta Lanata-divaricata Ochrosalmonea Paradoxa Penicillium* Ramigena Ramosa Roquefortorum* Sclerotiora Stolkia Thysanophora Torulomyces Turbata Cylindrosporum Divaricatum Inordinate Penicillium Undefined; similar to Lanata-divaricata P. janthinellum-type P. camemberti P. minioluteum Miscellaneous species and genera Undefined section Citromyces species Undefined section Funiculosa Lanata-divaricata Lanata-typica Luteo-virida Miscellanea (Monoverticillata)-stricta (Monoverticillata)-Ramigena Velutina P. minioluteum P. expansum P. arenicola P. oxalicum P. restrictum P. janthinellum Torulomyces Ramosum Penicillium Inordinate Geosmithia Eladia Divaricatum P. lagena P. lanosum P. expansum P. arenicola P. lavendulum P. sacculum P. janthinellum P. duclauxii P. minioluteum Exilicaulis Eladia Digitata* Citrina Cinnamopurpurea Chrysogena* Charlesii Canescentia Brevicompacta* P. viridicatum P. restrictum P. sacculum P. digitatum P. citrinum P. cinnamopurpureum P. chrysogenum P. charlesii P. canescens P. olsonii * Frisvad & Samson (2004) divided subgenus Penicillium in six sections. This sectional classification is supported by extrolite, phenotypic and physiological data and their subdivision is followed here. The results of our analysis based on partial RPB2 data (Fig. 13) do not confirm these sections; however, partial β-tubulin data largely confirmed their polyphasic classification (Samson et al. 2004). Simplicium Furcatum Exilicaulis P. italicum Coremigenum Biverticillium P. aurantiobrunneum Type species Fasiculate Penicillia e.g. P. hirsutum P. olsonii P. duclauxii Aspergilloides Fasciculata Section Coronatum Coremigenum P. glabrum Type species P. duclauxii Aspergilloides Section P. brevicompactum P. aurantiobrunneum Type species Coremigena Aspergilloides Brevi-compacta Section P. luteum Current study Type species Stolk & Samson (1985) Ascogena Pitt (1980) Section Thom (1930) Table 5. Overview of sectional classification in different studies of Penicillium Houbraken & Samson Phylogeny of Penicillium and Trichocomaceae CBS 347.59 P. thomii CBS 125543NT P. glabrum Clade 1: sect. Aspergilloides (Fig. 8) CBS 295.62NT P. fuscum 98/* CBS 122276T P. saturniforme CBS 117503T P. thiersii */* */* CBS 336.48NT P. herquei -/* CBS 647.95HT P. malachiteum Clade 2: sect. Sclerotiora (Fig. 8) 98/* CBS 229.60NT P. hirayamae 63/1.00 CBS 209.28 209 28LT P. P adametzii */* CBS 229.81NT P. fellutanum -/0.98 */* CBS 304.48T P. charlesii Clade 3: sect. Charlesii (Fig. 8) CBS 119387T P. coffeae CBS 277.58T P. griseolum */* CBS 206.57T P. taxi Clade 4: sect. Thysanophora 57/CBS 334.68T P. hennebertii */* CBS 489.66 P. ochrosalmoneum Clade 5: sect. Ochrosalmonea (Fig. 12) CBS 247.56T P. isariiforme */* CBS 112493T P. ellipsoideosporum 89/0 99 89/0.99 CBS 341.68 341 68T P. P idahoense Cl d 6: Clade 6 sect. t Cinnamopurpurea Ci (Fi 10) (Fig. */* CBS 228.89T P. shennangjianum 59/CBS 490.66 P. cinnamopurpureum */* CBS 251.56T P. ramusculum Clade 7: sect. Ramigena (Fig. 10) CBS 190.68T P. ornatum 92/* CBS 271.89HT P. cryptum */* CBS 185.65NT P. lagena Clade 8: sect. Torulomyces 74/CBS 277.70 P. lassenii */* CBS 351.67T P. inusitatum Clade 9: sect. Fracta CBS 124.68T P. fractum NT / */* CBS 367.48 367 48 P. P restrictum 91/0.93 CBS 247.67T P. katangense NT -/CBS 258.29 P. citreonigrum */* CBS 317.67HT P. alutaceum CBS 353 48NT P. namyslowskii 76/* Clade 10: sect. Exilicaulis (Fig. 10) */* CBS 343.48T P. lapidosum CBS 231.38 P. corylophilum 93/* -/68/0.94 CBS 352.67HT P. catenatum */* CBS 318.67HT P. erubescens */* CBS 203.84HT P. nepalense CBS 456.70 456 70T P. P dimorphosporum 97/* CBS 233.81 P. caperatum (NT of E. brefeldianum) 65/* CBS 341.48T P. javanicum Lineage 1 62/0.97 CBS 219.30NT P. oxalicum */* Aspergilloides CBS 340.48NT P. janthinellum Clade 11: sect. Lanata-divaricata (Fig. 11) 84/* */* CBS 246.67HT P. abidjanum NT 69/CBS 372.48 P. simplicissimum CBS 315.67HT P. stolkiae Clade 12: sect. Stolkia (Fig. 11) 97/* */* CBS 11687T P. macrosclerotiorum Clade 13: sect. Gracilenta (Fig. 10) CBS 599.73T P. gracilentum CBS 232.38 232 38 P. P citrinum (Type of P. P implicatum) */* CBS 139.45NT P. citrinum */* Clade 14: sect. Citrina (Fig. 12) CBS 290.48T P. shearii CBS 323.71NT P. euglaucum 97/* CBS 344.61T P. kewense Clade 15-19, details see Fig. 13: 76/0.93 CBS 306.48NT P. chrysogenum */* -/100 CBS 185.27NT P. griseofulvum sect. Fasiculata CBS 462.72HT P. osmophilum sect. Digitata NT 57/CBS 339.48 P. italicum 96/* NT P. expansum sect. Penicillium CBS 325.48 */* CBS 112082epiT P. P digitatum sect sect. Roquefortorum NT */* CBS 390.48 P. viridicatum */* */* sect. Chrysogena CBS 299.48AUT P. camemberti CBS 603.74NT P. verrucosum */* Clade 20, 21: sect. Turbata, Paradoxa CBS 527.65T Aspergillus paradoxus */* CBS 430.69T P. tularense Clade 22, 23: sect. Brevicompacta, */* CBS 232.60NT P. olsonii */* Ramosa (Fig. 13) NT CBS 106.11 P. lanosum Lineage 2 */* CBS 300.48NT P. canescens Clade 24: sect. Canescentia (Fig. 13) CBS 241.56NT P. atrovenetum s/g Penicillium */* */* CBS 231.61NT P. sacculum Clade 25: sect. sect Eladia (Fig. (Fig 13) CBS 316.67 P. senticosum CBS 513.88 Aspergillus niger ATCC 18227T Talaromyces (= Penicillium) marneffei 0.1 */* */* */* s/g Fig. 7. Best-scoring Maximum Likelihood tree using RAxML based on combined data set of partial Cct8, Tsr1, RPB1 and RPB2 sequences showing the relationship among members of Penicillium s. str. Penicillium s. str. is divided in two lineages (s/g Aspergilloides and Penicillium) and 25 sections. The BI posterior probabilities (pp) values and bootstrap (bs) percentages of the maximum likelihood (ML) analysis are presented at the nodes (bs/pp). Values less than 70 % supported in the ML or less than 0.95 in the Bayesian analysis are indicated with a hyphen, whereas asterisks indicate good support (100 % bs or 1.00 pp). The branches with more than 95 % bootstrap support and 1.00 posterior probability values are thickened. The bar indicates the number of substitutions per site. The tree is rooted with Penicillium (= Talaromyces) marneffei ATCC 18227T. Penicillium saturniforme (Wang & Zhuang) Houbraken & Samson, Stud. Mycol. 70: 48. 2011 (this study). Penicillium spinulosum Thom, Bull. Bur. Anim. Ind. U.S. Dep. Agric. 118: 76. 1910. Penicillium subericola Barreto, Frisvad & Samson, Fungal Diversity 49: 32. 2011. www.studiesinmycology.org Penicillium thiersii Peterson, Bayer & Wicklow, Mycologia 96: 1283. 2004. Penicillium thomii Maire, Bull. Soc. Hist. Nat. Afrique N. 8: 189. 1917. 31 Houbraken & Samson */* CBS 125096T P. subericola -/- CBS 374.48NT P. spinulosum CBS 336.79NT P. palmense CBS 347.59 P. thomii */98 */CBS 260.87HT P. patens CBS 745.70IsoT P. crocicola 0.96/72 */* CBS 229.28 P. glabrum */96 CBS 105.11 P. glabrum */99 CBS 125453NT P. glabrum NRRL 35684 P. glabrum (EF198601) */* CBS 324.83 P. asperosporum */96 /96 CBS 309.63 P. fuscum 0.99/94 CBS 295.62NT P. fuscum -/- CBS 235.60 P. fuscum -/*/99 CBS 127833HT “Eladia” inflata 0.98/90 CBS 310.63HT P. montanense 0.99/77 CBS 497.73NT P. ardesiacum NRRL 35682 P. species (EF198600) */99 294.62 62T P. P odoratum */99 CBS 294 CBS 347.48NT P. lividum */89 -/CBS 417.69IsoT P. quercetorum CBS 122276T P. saturniforme CBS 117503T P. thiersii */* CBS 305.48 “P. chermisinum” -/*/* CBS 231.81 “P. chermisinum” so P. -/87 CBS 115 115.63 63IsoT P indicum CBS 119387T P. coffeae */* CBS 249.32NT P. phoeniceum */* */95 CBS 330.59 P. charlesii -/95 CBS 326.59 P. charlesii */* CBS 304.48T P. charlesii -/IBT 15460NT P. fellutanum */* / CBS 330.90T P. nodositatum CBS 221.66NT P. bilaiae -/86 IBT 27051T P. angulare */* */82 CBS 313.59T P. adametzioides */99 CBS 192.87NT P. jugoslavicum CBS 116113HT P. brocae -/80 CBS 209.28NT P. adametzii */88 CBS 287.36NT P. sclerotiorum */* */96 */97 NRRL 2060 P. multicolor (EU427262) NRRL 143NT P. hirayamae (EU021625) */99 CBS 336.48NT P. herquei */97 */* CBS 347.51T P. luteocoeruleum CBS 647.95HT P. malachiteum NRRL 2162HT Aspergillus paradoxus (EF669670) */* */* CBS 325.48NT P. expansum CBS 231.61NT P. sacculum NRRL326NT Aspergillus niger CBS 310.38NT Talaromyces flavus */72 Clade 1: sect Aspergilloides sect. Clade 3: sect. Charlesii Clade 2: sect. Sclerotiora 0.1 Fig. 8. Best-scoring Maximum Likelihood tree using RAxML based on partial RPB2 sequences and giving an overview of the members accommodated in sections Aspergilloides, Sclerotiora and Charlesii. The BI posterior probabilities (pp) values and bootstrap (bs) percentages of the maximum likelihood (ML) analysis are presented at the nodes (pp/ bs). Values less than 70 % supported in the ML or less than 0.95 in the Bayesian analysis are indicated with a hyphen, whereas asterisks indicate good support (100 % bs or 1.00 pp). The branches with more than 95 % bootstrap support and 1.00 posterior probability values are thickened. The bar indicates the number of substitutions per site. The tree is rooted with Talaromyces flavus CBS 310.38NT. Clade 2: section Sclerotiora Houbraken & Samson, sect. nov. MycoBank MB563124. Sectio in Penicillio subgen. Aspergilloide. Mycelio saepe colorato, plus minusve flavido et/vel aurantiaco. Sclerotis/cleistotheciis claris. colore. 32 In: Penicillium subgenus Aspergilloides Type: Penicillium sclerotiorum van Beyma Phylogeny of Penicillium and Trichocomaceae Members of section Sclerotiora generally have monoverticillate conidiophores; however, exceptions are P. malachiteum, P. nodositatum and P. herquei, which form symmetrically biverticillate conidiophores. The mycelium of members of sect. Sclerotiora is pigmented in shades of yellow and/or orange, reverse colony colours in shades of yellow, orange or red, and sclerotia and cleistothecia are, if present, bright coloured. Species belonging to this section occur regularly in and are abundant upon substrata exposed to soil. This section corresponds with group 3 of Peterson (2000a). Our list of species belonging to this section was composed based on the data presented in Fig. 8 and studies by Peterson (2000a), Peterson et al. (2003, 2004), Peterson & Horn (2009), Nonaka et al. (2011) and Rivera & Seifert (2011). Isolate NRRL 2060 is included in Fig. 8 and Peterson & Horn (2009) treated this strain as the type of P. multicolor. However, Raper & Thom’s (1949) isolates of P. multicolor differ in significant features from the original description of Grigorieva-Manoilova & Poradielova (1915) (Pitt 1980), and Rivera & Seifert (2011) treated this species as a synonym of P. fellutanum. Penicillium nodositatum shares identical partial RPB2 sequences with P. bilaiae and might be conspecific with the latter species. More research is needed because the former species produces biverticillate conidiophores and the latter strictly monoverticillate structures (Pitt 1980, Valla et al. 1989). Type: Penicillium charlesii Smith Penicillium adametzii Zaleski, Bull. Int. Acad. Polon. Sci., Cl. Sci. Math., Sér. B, Sci. Nat., 1927: 507. 1927. Penicillium adametzioides Abe ex Smith, Trans. Br. Mycol. Soc. 46: 335. 1963. Penicillium angulare Peterson, Bayer & Wicklow, Mycologia 96: 1289. 2004. Penicillium bilaiae Chalabuda, Bot. Mater. Otd. Sporov. Rast. 6: 165. 1950. Penicillium brocae Peterson, Pérez, Vega & Infante, Mycologia 95: 143. 2003. Penicillium cainii Rivera & Seifert, Stud. Mycol. 70: 147. 2011. Penicillium guanacastense Rivera, Urb & Seifert, Mycotaxon, in press. 2011. Penicillium herquei Bainier & Sartory, Bull. Soc. Mycol. France 28: 121. 1912. Penicillium hirayamae Udagawa, J. Agric. Sci. Tokyo Nogyo Daigaku 5: 6. 1959. Penicillium jacksonii Rivera & Seifert, Stud. Mycol. 70: 151. 2011. Penicillium johnkrugii Rivera & Seifert, Stud. Mycol. 70: 151. 2011. Penicillium jugoslavicum Ramírez & Muntañola-Cvetkovic, Mycopathol. 88: 65. 1984. Penicillium malachiteum (Yaguchi & Udagawa) Houbraken & Samson, Stud. Mycol. 70: 47. 2011 (this study). Penicillium mallochii Rivera, Urb & Seifert Mycotaxon, in press. 2011. Penicillium nodositatum Valla, Plant and Soil 114: 146. 1989. Penicillium sclerotiorum van Beyma, Zentralbl. Bakteriol., 2. Abt., 96: 418. 1937. Penicillium viticola Nonaka & Masuma, Mycoscience 52: 339. 2011. Clade 4: section Thysanophora Houbraken & Samson, sect. nov. MycoBank MB563126. Clade 3: section Charlesia Houbraken & Samson, sect. nov. MycoBank MB563125. Sectio in Penicillio subgen. Aspergilloide. Solum in CYA, conidiophoris ad apicem inflatis. In: Penicillium subgenus Aspergilloides www.studiesinmycology.org The phylogeny of this section was studied by Peterson et al. (2005). In the same study, an overview was presented of phenotypic characters to differentiate species within section Charlesii. It was stated that the overall phenotypic similarity of these species is striking; however, no shared characters were given. With exception of P. indicum, all members of section Charlesii grow restricted on CYA and have conidiophores with an apical swelling. Species of this section can be strictly monoverticillate, but P. charlesii and P. fellutanum can also be irregularly biverticillate. Included species are based on the data presented in Fig. 8 and Peterson (2000a) and Peterson et al. (2005). Penicillium charlesii Smith, Trans. Br. Mycol. Soc. 18: 90. 1933. Penicillium coffeae Peterson, Vega, Posada & Nagai, Mycologia 97: 662. 2005. Penicillium fellutanum Biourge, Cellule 33: 262. 1923. Penicillium georgiense Peterson & Horn, Mycologia 101: 79. 2009. Penicillium indicum Sandhu & Sandhu, Can. J. Bot. 41: 1273. 1963 (syn. P. gerundense, Peterson & Horn 2009). Penicillium phoeniceum van Beyma, Zentralbl. Bakteriol., 2. Abt., 88: 136. 1933. Sectio in Penicillio subgen. Aspergilloide. Coloniis pullis, conidiophoris pigmentatis, compactis et incremento secundario stipitis per proliferationem penicillii apicali. In: Penicillium subgenus Aspergilloides Type: Sclerotium glauco-albidum Desmazières The genus Thysanophora is placed in synonymy with Penicillium (see above). The section is characterised by the formation dark coloured colonies, pigmented and stout conidiophores and the majority of species have secondary growth of the stipe by means of the proliferation of an apical penicillius. Nine specific epithets have been combined with Thysanophora, and eight are accepted species. Mercado-Sierra et al. (1998) is largely followed here and the following species belong in section Thysanophora: Penicillium asymmetricum (Subramanian & Sudha) Houbraken & Samson, Stud. Mycol. 70: 47. 2011 (this study). Penicillium coniferophilum Houbraken & Samson, Stud. Mycol. 70: 47. 2011 (this study). Penicillium glaucoalbidum (Desmazières) Houbraken & Samson, Stud. Mycol.70: 47. 2011 (this study). Penicillium hennebertii Houbraken & Samson, Stud. Mycol. 70: 47. 2011 (this study). Penicillium longisporum (Kendrick) Houbraken & Samson, Stud. Mycol. 70: 47. 2011 (this study). Penicillium melanostipe Houbraken & Samson, Stud. Mycol. 70: 47. 2011 (this study). Penicillium taiwanense (Matsushima) Houbraken & Samson, Stud. Mycol. 70: 48. 2011 (this study). Penicillium taxi Schneider, Zentralblatt für Bakteriologie und Parasitenkunde, Abteilung 2, 110: 43. 1956. Clade 5: section Ochrosalmonea Houbraken & Samson, sect. nov. MycoBank MB563127. 33 Houbraken & Samson Fig. 9. Penicillium isariiforme CBS 247.56. A. Colonies grown for 14 d at 25 °C, from left to right: MEA, YES, CYA. B–D. Conidiophores. E. Conidia. Scale bar = 10 µm. Sectio in Penicillio subgen. Aspergilloide. Mycelio conspicue pigmentoso, flavido; phialidibus ampulliformibus vel acerosis; conidiis apiculatis. In: Penicillium subgenus Aspergilloides Type: Penicillium ochrosalmoneum Udagawa Penicillium ochrosalmoneum and P. isariiforme are accommodated in section Ochrosalmonea (Fig. 5, clade 5). Both species seem macroscopically dissimilar. Penicillium isariiforme grows quickly on agar media MEA and CYA (Pitt 1980) and forms characteristic feather-like synnemata (Samson et al. 1976, Fig. 9). In contrast, P. ochrosalmoneum isolates grow slowly on agar media and forms a velutinous colony surface (Pitt 1980). However, both species form conspicuous yellow coloured mycelium, ampulliform to acerose shaped phialides and apiculate conidia. The classification of P. isariiforme in Penicillium was subject of various studies. This species was classified in subgenus Biverticillium (= Talaromyces s. str.) (Pitt 1980, Frisvad & Filtenborg 1983), but also in subgenus Penicillium (= Penicillium s. str.) (Ramírez 1982, Samson et al. 1976). Figure 7 shows that P. isariiforme phylogenetically belongs to subgenus Aspergilloides in Penicillium s. str. 34 The holotype of Eup. ochrosalmoneum is CBS 489.66 and CBS 231.60 is the ex-type of P. ochrosalmoneum. The strains share identical partial RPB2 sequences and therefore E. ochrosalmoneum is regarded as conspecific with P. ochrosalmoneum (Fig. 12). Based on the data presented in Fig. 12, the following species belong in section Ochrosalmonea. Penicillium isariiforme Stolk & Meyer, Trans. Br. Mycol. Soc. 40: 187. 1957. Penicillium ochrosalmoneum Udagawa, J. Agric. Sci. Tokyo Nogyo Daigaku 5: 10. 1959. Clade 6: section Cinnamopurpurea Houbraken & Samson, sect. nov. MycoBank MB563128. Sectio in Penicillio subgen. Aspergilloide. Sect. Ornatis similis, sed conidiophoris semper simplicibus vel biverticillate divaricates; stipitibus cum conidiophoris distincte vesiculosis. In: Penicillium subgenus Aspergilloides Type: Penicillium cinnamopurpureum Udagawa Phylogeny of Penicillium and Trichocomaceae Members of section Cinnamopurpurea grow slowly on MEA and CYA and can be strictly monoverticillate, but species with biverticillate conidiophores are also present in this section. The majority of the species have distinct vesicular conidiophores. This section is phenotypically related to section Ornata; however, statistical support for this relationship is lacking in our phylogenetic analysis (Fig. 7). Penicillium cinnamopurpureum was originally described by Abe (1956) without a Latin diagnosis, and validated by Udagawa (1959). Stolk & Samson (1983) considered P. dierckxii the anamorph of Eupenicillium cinnamopurpureum and Pitt (1980) linked P. phoeniceum to E. cinnamopurpureum. Our data show that P. phoeniceum (sect. Charlesii, Fig. 8) and P. dierckxii (sect. Ramigena, Fig. 10) are phylogenetically distinct from P. cinnamopurpureum. Furthermore, partial RPB2 data show that the type strains of P. cinnamopurpureum (CBS 847.68) and E. cinnamopurpureum (CBS 490.66) are similar (Fig. 10). Penicillium chermesinum is also placed in this section. This species was neotypified with NRRL 2048 (= CBS 231.81), because the type culture, NRRL 735, no longer adequately represented Biourge’s protologue (Pitt 1980). Molecular analysis shows that these two species are phylogenetically unrelated. The ITS-partial 28S rDNA sequences of NRRL 735T (= GenBank no. AF033413) is related to P. cinnamopurpureum (Peterson 2000a) while the neotype of this species, NRRL 2048NT, (AY742693) is related to P. indicum in section Charlesii. Based on the data presented in Fig. 10 and Peterson & Horn (2009), the following species are accommodated in Cinnamopurpurea. Penicillium chermesinum Biourge, Cellule 33: 284. 1923. Penicillium cinnamopurpureum Udagawa, J. Agric. Food Sci., Tokyo 5: 1. 1959. Penicillium ellipsoideosporum Wang & Kong, Mycosystema 19: 463. 2000. Penicillium idahoense Paden, Mycopath. Mycol. Appl. 43: 261. 1971 (Peterson & Horn 2009, this study). Penicillium incoloratum Huang & Qi, Acta Mycol. Sin. 13: 264. 1994. Penicillium malacaense Ramírez & Martínez, Mycopathologia 72: 186. 1980 (syn. P. ovetense, this study) (Peterson & Horn 2009). Penicillium nodulum Kong & Qi, Mycosystema 1: 108. 1988. Penicillium parvulum Peterson & Horn, Mycologia 101: 75. 2009. Penicillium shennangjianum Kong & Qi, Mycosystema 1: 110. 1988. Clade 7: section Ramigena Thom, The Penicillia: 225. 1930. In: Penicillium subgenus Aspergilloides Type: Penicillium cyaneum (Bainier & Sartory) Biourge This section is based on Thom’s section Ramigena. Thom (1930) introduced this section for species where monoverticillate conidiophores are evident, but divaricate branching at various levels without a definiteness of organisation or arrangement is consistently observed. Most species illustrated by Banier & Sartory (1913) as species of Citromyces are accommodated in this section (fide Thom 1930). Members of the section Ramigena share the following characters: a slow growth rate on agar media, a monoverticillate branching system with non-vesiculate stipes. Conidia are relatively large (3–4 µm), smooth and ellipsoidal or pyriform (Pitt 1980). Penicillium ornatum is the sole member known in this section with a teleomorph (Udagawa 1968, Pitt 1980). The ascospores of this www.studiesinmycology.org species are ornamented with two and sometimes four longitudinal flanges. The ex-type culture of P. implicatum in the CBS collection (CBS 232.38) is a Penicillium citrinum, and therefore this species is not accepted as distinct (Frisvad et al. 1990b, Houbraken et al. 2010b). Pitt (1980) neotypified P. implicatum with CBS 184.81 and Fig. 10 shows that this strain is closely related to the type of Penicillium hispanicum CBS 691.77. This neotypification is not accepted here and P. implicatum sensu Pitt is considered as a synonym of P. hispanicum. Pitt et al. (2000) accepted P. dierckxii, P. cyaneum and P. sublateritium as single species in their overview of accepted species in Penicillium. This concept is followed here; however, partial RPB2 data (Fig. 10) shows that these three species are very closely related and might represent one species. Penicillium capsulatum Raper & Fennell, Mycologia 40: 528. 1948. Penicillium cyaneum (Bainier & Sartory) Biourge, Cellule 33: 102. 1923. Penicillium dierckxii Biourge, Cellule 33: 313. 1923. Penicillium hispanicum Ramírez, Martínez & Ferrer, Mycopathol. 66: 77. 1978 (syn. Penicillium implicatum sensu Pitt). Penicillium ornatum Udagawa, Trans. Mycol. Soc. Japan 9: 49. 1968. Penicillium ramusculum Batista & Maia, Anais Soc. Biol. Pernamb. 13: 27. 1955 (syn. P. brevissimum Rai & Wadhwani) (this study, Peterson & Horn 2009). Penicillium sublateritium Biourge, Cellule 33: 315. 1923. Clade 8: section Torulomyces (Delitsch) Stolk & Samson, Adv. Pen. Asp. Syst.: 169. 1985. In: Penicillium subgenus Aspergilloides Type: Penicillium lagena (Delitsch) Stolk & Samson The genus Torulomyces is synonymised with Penicillium and consequently the majority of the species described in Torulomyces are transferred to Penicillium (this study). Figure 7 shows that P. lagena is related to P. cryptum and P. lassenii. These species have a slow growth rate on the agar media CYA and MEA and form shortstiped monoverticillate or terminal biverticillate conidiophores. Phialides are predominantly singly formed in P. lagena, short, 4–7 µm long, with a narrowed base and a swollen middle that tapers abruptly into a narrow neck (Fig. 6). Penicillium cryptum Gochenaur, Mycotaxon 26: 349. 1986. Penicillium lagena (Delitsch) Stolk & Samson, Stud. Mycol. 23: 100. 1983. Penicillium laeve (K. Ando & Manoch) Houbraken & Samson, Stud. Mycol. 70: 47. 2011 (this study). Penicillium lassenii Paden, Mycopathol. Mycol. Appl. 43: 266. 1971. Penicillium ovatum (K. Ando & Nawawi) Houbraken & Samson, Stud. Mycol. 70: 48. 2011 (this study). Penicillium parviverrucosum (K. Ando & Pitt) Houbraken & Samson, Stud. Mycol. 70: 48. 2011 (this study). Penicillium porphyreum Houbraken & Samson, Stud. Mycol. 70: 48. 2011 (this study). Clade 9: section Fracta Houbraken & Samson, sect. nov. MycoBank MB563129. Sectio in Penicillio subgen. Aspergilloide. Coloniis in agaro tarde crescentibus; ascosporis spinulosis; phialidibus ampullifomibus vel lanceolatis; conidiis ellipsoideis. 35 Houbraken & Samson CBS 261.87HT P. sabulosum CBS 256.87T P. corynephorum 0.99/74 CBS 276.83NT P. smithii */* CBS 280.58 P. melinii CBS 218.30NT P. melinii 0.97/CBS 380.75IsoT P. atrosanguineum CBS 224.28NT P. raciborskii */99 -/81 CBS 622.72IsoT P. luzoniacum -/- CBS 313.67HT P. terrenum */99 /99 CBS 255.87 P.chalybeum */* CBS 325.89T P. burgense */* CBS 343.48T P. lapidosum -/CBS 353.48NT P. namyslowskii */* CBS 330.79 P. corylophilum */* CBS 231.38 P. corylophilum CBS 145.83HT P. rubefaciens CBS 689.77T P. fagi */99 CBS 230.81NT P. decumbens CBS 317.67HT P. alutaceum */83 CBS 226.89NT P. heteromorphum -/81 /81 CBS 222.66IsoT P. cinereoatrum */CBS 247.67T P. katangense */91 */* CBS 367.48NT P. restrictum CBS 623.72AUT P. philippinense CBS 314.67HT P. meridianum 0.99/93 */* NRRL 1187 P. citreonigrum (EF198501) */* NRRL 2046 P. citreonigrum (EF198502) NRRL 3127 P. toxicarium (EF198486) */98 NRRL 6172 P. toxicarium (EF198499) */* CBS 609.73HT P. rubidurum */90 CBS 102479HT P. pimiteouiense -/*/* CBS 570.73IsoT P. papuaneum */75 CBS 359.48NT P. parvum 0.96/70 CBS 389.48NT P. vinaceum CBS 318.67HT P. erubescens */99 CBS 705.68HT P. striatisporum -/CBS 352.67HT P. catenatum */95 0.95/CBS 203.84HT P. nepalense CBS 456.70T P. dimorphosporum */* CBS 341.68T P. idahoense -/CBS 112493T P. ellipsoideosporum */* CBS 163.81 P. malacaense 0.99/88 CBS 160.81T P. malacaense -/- CBS 227.89NT P. nodulum */* CBS 228.89T P. shennangjianum */* -/CBS 101753HT P. incoloratum */* CBS 847.68SynT P. cinnamopurpureum CBS 490.66 P. cinnamopurpureum CBS 315.48NT P. cyaneum */* CBS 267.29NT P. sublateritium */* CBS 185.81NT P. dierckxii */* CBS 184.81 “P. implicatum” sensu Pitt -/73 -/CBS 691.77T P. hispanicum CBS 190.68T P. ornatum */92 CBS 251.56T P. ramusculum */* CBS 763.68T P. brevissimum */* -/NRRL 2279 P. ramusculum (EU427260) CBS 301.48NT P. capsulatum CBS 125543NT P. glabrum */99 CBS 599.73T P. gracilentum */100 CBS 116871T P. macrosclerotiorum CBS 202.84HT P. angustiporcatum CBS 340.48NT P. janthinellum CBS 315.67HT P. stolkiae */* CBS 325.48NT P. expansum */* NRRL 2162HT Aspergillus paradoxus (EF669670) CBS 231.61NT P. sacculum NRRL326NT Aspergillus niger CBS 310.38NT Talaromyces flavus 0.99/98 */* Clade 10: sect. t Exilicaulis E ili li Clade 6: sect. Cinnamopurpurea Clade 7: sect. Ramigena */87 0.1 Clade 13: sect. Gracilenta Fig. 10. Best-scoring Maximum Likelihood tree using RAxML based on partial RPB2 sequences and giving an overview of the members accommodated in sections Exilicaulis, Cinnamopurpurea, Ramigena and Gracilenta. The BI posterior probabilities (pp) values and bootstrap (bs) percentages of the maximum likelihood (ML) analysis are presented at the nodes (pp/bs). Values less than 70 % supported in the ML or less than 0.95 in the Bayesian analysis are indicated with a hyphen, whereas asterisks indicate good support (100 % bs or 1.00 pp). The branches with more than 95 % bootstrap support and 1.00 posterior probability values are thickened. The bar indicates the number of substitutions per site. The tree is rooted with Talaromyces flavus CBS 310.38NT. In: Penicillium subgenus Aspergilloides Type: Penicillium ornatum Udagawa 36 Penicillium inusitatum and P. fractum belong to section Fracta and both are able to form a teleomorph. Pitt (1980) noted that these two species are closely related, differing principally in conidiophore structure. Both species share unusual ascospore morphology for Phylogeny of Penicillium and Trichocomaceae Penicillium species: the ascospores are spheroidal without flanges or furrows and ornamented by spines. Furthermore, both species grow slowly on agar media, form ampulliform to lanceolate phialides and ellipsoidal conidia. Phylogenetically, section Fracta might be related to section Torulomyces (72 % bs, < 0.95 pp). However, ascospores produced by the members of the latter section have two ridges (P. lagena, P. lassenii, P. cryptum). Penicillium fractum Udagawa, Trans. Mycol. Soc. Japan 9: 51. 1968. Penicillium inusitatum Scott, Mycopathol. Mycol. Appl. 36: 20. 1968. Clade 10: section Exilicaulis Pitt, The Genus Penicillium: 205. 1980. In: Penicillium subgenus Aspergilloides Type: Penicillium restrictum Gilman & Abbott = Eupenicillium section Lapidosa (Pitt) Stolk & Samson, Stud. Mycol. 23: 55. 1983. Pitt (1980) defined section Exilicaulis for monoverticillate species with stipes lacking a terminal vesicular swelling. The phylogenetic delimitation is broader and also several species with an additional branch are included (e.g. P. raciborski, P. melinii, P. velutinum, P. corylophilum). This section largely corresponds with group 4 of Peterson (2000a); the only difference is that Peterson placed P. turbatum in this clade, while our data shows that this species belongs to section Turbata (group 6 fide Peterson (2000a)). Based on Fig. 10 and data of Peterson et al. and Peterson 2000a, the following species are included in section Exilicaulis: Penicillium alutaceum Scott, Mycopathol. Mycol. Appl. 36: 17. 1968. Penicillium atrosanguineum Dong, Ceská Mycol. 27: 174. 1973. Penicillium burgense Quintanilla, Avances Nutr. Mejora Anim. Aliment. 30: 176. 1990. Penicillium catenatum Scott, Mycopathol. Mycol. Appl. 36: 24. 1968. Penicillium chalybeum Pitt & Hocking, Mycotaxon 22: 204. 1985. Penicillium cinerascens Biourge, Cellule 33: 308. 1923. Penicillium cinereoatrum Chalabuda, Bot. Mater. Otd. Sporov. Rast. 6: 167, 1950 (Frisvad et al. 1990c). Penicillium citreonigrum Dierckx, Ann. Soc. Sci. Bruxelles 25: 86. 1901. Penicillium corylophilum Dierckx, Ann. Soc. Sci. Bruxelles 25: 86. 1901. Penicillium decumbens Thom, Bull. Bur. Anim. Ind. U.S. Dep. Agric. 118: 71. 1910. Penicillium dimorphosporum Swart, Trans. Br. Mycol. Soc. 55: 310. 1970. Penicillium dravuni Janso, Mycologia 97: 445. 2005. Penicillium erubescens Scott, Mycopathol. Mycol. Appl. 36: 14. 1968. Penicillium fagi Ramírez & Martínez, Mycopathol. 63: 57. 1978. Penicillium flavidostipitatum Ramírez & González, Mycopathol. 88: 3. 1984 (preliminary sequencing results show that this species is closely related to P. namyslowskii). Penicillium guttulosum Gilman & Abbott, Iowa State Coll. J. Sci. 1: 298. 1927 (Peterson et al. 2011). Penicillium heteromorphum Kong & Qi, Mycosystema 1: 107. 1988. Penicillium katangense Stolk, Ant. van Leeuwenhoek 34: 42. 1968. www.studiesinmycology.org Penicillium lapidosum Raper & Fennell, Mycologia 40: 524. 1948. Penicillium maclennaniae Yip, Trans. Br. Mycol. Soc. 77: 202. 1981. Penicillium melinii Thom, Penicillia: 273. 1930. Penicillium menonorum Peterson, IMA Fungus 2: 122. 2011. Penicillium meridianum Scott, Mycopathol. Mycol. Appl. 36: 12. 1968. Penicillium namyslowskii Zaleski, Bull. Int. Aead. Polonc. Sci., Cl. Sci. Math., Sér. B, Sci. Nat., 1927: 479. 1927. Penicillium nepalense Takada & Udagawa, Trans. Mycol. Soc. Japan 24: 146. 1983. Penicillium parvum Raper & Fennell, Mycologia 40: 508. 1948 (this study). Penicillium philippinense Udagawa & Y. Horie, J. Jap. Bot. 47: 341. 1972. Penicillium pimiteouiense Peterson, Mycologia 91: 271. 1999. Penicillium raciborskii Zaleski, Bull. Int. Acad. Polon. Sci., Cl. Sci. Math., Sér. B, Sci. Nat., 1927: 454. 1927. Penicillium restrictum Gilman & Abbott, Iowa State Coll. J. Sci. 1: 297. 1927. Penicillium rubefaciens Quintanilla, Mycopathol. 80: 73. 1982. Penicillium rubidurum Udagawa & Horie, Trans. Mycol. Soc. Japan 14: 381. 1973. Penicillium smithii Quintanilla, Avances Nutr. Mejora Anim. Aliment. 23: 340. 1982 (syn. P. corynephorum, P. sabulosum). Penicillium striatisporum Stolk, Ant. van Leeuwenhoek 35: 268. 1969. Penicillium terrenum Scott, Mycopathol. Mycol. Appl. 36: 1. 1968. Penicillium toxicarium Miyake, Rep. Res. Inst. Rice Improvement 1: 1. 1940 (nom. inval., Art. 36) (Serra et al. 2008). Penicillium velutinum van Beyma, Zentralbl. Bakteriol., 2. Abt., 91: 353. 1935. Penicillium vinaceum Gilman & Abbott, Iowa State Coll. J. Sci. 1: 299. 1927. Clade 11: Section Lanata-divaricata Thom, The Penicillia: 328. 1930. = section Funiculosa Thom, The Penicillia: 358. 1930. = section Divaricatum Pitt, The Genus Penicillium: 238. 1980. = section Furcatum Pitt, The Genus Penicillium: 272. 1980. = Eupenicillium section Javanica (Pitt) Stolk & Samson, Stud. Mycol. 23: 55. 1983. In: Penicillium subgenus Aspergilloides Type: Penicillium janthinellum Biourge Most of the species, but not all, of section Lanata-divaricata grow rapidly and form broadly spreading colonies. The majority of the species belonging to this section are strongly divaricate and the metulae are born terminally, subterminally and in intercalary positions, and in the latter case intergrading with monoverticillate conidiophores. Furthermore, the terminal cluster often consists of a prolongation of the main axis. Species belonging to section Lanatadivaricata are mainly soil inhabitants, but may also occur on leaf litter and vegetable remains in the later stage of decomposition (Raper & Thom 1949, Houbraken et al. 2011c). Many species of this section are unusually tolerant for heavy metals and some species have been proposed as efficient biosorbent agents in the bioleaching of zinc oxide, copper, lead and nickel (Burgstaller et al. 1992, Valix et al. 2001, Li et al. 2008). Section Funiculosa is placed in synonymy with this section. Thom (1930) already noted that species belonging section 37 Houbraken & Samson Funiculosa have affinity with members of section Lanata-typica and that separation is hard to define. This observation is supported by our data: many species mentioned in Thom’s section Funiculosa belong to section Lanata-divaricata. Raper & Thom’s (1949) subsection Divaricata largely corresponds with our section Lanatadivaricata. They noted that members of their subsection have a definite relationship to Penicillium javanicum. Stolk & Samson (1983) also discussed this relationship and they placed 26 species in synonymy with Eupenicillium javanicum and P. simplicissimum. Recently, a phylogenetic study showed that many of these synonyms should be treated as separate species (Peterson 2000a, Houbraken et al. 2011c). This section largely corresponds with Peterson’s (2000a) group 5 and the list provided here for this section is mainly based on this data supplemented with data of Houbraken et al. (2011c). Penicillium cluniae, P. griseopurpureum and P. glaucoroseum were not included in these studies, though unpublished data shows that these three species also belong to this section. The typification of P. brefeldianum, P. javanicum, P. levitum and P. ehrlichii warrants further attention. Dodge (1933) described P. brefeldianum as a holomorphic species. Pitt (1980) did not accept teleomorph species in Penicillium and a neotype (CBS 233.81 = FRR 71 = IMI 216895) was selected because the original type culture of P. brefeldianum distributed by Dodge no longer produced cleistothecia. Subsequently, Dodge’s strain (CBS 235.81 = FRR 710 = IMI 216896 = NRRL 710) was used for the description of the anamorph of Eupenicillium brefeldianum (as Penicillium dodgei). Teleomorphs are allowed in Penicillium and therefore Dodge’s P. brefeldianum is re-instated. Furthermore, Fig. 11 shows that Dodge’s type strain (CBS 235.81) differs from Pitt’s neotype (CBS 233.81) and this neotype is similar to the type of P. caperatum (CBS 443.75T). Penicillium levitum, P. javanicum and P. ehrlichii were described including a teleomorph. Pitt (1980) introduced the new species names P. rasile, P. indonesiae and P. klebahnii respectively, for the anamorphs of P. levitum, P. javanicum and P. ehrlichii. These names are not used here for the same the reason as mentioned under P. brefeldianum. Penicillium abidjanum Stolk, Ant. van Leeuwenhoek 34: 49. 1968. Penicillium araracuarense Houbraken, C. López-Q, Frisvad & Samson, Int. J. Syst. Evol. Microbiol. 61: 1469. 2011. Penicillium brasilianum Batista, Anais Soc. Biol. Pernambuco 15: 162. 1957. Penicillium brefeldianum Dodge, Mycologia 25: 92. 1933 (syn. P. dodgei). Penicillium caperatum Udagawa & Horie, Trans. Mycol. Soc. Japan 14: 371. 1973 (syn. E. brefeldianum sensu Pitt). Penicillium cluniae Quintanilla, Avances Nutr. Mejora Anim. Aliment. 30: 174. 1990. (unpubl. data) Penicillium coeruleum Sopp apud Biourge, Cellule 33: 102. 1923. Penicillium cremeogriseum Chalabuda, Bot. Mater. Otd. Sporov. Rast. 6: 168. 1950. Penicillium daleae Zaleski, Bull. Int. Acad. Polon. Sci., Cl. Sci. Math., Sér. B, Sci. Nat., 1927: 495. 1927. Penicillium ehrlichii Klebahn, Ber. Deutsch. Bot. Ges. 48: 374. 1930. Penicillium elleniae Houbraken, C. López-Q, Frisvad & Samson, Int. J. Syst. Evol. Microbiol. 61: 1470. 2011. Penicillium glaucoroseum Demelius, Verh. Zool.-Bot. Ges. Wien 72: 72. 1923. (unpubl. data) Penicillium griseopurpureum Smith, Trans. Br. Mycol. Soc. 48: 275. 1965 (unpubl. data). 38 Penicillium janthinellum Biourge, Cellule 33: 258. 1923. Penicillium javanicum van Beyma, Verh. Kon. Ned. Akad. Wetensch., Afd. Natuurk., Tweede Sect., 26: 17. 1929 (syn. P. oligosporum, P. indonesiae). Penicillium levitum Raper & Fennell, Mycologia 40: 511. 1948 (syn. P. rasile). Penicillium limosum Ueda, Mycoscience 36: 451. 1995. Penicillium lineolatum Udagawa & Horie, Mycotaxon 5: 493. 1977. Penicillium ludwigii Udagawa, Trans. Mycol. Soc. Japan 10: 2. 1969. Penicillium mariaecrucis Quintanilla, Avances Nutr. Mejora Anim. Aliment. 23: 334. 1982. Penicillium meloforme Udagawa & Horie, Trans. Mycol. Soc. Japan 14: 376. 1973. Penicillium ochrochloron Biourge, Cellule 33: 269. 1923. Penicillium onobense Ramírez & Martínez, Mycopathol. 74: 44. 1981. Penicillium oxalicum Currie & Thom, J. Biol. Chem. 22: 289. 1915. Penicillium paraherquei Abe ex Smith, Trans. Br. Mycol. Soc. 46: 335. 1963. Penicillium penarojense Houbraken, C. López-Q, Frisvad & Samson, Int. J. Syst. Evol. Microbiol. 61: 1471. 2011. Penicillium piscarium Westling, Ark. Bot. 11: 86. 1911. Penicillium pulvillorum Turfitt, Trans. Br. Mycol. Soc. 23: 186. 1939 (Syn. P. ciegleri). Penicillium raperi Smith, Trans. Br. Mycol. Soc. 40: 486. 1957. Penicillium reticulisporum Udagawa, Trans. Mycol. Soc. Japan 9: 52. 1968. (syn. P. arvense). Penicillium rolfsii Thom, Penicillia: 489. 1930. Penicillium simplicissimum (Oudemans) Thom, Penicillia: 335. 1930. Penicillium skrjabinii Schmotina & Golovleva, Mikol. Fitopatol. 8: 530. 1974. Penicillium svalbardense Frisvad, Sonjak & Gunde-Cimerman, Ant. van Leeuwenhoek 92: 48. 2007. Penicillium vanderhammenii Houbraken, C. López-Q, Frisvad & Samson, Int. J. Syst. Evol. Microbiol. 61: 1473. 2011. Penicillium vasconiae Ramírez & Martínez, Mycopathol. 72: 189. 1980. Penicillium wotroi Houbraken, C. López-Q, Frisvad & Samson, Int. J. Syst. Evol. Microbiol. 61: 1474. 2011. Penicillium zonatum Hodges & Perry, Mycologia 65: 697. 1973. Clade 12: section Stolkia Houbraken & Samson, sect. nov. MycoBank MB563130. Sectio in Penicillio subgen. Aspergilloide. Conidiophoris pigmentatis, metulis subapicalibus sympodialiter proliferantibus; phialidibus nullis. In: Penicillium subgenus Aspergilloides Type: Penicillium stolkiae Scott Brown conidiophores occur in two phylogenetic unrelated sections of Penicillium s. str. One includes species belonging to section Thysanophora (previously assigned to the genus Thysanophora) (Iwamoto et al. 2002, Peterson & Sigler 2002) and the second lineage is centered around P. stolkiae, another species with conidiophores that also may be hyaline to definitely brown (Stolk & Samson 1983). Peterson & Sigler (2002) described four species with darkly melanised conidiophores, which are all closely related to P. stolkiae, namely P. subarticum, P. canariense, P. pullum and Phylogeny of Penicillium and Trichocomaceae */* CBS 121.68T P. reticulisporum CBS 513.74T P. reticulisporum */* CBS 233.81 ”P. brefeldianum” sensu Pitt 0.98/82 CBS 443 443.75 75T P. P caperatum T P. javanicum CBS 341.48 */* 0.99/86 CBS 349.51T P.oligosporum -/CBS 118135T P. elleniae */* CBS 345.48NT P. levitum CBS 141.45 P. coeruleum CBS 339.97T P. limosum -/*/* CBS 235 235.81 81T P. P brefeldianum -// NT P. cremeogriseum CBS 223.66 */94 -/CBS 340.48NT P. janthinellum 0.99/79 */93 CBS 281.58NT P. raperii CBS 188.77T P. lineolatum CBS 324.48T P. ehrlichii -/-/CBS 445.74T P. meloforme CBS 126216T P. P vanderhammenii d h ii */99 -/CBS 113178T P. penarojense -/CBS 211.28T P. daleae 0.96/CBS 246.67T P. abidjanum CBS 992.72T P. zonatum -/*/91 CBS 253.55T P. brasilianum -/91 CBS 430.65T P. paraherqei */* CBS 174.81NT P.onobense -/- -/74 CBS 439.75NT P. skrjabinii CBS 271.83T P. mariaecrucis -/-/87 CBS 328.59T P. echinulonalgiovense nom. inval. CBS 372.48NT P. simplicissimum 0.98/70 -/78 CBS 118171T P. wotroi CBS 113149T P. araracuarense */98 CBS 122416T P. svalvardense -/CBS 357.48NT P. ochrochloron -/CBS 275.83T P. ciegleri -/- */* CBS 280.39NT P. pulvillorum */94 CBS 362.48T P. piscarium CBS 368.48T P. rolfsii -/CBS 339.79T P. vasconiae CBS 111720HT P. canariense -/CBS 331.48 P. pullum */97 CBS 111717 P. boreae CBS 315.67HT P. stolkiae */* -/- CBS 111719HT P. subarcticum CBS 188.72HT P. donkii CBS C S 125543 55 3T P.glabrum g ab u Clade 11: sect. Lanata‐divaricata Clade 12: sect. Stolkia 0.1 Fig. 11. Best-scoring Maximum Likelihood tree using RAxML based on partial β-tubulin sequences and giving an overview of the members accommodated in sections Lanatadivaricata and Stolkia. The BI posterior probabilities (pp) values and bootstrap (bs) percentages of the maximum likelihood (ML) analysis are presented at the nodes (pp/bs). Values less than 70 % supported in the ML or less than 0.95 in the Bayesian analysis are indicated with a hyphen, whereas asterisks indicate good support (100 % bs or 1.00 pp). The branches with more than 95 % bootstrap support and 1.00 posterior probability values are thickened. The bar indicates the number of substitutions per site. The tree is rooted with Penicillium glabrum CBS 125543T. P. boreae. None of these species demonstrate the sympodial proliferation of subapical metulae and phialides present in section Thysanophora. The following species are placed in section Stolkia based on the data presented in Fig. 11 and of Peterson & Sigler (2002). www.studiesinmycology.org Penicillium boreae Peterson & Sigler, Mycol. Res. 106: 1112. 2002. Penicillium canariense Peterson & Sigler, Mycol. Res. 106: 1113. 2002. Penicillium donkii Stolk, Persoonia 7: 333. 1973. Penicillium pullum Peterson & Sigler, Mycol. Res. 106: 1115. 2002. 39 Houbraken & Samson Penicillium stolkiae Scott, Mycopathol. Mycol. Appl. 36: 8. 1968. Penicillium subarcticum Peterson & Sigler, Mycol. Res. 106: 1116. 2002. Clade 13: section Gracilenta Houbraken & Samson, sect. nov. MycoBank MB563131. Sectio in Penicillio subgen. Aspergilloide. Coloniis 37 °C haud crescentibus, reverso olivaceo-brunneo vel brunneo, conidiis saepe late ellipsoideis vel ellipsoideis. In: Penicillium subgenus Aspergilloides Type: Penicillium gracilentum Udagawa & Horie Four species are placed in section Gracilenta. Comparison of the phenotypic characters did not reveal many significant similarities among these species. All species did not grow at 37 °C and have an olive-brown to brown reverse on agar media. With exception of P. macrosclerotiorum, all species produced broadly ellipsoidal to ellipsoidal conidia (Abe 1956, Udagawa & Horie 1973, Pitt 1980, Takada & Udagawa 1983, Wang et al. 2007). The taxonomy and phylogeny of these species is not well studied and future research might reveal more shared characters. Penicillium angustiporcatum Takada & Udagawa, Trans. Mycol. Soc. Japan 24: 143. 1983. Penicillium estinogenum Komatsu & Abe ex Smith, Trans. Br. Mycol. Soc. 46: 335. 1963. Penicillium macrosclerotiorum Wang, Zhang & Zhuang, Mycol. Res. 111: 1244. 2007. Penicillium gracilentum Udagawa & Horie, Trans. Mycol. Soc. Japan 14: 373. 1973. Clade 14: section Citrina Houbraken & Samson, sect. nov. MycoBank MB563132. Sectio in Penicillio subgen. Aspergilloide. Formatione conidiophorum symmetricorum biverticillatorum. In: Penicillium subgenus Aspergilloides Type: Penicillium citrinum Thom Species of section Citrina are commonly occurring in soil and the majority of the species form symmetrical biverticillate conidiophores. This section corresponds with group 1 of Peterson (2000a). The taxonomy of section Citrina is recently revised by Houbraken et al. (2010b, 2011b) and based on this data and Fig. 12, the following species are placed in section Citrina: Penicillium anatolicum Stolk, Ant. van Leeuwenhoek 34: 46. 1968. Penicillium argentinense Houbraken, Frisvad & Samson, Stud. Mycol. 70: 78. 2011. Penicillium atrofulvum Houbraken, Frisvad & Samson, Stud. Mycol. 70: 80. 2011. Penicillium aurantiacobrunneum Houbraken, Frisvad & Samson, Stud. Mycol. 70: 80. 2011. Penicillium cairnsense Houbraken, Frisvad & Samson, Stud. Mycol. 70: 83. 2011. Penicillium christenseniae Houbraken, Frisvad & Samson, Stud. Mycol. 70: 85. 2011. Penicillium chrzaszczii Zaleski, Bull. Int. Acad. Polon. Sci., Cl. Sci. Math., Sér. B, Sci. Nat., 1927: 464. 1927. 40 Penicillium citrinum Thom, Bull. Bur. Anim. Ind. U.S. Dep. Agric. 118: 61. 1910. Penicillium copticola Houbraken, Frisvad & Samson, Stud. Mycol. 70: 88. 2011. Penicillium cosmopolitanum Houbraken, Frisvad & Samson, Stud. Mycol. 70: 91. 2011. Penicillium decaturense Peterson, Bayer & Wicklow, Mycologia 96: 1290. 2004. Penicillium euglaucum van Beyma, Ant. van Leeuwenhoek 6: 269. 1940. Penicillium galliacum Ramírez, Martínez & Berenguer, Mycopathol. 72: 30. 1980. Penicillium godlewskii Zaleski, Bull. Int. Acad. Polon. Sci., Cl. Sci. Math., Sér. B, Sci. Nat., 1927: 466. 1927. Penicillium gorlenkoanum Baghdadi, Nov. Sist. Niz. Rast. 5: 97. 1968. Penicillium hetheringtonii Houbraken, Frisvad & Samson, Fung. Div. 44: 125. 2010. Penicillium manginii Duché & Heim, Trav. Cryptog. Louis L. Mangin: 450. 1931 (syn. P. pedemontanum, Houbraken et al. 2011b). Penicillium miczynskii Zaleski, Bull. Int. Acad. Polon. Sci., Cl. Sci. Math., Sér. B, Sci. Nat., 1927: 482. 1927. Penicillium neomiczynskii Cole, Houbraken, Frisvad & Samson, Stud. Mycol. 70: 105. 2011. Penicillium nothofagi Houbraken, Frisvad & Samson, Stud. Mycol. 70: 105. 2011. Penicillium pancosmium Houbraken, Frisvad & Samson, Stud. Mycol. 70: 108. 2011. Penicillium pasqualense Houbraken, Frisvad & Samson, Stud. Mycol. 70: 108. 2011. Penicillium paxilli Bainier, Bull. Soc. Mycol. France 23: 95. 1907. Penicillium quebecense Houbraken, Frisvad & Samson, Stud. Mycol. 70: 111. 2011. Penicillium raphiae Houbraken, Frisvad & Samson, Stud. Mycol. 70: 114. 2011. Penicillium roseopurpureum Dierckx, Ann. Soc. Sci. Bruxelles 25: 86. 1901. Penicillium sanguifluum (Sopp) Biourge, La Cellule 33: 105. 1923. Penicillium shearii Stolk & Scott, Persoonia 4: 396. 1967. Penicillium sizovae Baghdadi, Novosti Sist. Nizs. Rast. 1968: 103. 1968. Penicillium steckii Zaleski, Bull. Int. Acad. Polon. Sci., Cl. Sci. Math., Sér. B, Sci. Nat., 1927: 469. 1927. Penicillium sumatrense Szilvinyi, Archiv. Hydrobiol. 14, Suppl. 6: 535. 1936. Penicillium terrigenum Houbraken, Frisvad & Samson, Stud. Mycol. 70: 125. 2011. Penicillium tropicoides Houbraken, Frisvad & Samson, Fung. Div. 44: 127. 2010. Penicillium tropicum Houbraken, Frisvad & Samson, Fung. Div. 44: 129. 2010. Penicillium ubiquetum Houbraken, Frisvad & Samson, Stud. Mycol. 70: 127. 2011. Penicillium vancouverense Houbraken, Frisvad & Samson, Stud. Mycol. 70: 131. 2011. Penicillium waksmanii Zaleski, Bull. Int. Acad. Polon. Sci., Cl. Sci. Math., Sér. B, Sci. Nat., 1927: 468. 1927. Penicillium wellingtonense Cole, Houbraken, Frisvad & Samson, Stud. Mycol. 70: 133. 2011. Penicillium westlingii Zaleski, Bull. Int. Acad. Polon. Sci., Cl. Sci. Math., Sér. B, Sci. Nat., 1927: 473. 1927. Phylogeny of Penicillium and Trichocomaceae CBS 230.28T P. waksmanii CBS 215.28T P. godlewskii g 0.99/78 CBS 217.28T P. chrzaszczii CBS 117509T P. decaturense CBS 231.28T P. westlingii CBS 265.65T P. pedemontanum */* CBS 253.31NT P. manginii CBS 101623T P. quebencense */98 CBS 220 220.28 28T P. P miczynskii T */93 CBS 126236 P. christenseniae CBS 126234T P. raphiae 0.95/76 CBS 122402T P. pasqualense CBS 130375T P. wellingtonense CBS 109.66T P. atrofulvum CBS 290.48T P. shearii CBS 360 360.48 48NT P. P paxilli NRRL 779T P. sumatrense */* NRRL 6181 P. sumatrense CBS 416.69 P. sumatrense */* NRRL 35755 P. alicantinum CBS 167.81T P. galliacum CBS 148.83 P. sanguifluum */* / CBS 685 685.85 85 P. P sanguifluum ifl CBS 266.29 P. roseopurpureum */* CBS 323.71NT P. euglaucum CBS 479.66T P. anatolicum */* CBS 232.38 P. citrinum */* CBS 139.45T P. citrinum -/70 CBS 122392T P. hetheringtonii CBS 413.69NT P. sizovae */99 */91 CBS 112584T P. tropicum CBS 122410T P. tropicoides CBS 260.55NT P. steckii */99 CBS 408.69T P. gorlenkoanum */* CBS 127354T P. terrigenum CBS 127355T P. copticola p NT P. expansum */* CBS 325.48 */*/99 NRRL 35686 P. commune NRRL 2162HT Aspergillus paradoxus (EF669670) */* CBS 231.60 P. ochrosalmoneum */94 CBS 489.66 P. ochrosalmoneum CBS 247.56T P. isariiforme NRRL326NT Aspergillus niger CBS 310.38NT Talaromyces flavus Clade 14: sect. Citrina Clade 5: sect. Ochrosalmonea 0.1 Fig. 12. Best-scoring Maximum Likelihood tree using RAxML based on partial RPB2 sequences and giving an overview of the members accommodated in sections Citrina and Ochrosalmonea. The BI posterior probabilities (pp) values and bootstrap (bs) percentages of the maximum likelihood (ML) analysis are presented at the nodes (pp/bs). Values less than 70 % supported in the ML or less than 0.95 in the Bayesian analysis are indicated with a hyphen, whereas asterisks indicate good support (100 % bs or 1.00 pp). The branches with more than 95 % bootstrap support and 1.00 posterior probability values are thickened. The bar indicates the number of substitutions per site. The tree is rooted with Talaromyces flavus CBS 310.38NT. Clade 15: Section Fasciculata Thom, The Penicillia: 374. 1930. = Section Lanata-typica Thom, The Penicillia: 305. 1930. = Section Viridicata Frisvad & Samson, Stud. Mycol. 49: 27. 2004. In: Penicillium subgenus Penicillium Type: Penicillium hirsutum Dierckx www.studiesinmycology.org Sections Lanata-typica and Viridicata are placed in synonymy with section Fasciculata. Lanata-typica was erected for species with vegetative aerial mycelium consisting of lanose, cottony or floccose colonies and only a small portion of the species currently present this section produce such structures (P. camemberti, P. commune, P. caseifulvum). Most species of section Fasciculata have a granulose or fasciculate colony texture and therefore the name Fasciculata is given priority to Lanata-typica. The current definition of Fasciculata 41 Houbraken & Samson is similar to that of Viridicata (Frisvad & Samson 2004). All species grow rather quickly, except species in series Verrucosa, which grow slowly. Most species this section have globose conidia and rough-walled conidiophore stipes. All species are psychrotolerant and grow well at low water activities (Frisvad & Samson 2004). Frisvad & Samson (2004) accommodated 28 species in section Viridicata (= Fasciculata). We excluded P. atramentosum from this section and placed this species in section Paradoxa. This species was placed in section Fasciculata based on its ability to grow on creatine as sole nitrogen source and its occurrence on cheese. However, Frisvad & Samson (2004) also noted that its ability to grow at very high pH values and the formation of smoothwalled stipes sets it apart from section Fasciculata. Penicillium osmophilum is tentatively accommodated in section Viridicata. Figure 13 shows that this species is most closely related to this section, but bootstrap support is lacking. Penicillium albocoremium (Frisvad) Frisvad, Int. Mod. Tax. Meth. Pen. Asp. Clas.: 275. 2000. Penicillium allii Vincent & Pitt, Mycologia 81: 300. 1989. Penicillium aurantiogriseum Dierckx, Ann. Soc. Scient. Brux. 25: 88. 1901. Penicillium camemberti Thom, Bull. Bur. Anim. Ind. USDA 82: 33. 1906. Penicillium caseifulvum Lund, Filt. & Frisvad, J. Food Mycol. 1: 97. 1998. Penicillium cavernicola Frisvad & Samson, Stud. Mycol. 49: 31. 2004. Penicillium commune Thom, Bull. Bur. Anim. Ind. USDA 118: 56. 1910. Penicillium crustosum Thom, Penicillia: 399. 1930. Penicillium cyclopium Westling, Ark. Bot. 11: 90. 1911. Penicillium discolor Frisvad & Samson, Ant. Van Leeuwenhoek, 72: 120. 1997. Penicillium echinulatum Fassatiová, Acta Univ. Carol. Biol. 12: 326. 1977. Penicillium freii Frisvad & Samson, Stud. Mycol. 49: 28. 2004. Penicillium hirsutum Dierckx, Ann. Soc. Scient. Brux. 25: 89. 1901. Penicillium hordei Stolk, Ant. van Leeuwenhoek 35: 270. 1969. Penicillium melanoconidium (Frisvad) Frisvad & Samson, Stud. Mycol. 49: 28. 2004. Penicillium neoechinulatum (Frisvad, Filt. & Wicklow) Frisvad & Samson, Stud. Mycol. 49: 28. 2004. Penicillium nordicum Dragoni & Cantoni ex Ramírez, Adv. Pen. Asp. Syst.: 139. 1985. Penicillium osmophilum Stolk & Veenbaas-Rijks, Ant. van Leeuwenhoek 40: 1. 1974. Penicillium palitans Westling, Ark. Bot. 11: 83. 1911. Penicillium polonicum Zaleski, Bull. Int. Acad. Pol. Sci. Lett., Sér. B 1927: 445. 1927. Penicillium radicicola Overy & Frisvad, Syst. Appl. Microbiol.: 633. 2003. Penicillium solitum Westling, Ark. Bot. 11: 65. 1911. Penicillium thymicola Frisvad & Samson, Stud. Mycol. 49: 29. 2004. Penicillium tricolor Frisvad, Seifert, Samson & Mills, Can. J. Bot. 72: 937. 1994. Penicillium tulipae Overy & Frisvad, Syst. Appl. Microbiol. 634. 2003. Penicillium venetum (Frisvad) Frisvad, Int. Mod. Tax. Meth. Pen. Asp. Clas.: 275. 2000. Penicillium verrucosum Dierckx, Ann. Soc. Scient. Brux. 25: 88. 1901. 42 Penicillium viridicatum Westling, Ark. Bot. 11: 88. 1911. Clade 16: Section Digitata (as "Digitatum") Frisvad & Samson, Stud. Mycol. 49: 26. 2004. In: Penicillium subgenus Penicillium Type: Penicillium digitatum (Pers.:Fr.) Sacc. Section Digitata is represented by one species, P. digitatum. This species is unique in its combination of features. Conidiophore and conidial structures are irregular and exceptionally large for Penicillium, usually biverticillate rather than terverticillate and the conidia are olive-green. The conidia are large and ellipsoidal to cylindrical (Frisvad & Samson 2004). Partial β-tubulin (Samson et al. 2004) and RPB2 data (Fig. 13) shows that this section is situated in subgenus Penicillium. Frisvad & Samson (2004) is followed here and this section is retained for P. digitatum. Penicillium digitatum (Pers.:Fr.) Sacc., Fung. Ital.: 894. 1881. Clade 17: Section Penicillium = Bulliardium Biourge, La Cellule 33: 107. 1923 (= Asymetrica). In: Penicillium subgenus Penicillium Type: Penicillium expansum Link Frisvad & Samson (2004) are followed here in their delimitation of section Penicillium. The recently described species P. brevistipitatum is added to this list, because it is closely related to P. coprophilum (Fig. 13). The analysis of our partial RPB2 data (Fig. 13) indicate sthat this section is polyphyletic. In contrast, partial β-tubulin data (Samson et al. 2004) showed that members of this section are on a single branch with 100 % bootstrap support. Frisvad & Samson (2004) are followed and the following species are accommodated in section Penicillium: Penicillium brevistipitatum Wang & Zhuang, Mycotaxon 93: 234. 2005. Penicillium clavigerum Demelius, Verh. Zool.-Bot. Ges. Wien 72: 74. 1922. Penicillium concentricum Samson, Stolk & Hadlok, Stud. Mycol. 11: 17. 1976. Penicillium coprobium Frisvad, Mycologia 81: 853. 1989. Penicillium coprophilum (Berk. & Curt.) Seifert & Samson, Adv. Pen. Asp. Syst.: 145. 1985. Penicillium dipodomyicola (Frisvad, Filt. & Wicklow) Frisvad, Int. Mod. Meth. Pen. Asp. Clas.: 275. 2000. Penicillium expansum Link, Ges. Naturf. Freunde Berlin Mag. Neuesten Entdeck. Gesammten Naturk. 3: 16. 1809. Penicillium formosanum Hsieh, Su & Tzean, Trans. Mycol. Soc. R.O.C. 2: 159. 1987. Penicillium gladioli McCulloch & Thom, Science, N.Y. 67: 217. 1928. Penicillium glandicola (Oud.) Seifert & Samson, Adv. Pen. Asp. Syst.: 147. 1985. Penicillium griseofulvum Dierckx, Ann. Soc. Scient. Brux. 25: 88. 1901. Penicillium italicum Wehmer, Hedwigia 33: 211. 1894. Penicillium marinum Frisvad & Samson, Stud. Mycol. 49: 20. 2004. Phylogeny of Penicillium and Trichocomaceae Penicillium sclerotigenum Yamamoto, Scient. Rep. Hyogo Univ. Agric., Agric. Biol. Ser. 2, 1: 69. 1955. Penicillium ulaiense Hsieh, Su & Tzean, Trans. Mycol. Soc. R.O.C. 2: 161. 1987. Penicillium vulpinum (Cooke & Massee) Seifert & Samson, Adv. Pen. Asp. Syst.: 144. 1985. Clade 18: section Roquefortorum (as "Roqueforti") Frisvad & Samson, Stud. Mycol. 49: 16. 2004. In: Penicillium subgenus Penicillium Type: Penicillium roqueforti Thom Frisvad & Samson (2004) erected section Roqueforti for rapidly growing species forming strictly velutinous colonies. All species form terverticillate rough walled conidiophores and are able to grow at low pH values (e.g. on media containing 0.5 % acetic acid), at high alcohol concentrations and at elevated CO2 levels. Members of this section appear to have a symbiotic relationship with lactic acid bacteria and certain acid-tolerant yeasts. Currently, four species are described in this section (Frisvad & Samson 2004, Houbraken et al. 2010a): Penicillium carneum (Frisvad) Frisvad, Microbiology, UK, 142: 546. 1996. Penicillium paneum Frisvad, Microbiology (UK) 142: 546. 1996. Penicillium psychrosexualis Houbraken & Samson, IMA Fungus 1:174. 2010. Penicillium roqueforti Thom, Bull. Bur. Anim. Ind. US Dept. Agric. 82: 35, 1906. Clade 19: section Chrysogena Frisvad & Samson, Stud. Mycol. 49: 17. 2004. In: Penicillium subgenus Penicillium Type: Penicillium chrysogenum Thom Members of the section Chrysogena are characterised by the formation of ter- and/or quarterverticillate, smooth walled conidiophores with relatively small phialides. Colonies have a velvety texture and species are tolerant to salt and the majority is capable to produce penicillin (Frisvad & Samson 2004). Four teleomorph species belong to section Chrysogena: P. sinaicum, P. egyptiacum, P. molle and P. kewense (Fig. 13). Penicillium egyptiacum was described as a holomorphic species (van Beyma 1933). Pitt (1980) transferred the teleomorphic state to Eupenicillium (E. egyptiacum) and introduced a new name for the Penicillium morph (P. nilense). This name is not used here and P. egyptiacum is re-instated. There are several taxonomic problems concerning P. kewense. Brefeld (1874) was the first who described the formation of a teleomorph in Penicillium. He identified the studied species as “Penicillium crustaceum Fries, Penicillium glaucum Link”. It is, however, very questionable whether the strains studied by Brefeld truly represented the species described by Link and Fries (Stolk & Scott 1967). Stolk & Scott (1967) are followed here; they agreed that the fungus described by Smith (1961b) as Penicillium kewense resembles Brefeld’s fungus. Based on the data of Samson et al. (2004), Houbraken et al. (2011a) and Fig. 13, the following species are accommodated in section Chrysogena. Penicillium aethiopicum Frisvad, Mycologia 81: 848. 1990. Penicillium chrysogenum Thom, Bull. Bur. Anim. Ind. U.S. Dep. Agric. 118: 58. 1910. www.studiesinmycology.org Penicillium confertum (Frisvad et al.) Frisvad, Mycologia 81: 852. 1990. Penicillium dipodomyis (Frisvad, Filtenborg & Wicklow) Banke, Frisvad & Rosendahl, Int. Mod. Meth. Pen. Asp. Clas., 270. 2000. Penicillium egyptiacum van Beyma, Zentralbl. Bakteriol., 2. Abt., 88: 137. 1933. (syn. P. nilense). Penicillium flavigenum Frisvad & Samson, Mycol. Res. 101: 620. 1997. Penicillium kewense Smith, Trans. Br. Mycol. Soc. 44: 42. 1961 (syn. E. crustaceum). Penicillium molle Pitt, The Genus Penicillium: 148, 1980 [“1979”]. Penicillium mononematosum (Frisvad et al.) Frisvad, Mycologia 81: 857. 1990. Penicillium nalgiovense Laxa, Zentralbl. Bakteriol., 2. Abt., 86: 160. 1932. Penicillium persicinum Wang, Zhou, Frisvad & Samson, Ant. van Leeuwenhoek 86: 177. 2004. Penicillium rubens Biourge, Cellule 33: 265. 1923. Penicillium sinaicum Udagawa & Ueda, Mycotaxon 14: 266. 1982. Clade 20: section Turbata Houbraken & Samson, sect. nov. MycoBank MB563133. Sectio in Penicillio subgen. Penicillo. Conidiophoris delicatis et symmetricis, biverticillatis; formatione acoris extroliti penicillici. In: Penicillium subgenus Penicillium Type: Penicillium turbatum Westling Section Turbata is phylogenetically closely related to section Paradoxa, and P. matriti, P. bovifimosum and P. turbatum are accommodated in this section. These species form rather delicate and symmetric biverticillate Penicillium conidiophores. Furthermore, penicillic acid is produced by all these species, and P. bovifimosum, P. turbatum and selected strains of P. matriti produce a fumagillinlike compound (Tuthill & Frisvad 2002). Penicillium bovifimosum (Tuthill & Frisvad) Houbraken & Samson, Stud. Mycol. 70: 47. 2011 (this study). Penicillium matriti Smith, Trans. Br. Mycol. Soc. 44: 44. 1961. Penicillium turbatum Westling, Ark. Bot. 11: 128. 1911 (syn. E. baarnense, P. baarnense, this study). Clade 21: section Paradoxa Houbraken & Samson, sect. nov. MycoBank MB563134. Sectio in Penicillio subgen. Penicillo. Speciebus saepe cum conidiophoris typi Aspergillus et odore molesti efferenti. In: Penicillium subgenus Penicillium Type: Aspergillus paradoxus Fennell & Raper Aspergillus paradoxus, A. malodoratus, A. crystallinus and P. atramentosum form a well-supported clade (85 % bs, 1.00 pp). Phylogenetic and extrolite analysis shows that the first three species belong in Penicillium and will be transferred to this genus (R.A. Samson, unpubl. data). Besides a similar type of Aspergillus anamorph, these three species also produce a strong, unpleasant smell. Penicillium atramentosum is phylogenetically basal to these three species. This species is alkaliphilic and unpublished results show that this character is shared with A. paradoxus. More research 43 Houbraken & Samson CBS 222.28T P. polonicum CBS 390.48NT P. viridicatum CBS 324.89NT P. aurantiogriseum CBS 641.95 P. melanoconidium Clade 15: sect. sect Fasciculata CBS 603.74NT P. verrucosum T */* CBS 135.41 P. hirsutum NRRL 35686 P. commune (EF198602) -/CBS 332.48NT P. gladioli CBS 462.72HT P. osmophilum 0.97/74 CBS 112082epiT P. digitatum 0.96/84 Clade 16: sect. Digitata */98 CBS 325.48NT P. expansum -/NT Clade 17: sect. Penicillium CBS 339.48 P. italicum CBS 101033T P. sclerotigenum CBS 498.75epiT P. glandicola -/*/99 CBS 221.30NT P. roqueforti */* CBS 112297T P. carneum -/- */* Clade 18: sect. Roquefortorum CBS 128036HT P. psychrosexualis CBS 465.95 P. paneum */* CBS 110760 P. coprophilum DTO 105I7T P. brevistipitatum */* CBS 306.48NT P. chrysogenum CBS 205.57 P. rubens */96 -/CBS 419.89HT P. flavigenum -/CBS 171.87HT P. confertum -// CBS 484.84HT P. aethiopicum */82 Clade 19: sect. Chrysogena CBS 352.48NT P. nalgiovense 0.97/76 CBS 111235HT P. percisinum 0.97/CBS 244.32NT P. egyptiacum CBS 456.72HT P. molle */99 CBS 344.61T P. kewense */93 -/CBS 279.82HT P. sinaicum CBS 185.27NT P. griseofulvum CBS 211.92HT P. formosanum */* CBS 339.61 P. turbatum */* CBS 134.41 P. turbatum */97 CBS 383.48NT P. turbatum CBS 116986 Penicillium sp. Clade 20: sect. Turbata */* -/CBS 102825T P. bovifimosum */* CBS 170.81 P. madriti CBS 347.61HT P. madriti */* NRRL 4695 Asp. paradoxus (EF669671) */82 -/NRRL 2162HT Asp. paradoxus (EF669670) */* NRRL 5083NT Asp. malodoratus (EF669672) NRRL 5082NT Asp. p crystallinus y ((EF669669)) Clade 21: sect. sect Paradoxa */85 /85 CBS 291.48NT P. atramentosum T 0.99/97 CBS 122428 P. neocrassum -/87 CBS 257.29T P. brevicompactum */* CBS 711.68 P. fennelliae -/CBS 227.28T P. bialowiezense CBS 117192 Penicillium sp. -/Clade 22: sect. Brevicompacta */93 CBS 117181 Penicillium sp. */88 T CBS 430.69 P. tularense */95 -/CBS 122427T P. astrolabium CBS 232.60NT P. olsonii CBS 226.28NT P. soppii CBS 114838isoT P. virgatum -/79 CBS 119391T P. swiecickii -/-/CBS 102888T P. jamesonlandense CBS 127809T P. ribeum -/80 Clade 23: sect. Ramosa CBS 345.61T P. kojigenum -/80 NT */* CBS 106.11 P. lanosum */* */* CBS 261.33NT P. raistrickii CBS 277.83NT P. sajarovii CBS 683.89HT P. scabrosum */87 */88 -/0 99/86 0.99/86 */90 */* Fig. 13. Best-scoring Maximum Likelihood tree using RAxML based on partial RPB2 sequences and giving an overview of the members accommodated in subgenus Penicillium (clades 15–25). The BI posterior probabilities (pp) values and bootstrap (bs) percentages of the maximum likelihood (ML) analysis are presented at the nodes (pp/bs). Values less than 70 % supported in the ML or less than 0.95 in the Bayesian analysis are indicated with a hyphen, whereas asterisks indicate good support (100 % bs or 1.00 pp). The branches with more than 95 % bootstrap support and 1.00 posterior probability values are thickened. The bar indicates the number of substitutions per site. The tree is rooted with Talaromyces flavus CBS 310.38NT. 44 Phylogeny of Penicillium and Trichocomaceae CBS 161.81T P. murcianum CBS 300.48NT P. canescens CBS 410.69IsoT P. yarmokense -/CBS 216.28T P. jensensii CBS 221.28NT P. janczewskii */97 */99 CBS 100492T P. antarcticum -/CBS 241.56NT P. atrovenetum -/CBS 137.41NT P. novae-zeelandiae 0.97/85 */72 CBS 123.65NT P. coralligerum */* CBS 316.67HT P. senticosum -/CBS 231 231.61 61NT P. P sacculum -/IBT 15460T P. fellutanum CBS 139.45NT P. citrinum */* CBS 340.48NT P. janthinellum -/CBS 315.67HT P. stolkiae -/CBS 125543T P. glabrum CBS 599.73HT P. gracilentum -/- */72 CBS 367.48NT P. restrictum CBS 185.65NT P. lagena CBS 287.36NT P. sclerotiorum NRRL 326NT Aspergillus niger CBS 310.38NT Talaromyces y flavus 0.1 0.99/97 */97 */99 Clade 24: sect. Canescentia Clade 25: section Eladia Fig. 13. (Continued). is needed to determine whether A. malodoratus and A. crystallinus also share this feature. Penicillium atramentosum Thom, Bull. Bur. Anim. Ind. US Dept. Agric. 118: 65. 1910. Aspergillus crystallinus Kwon-Chung & Fennell, The Genus Aspergillus: 471. 1965. Aspergillus malodoratus (Kwon-Chung & Fennell), The Genus Aspergillus: 468. 1965. Aspergillus paradoxus Fennell & Raper, Mycologia 47: 69. Clade 22: section Brevicompacta Thom, The Penicillia: 289. 1930. = section Coronata Pitt, The Genus Penicillium: 392, 1980. In: Penicillium subgenus Penicillium Type: Penicillium brevicompactum Dierckx Members of the section Brevicompacta are characterised by conidiophores with long and broad stipes. The conidial heads look superficially like Aspergillus heads in the stereomicroscope. Section Coronata, typified with P. olsonii, is placed here in synonymy. Recently, P. neocrassum and P. astrolobatum were described in this section (Serra & Peterson 2007) and partial RPB2 data (Fig. 13) show that also P. tularense and P. fennelliae belong here. The production of the extrolites asperphenamate and the unknown metabolite O (Frisvad & Samson 2004) is shared by P. olsonii, P. brevicompactum and P. bialowiezense. More research in needed to determine whether these metabolites are also produced by the other members of section Brevicompacta. Based on literature (Frisvad & Samson 2004, Peterson 2004, Serra & Peterson 2007) and partial RPB2 data (Fig. 13) the following species are accommodated in section Brevicompacta: Penicillium astrolobatum Serra & Peterson, Mycologia 99: 80. 2007. Penicillium bialowiezense Zaleski, Bull. Int. Acad. Pol. Sci. Lett., Sér. B, 1927: 462. 1927 (syn. P. biourgeianum). Penicillium brevicompactum Dierckx, Ann. Soc. Scient. Brux. 25: 88. 1901. www.studiesinmycology.org Penicillium fennelliae Stolk, Ant. van Leeuwenhoek 35: 261. 1969. Penicillium neocrassum Serra & Peterson, Mycologia 99: 81. 2007. Penicillium olsonii Bainier & Sartory, Ann. Mycol. 10: 398. 1912. Penicillium tularense Paden, Mycopathol. Mycol. Appl. 43: 264. 1971. Clade 23: section Ramosa (as “Ramosum”) Stolk & Samson, Adv. Pen. Asp. Syst.: 179. 1985. In: Penicillium subgenus Penicillium Type: Penicillium lanosum Westling Figure 13 shows that section Ramosa is not well resolved and members of this section are on a well-supported branch with section Brevicompacta members (100 % bs, 1.00 pp). We split this clade in two sections based on phenotypic characters and extrolite patterns. Members of the section Lanosa form biverticillate or terverticillate conidiophores with divergent rami (twice biverticillate), while members of sect. Brevicompacta have appressed branches. Penicillium jamesonlandense, P. lanosum, P. ribeum, P. raistrickii, P. soppii and P. swiecickii produce different combinations of cycloaspeptide, kojic acid and griseofulvin (Frisvad & Filtenborg 1990, Frisvad et al. 2006) and these extrolites are not been found in section Brevicompacta (Frisvad & Samson 2004). More research is needed to determine if the other members of this section also produce cycloaspeptide, kojic acid and/or griseofulvin. Penicillium scabrosum is basal to the members of sections Brevicompacta and Ramosa. This species is tentatively accommodated in sect. Ramosa based on the formation of divaricate branches (Frisvad et al. 1990a). In contrast, cyclopenin, cyclopenol, viridicatin, penigequinolone A and B and fumagillin are produced by P. scabrosum and these extrolites are not detected in species belonging to sect. Ramosa (Frisvad et al. 1990a, Larsen et al. 1999). In the original description of P. virgatum, a relationship with P. daleae was suggested (Kwasna & Nirenberg 2005). However, these two species are unrelated and our partial RPB2 data suggest P. virgatum is related to members of section Ramosa (Fig. 13). Based on data presented in Fig. 13 and in Frisvad et al. (2006), the following species are placed in section Ramosa: 45 Houbraken & Samson Penicillium jamesonlandense Frisvad & Overy, Int. J. Syst. Evol. Microbiol. 56: 1435. 2006. Penicillium kojigenum Smith, Trans. Br. Mycol. Soc. 44: 43. 1961. Penicillium lanosum Westling, Ark. Bot. 11: 97. 1911. Penicillium raistrickii Smith, Trans. Br. Mycol. Soc.18: 90. 1933. Penicillium ribeum Frisvad & Overy, Int. J. Syst. Evol. Microbiol. 56: 1436. 2006. Penicillium sajarovii Quintanilla, Avances Nutr. Mejora Anim. Aliment. 22: 539. 1981. Penicillium scabrosum Frisvad, Samson & Stolk, Persoonia 14: 177. 1990. Penicillium simile Davolos, Pietrangeli, Persiani & Maggi, J. Syst. Evol. Microbiol., in press. Penicillium soppii Zaleski, Bull. Int. Acad. Polon. Sci., Cl. Sci. Math., Sér. B, Sci. Nat., 1927: 476. 1927. Penicillium swiecickii Zaleski, Bull. Int. Acad. Pol. Sci. Lett., Sér. B 1927: 474. 1927. Penicillium virgatum Nirenberg & Kwasna, Mycol. Res. 109: 977. 2005. Type: Penicillium sacculum Dale Clade 24: section Canescentia Houbraken & Samson, sect. nov. MycoBank MB563135. Over 250 Penicillium and Eupenicillium species are mentioned in the list of accepted Penicillium species (Pitt et al. 2000) and a fair amount of these do not belong to Penicillium s. str. The majority of these excluded species are currently classified in Talaromyces and an overview of species is given by Samson et al. (2011). Only a small number of species do not belong to either genus. These include P. arenicola, P. inflatum, P. kabunicum, P. lineatum, P. megasporum and P. moldavicum. Figure 1 shows that P. arenicola is closely related to Phialomyces (clade 6) and P. megasporum belongs to the clade 3 (Hamigera/Warcupiella). Both species should be transferred to other genera. Unpublished data (R.A. Samson) shows that P. inflatum belongs to Aspergillus and this species will be combined in that genus. Penicillium kabunicum and P. moldavicum are phylogenetically related and were included in the initial analyses of Trichocomaceae. Both species were together on a single branch and did not fit with any members of this family (J. Houbraken, unpubl. data). These two species belong to another (related) family and might represent a new genus. Penicillium lineatum was described as the anamorph of Hamigera striata (Pitt 1980). Hamigera striata is accommodated in clade 3 (Fig. 1) and does therefore not belong to Penicillium s. str. Penicillium syriacum was included in the list of accepted names (Pitt et al. 2000), but the illustration and description of P. syriacum by Baghdadi (1968) and examination of ex-type material from ATCC, CBS and IMI indicated a mixed culture. This species is considered a nomen ambiguum (Christensen et al. 1999). The phylogenetic position of P. resedanum needs further attention. Pitt (1980) and Ramírez (1982) placed P. resedanum in section Aspergilloides based on the formation of monoverticillate conidiophores. Pitt (1980) already noted that this species form acerose phialides with weak growth on G25N, suggesting a relationship with Talaromyces (and subgenus Biverticillium). A BLAST search on GenBank with ITS sequences of NRRL 578T (AF033398) indicates a relationship with Talaromyces. Penicillium griseolum is listed as a synonym of P. restrictum (Pitt et al. 2000). However, Fig. 7 shows that these species are phylogenetically unrelated. In our study, we did not find any species closely related to P. griseolum and this species might represent a separate section. We have chosen not to proceed with the description of this new section for this species until additional related species are described. Sectio in Penicillio subgen. Penicillo. Structuris symmetricis biverticillatis, raro cum ramulis pluribus. Phialidibus simplicibus, brevibus (7–9 µm), cum collo brevi, interdum distincte attenuato. In: Penicillium subgenus Penicillium Type: Penicillium canescens Sopp Members of section Canescentia are soil-borne and are characterised by the formation of symmetrical biverticillate structures with infrequently an additional branch. Phialides are simple and short (7–9 µm) with a broadly cylindrical to slightly or more definitely swollen base and a short, occasionally more pronounced narrowed neck. This section has not been a subjected to a thorough phylogenetic study and unpublished sequence results show that several synonyms should be raised to species level. Partial RPB2 data (Fig. 13) shows that following species are placed in section Canescentia. Penicillium canescens Sopp, Skr. Vidensk.-Selsk. Christiana, Math.-Naturvidensk. Kl. 11: 181. 1912. Penicillium jensenii Zaleski, Bull. Int. Acad. Polon. Sci., Cl. Sci. Math., Sér. B, Sci. Nat., 1927: 494. 1927. Penicillium yarmokense Baghdadi, Nov. Sist. Niz. Rast. 5: 99. 1968. Penicillium janczewskii Zaleski, Bull. Int. Acad. Polon. Sci., Cl. Sci. Math., Sér. B, Sci. Nat., 1927: 488. 1927. Penicillium antarcticum Hocking & McRae, Polar Biology 21: 103. 1999. Penicillium atrovenetum Smith, Trans. Br. Mycol. Soc. 39: 112. 1956. Penicillium novae-zeelandiae van Beyma, Ant. van Leeuwenhoek 6: 275. 1940. Penicillium coralligerum Nicot & Pionnat, Bull. Soc. Mycol. France 78: 245. 1963 [“1962”]. Clade 25: section Eladia (Smith) Stolk & Samson, Adv. Pen. Asp. Syst.: 169. 1985. In: Penicillium subgenus Penicillium 46 The genus Eladia is synonymised with Penicillium and two species are placed here in section Eladia: P. sacculum and P. senticosum (Fig. 7, clade 25 and Fig. 13). Penicillium sacculum and P. senticosum grow rather well on MEA (and poorly on Czapek agar) and their colonies on MEA are velvety and dull-green, brownishgreen or olive-brown coloured. Phialides are born irregularly on the stipes, subterminally as well as terminally, short, 4–7 µm, with a swollen base, and at the apex tapering abruptly into a short narrow neck. Conidia are distinctly ornamented (Smith 1961b, Pitt 1980, Stolk & Samson 1983, Stolk & Samson 1985). No type material could be obtained from Eladia pachyphialis and Eladia tibetensis and their taxonomic position remains uncertain. Based on their protologues, it is likely that these species belong to Penicillium. Penicillium sacculum Dale apud Biourge, Cellule 33: 323. 1923. Penicillium senticosum Scott, Mycopathol. Mycol. Appl. 36: 5. 1968. Excluded and unclassified Penicillia Phylogeny of Penicillium and Trichocomaceae Penicillium arenicola Chalabuda, Bot. Mater. Otd. Sporov. Rast. 6: 162. 1950 (= clade 6, related to Phialomyces). Penicillium inflatum Stolk & Malla, Persoonia 6: 197. 1971. (= Aspergillus inflatus, R.A. Samson, unpubl. data). Penicillium kabunicum Baghdadi, Novosti Sist. Nizs. Rast.: 98. 1968 (unrelated to Penicillium, J. Houbraken, unpubl. data). Penicillium lineatum Pitt, The Genus Penicillium: 485. 1980 [“1979”] (= Hamigera striata). Penicillium megasporum Orpurt & Fennell, Mycologia 47: 233. 1955 (= clade 3, related to Hamigera and Warcupiella). Penicillium moldavicum Milko & Beliakova, Novosti Sist. Nizs. Rast. 1967: 255. 1967 (unrelated to Penicillium, J. Houbraken, unpubl. data). Penicillium syriacum Baghdadi, Novosti Sist. Nizs. Rast. 1968: 111. 1968 (nomen ambiguum, Christensen et al. 1999). Character analysis Penicillium coniferophilum Houbraken & Samson, nom. nov. MycoBank MB561968. Basionym: Thysanophora striatispora Barron & Cooke, Mycopathologia et Mycologia Applicata 40: 353. 1970, non Penicillium striatisporum Stolk, Ant. van Leeuwenhoek 35: 268. 1969. Note: The name P. striatisporum is already occupied and therefore a new name is proposed. Penicillium glaucoalbidum (Desmazières) Houbraken & Samson, comb. nov. MycoBank MB561965. Basionym: Sclerotium glaucoalbidum Desmazières, Annales des Sciences Naturelles, Botanique 16: 329. 1851. = Thysanophora glaucoalbida (Desm.) Morelet, Annales de la Société des Sciences Naturelles et Archéologie de Toulon et Var 20: 104. 1968. = Thysanophora penicillioides (Roumeguère) Kendrick, Can. J. Bot. 39: 820. 1961. The classification proposed in the monographs of Raper & Thom (1949), Pitt (1980) and Ramírez (1982) is not concordant with the new classification system proposed here. One of the most important characters in these monographs is the branching pattern of the Penicillium conidiophore. Our study shows that monoverticillate (Aspergilloid) conidiophores occur in various sections (e.g. clades 1, 2, 6, 8, 10, 12, 25). Sections Aspergilloides (clade 1) and Eladia (clade 25) comprise only strictly monoverticillate species, while mono- and biverticillate species are intermingled in the other clades. The occurrence of both structures in multiple phylogenetic clades (sections) indicates that reduction of the Penicillium conidiophore might have occurred various times. Most of the species belonging to section Citrina (clade 14) are symmetrically biverticillate and occasionally additional branches with the same branching pattern as the main axis (“double symmetrically biverticillate”) occurs. Species belonging to section Lanata-divaricata are mainly divaricate and the metulae are borne terminally, subterminally and in intercalary positions. Terverticillate conidiophores mainly occur in clades 15–18 and section Chrysogena (clade 19) comprises species with quarterverticillate condiophores. The monoverticillate species Penicillium sacculum and P. senticosum belong to clade 25. This clade is positioned in subgenus Penicillium and has therefore a unique branching pattern for this subgenus. Growth rates on agar media are also frequently used for classification. Some sections mainly comprise fast growing species (e.g. clades 1, 2, 11, 16, 18, 19, 25) while in other clades slow growing species predominate (e.g. clades 3, 6, 8, 9). The new proposed sectional classification will serve as a starting point to investigate phenotypic characters used for classification. Note: Virtually all of the published information relating to P. glaucoalbidum has used the binomial Thys. penicillioides. Iwamoto et al. (2005) aggregated sequence data of seven European and North American P. glaucoalbidum (as Thys. penicillioides) strains with Japanese strains. The strains formed nine lineages and according to phylogenetic species recognition by the concordance of genealogies, respective lineages correspond to phylogenetic species. Taxonomic implications Basionym: Chromocleista malachitea Yaguchi & Udagawa, Trans. Mycol. Soc. Japan 34: 102. 1993. Penicillium asymmetricum (Subramanian & Sudha) Houbraken & Samson, comb. nov. MycoBank MB561963. Basionym: Thysanophora asymmetrica Subramanian & Sudha, Kavaka 12: 88. 1985. Penicillium bovifimosum (Tuthill & Frisvad) Houbraken & Samson, comb. nov. MycoBank MB561957. Basionym: Eupenicillium bovifimosum Tuthill & Frisvad, Mycologia 94: 241. 2002. www.studiesinmycology.org Penicillium hennebertii Houbraken & Samson, nom. nov. MycoBank MB561964. Basionym: Thysanophora canadensis Stolk & Hennebert, Persoonia 5: 189. 1968, non Penicillium canadense Smith, Trans. Br. mycol. Soc. 39: 113. 1956. Note: A new name was sought for this species, as the species name “canadensis” is already occupied. Penicillium laeve (K. Ando & Manoch) Houbraken & Samson, comb. nov. MycoBank MB561960. Basionym: Torulomyces laevis K. Ando & Manoch, Mycoscience 39: 317. 1998. Penicillium longisporum (Kendrick) Houbraken & Samson, comb. nov. MycoBank MB561966. Basionym: Thysanophora longispora Kendrick, Can. J. Bot. 39: 826. 1961. Penicillium malachiteum (Yaguchi & Udagawa) Houbraken & Samson, comb. nov. MycoBank MB561971. = Geosmithia malachitea Yaguchi & Udagawa, Trans. Mycol. Soc. Japan 34: 102. 1993. Penicillium melanostipe Houbraken & Samson, nom. nov. MycoBank MB561970. Basionym: Thysanophora verrucosa Mercado, Gené & Guarro, Mycotaxon 67: 419. 1998, non Penicillium verrucosum Dierckx, Annales de la Société Scientifique de Bruxelles 25: 88. 1901. Note: The name Penicillium verrucosus is already occupied and therefore the name melanostipe, which is referring to the pigmented stipe of this species, is proposed. 47 Houbraken & Samson Penicillium ovatum (K. Ando & Nawawi) Houbraken & Samson, comb. nov. MycoBank MB561961. Basionym: Torulomyces ovatus K. Ando & Nawawi, Mycoscience 39: 317. 1998. Penicillium parviverrucosum (K. Ando & Pitt) Houbraken & Samson, comb. nov. MycoBank MB561962. Basionym: Torulomyces parviverrucosus K. Ando & Pitt, Mycoscience 39: 317. 1998. Penicillium porphyreum Houbraken & Samson, nom. nov. MycoBank MB561959. Basionym: Monocillium humicola Barron var. brunneum M. Christensen & Backus, Mycologia 56: 498. 1964, non Penicillium brunneum Udagawa, J. agric. Sci. Tokyo Nogyo Daigaku 5: 16. 1959. = Torulomyces brunneus (M. Christensen & Backus) K. Ando, Mycoscience 39: 314. 1998. Note: The name Penicillium brunneum is already occupied (Udagawa et al. 1959) and therefore the name P. porphyreum is proposed. The epithet porphyreum refers to the red-brown reverse of this species. Penicillium saturniforme (Wang & Zhuang) Houbraken & Samson, comb. nov. MycoBank MB561958. Basionym: Eupenicillium saturniforme Mycopathologia 167: 300. 2009. Wang & Zhuang, Penicillium taiwanense (Matsushima) Houbraken & Samson, comb. nov. MycoBank MB561969. Basionym: Phialomyces taiwanensis Matsushima, Matsushima Mycological Memoirs 4: 12. 1985. = Thysanophora taiwanensis (Matsush.) Mercado, Gené & Guarro, Mycotaxon 67: 421. 1998. Note: This species was originally described as Phialomyces taiwanensis. Based on micro-morphological features, MercadoSierra et al. (1998) transferred this species to Thysanophora taiwanensis. 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Aspergillus crystallinus NRRL 5082NT = CBS 479.65 = ATCC 16833 = IMI 139270 Forest soil, Costa Rica EF669669RPB2 Aspergillus malodoratus NRRL 5083NT = CBS 490.65 = IMI 172289 = ATCC 16834 Forest soil, Costa Rica EF669672RPB2 Aspergillus paradoxus NRRL 2162HT = ATCC 16918 = IMI 061446 Holotype of Hemicarpenteles paradoxus; dung of opossum, Wellington, New-Zealand EF669670RPB2 NRRL 4695 = IMI 086829 Unknown source, India EF669671RPB2 Eladia infata CBS 127833HT Soil, Sichuan Prov., Kangding County, China JN406643RPB2 P. abidjanum CBS 246.67 = ATCC 18385 = IMI 136244 Savannah soil, Ivory Coast GU981650BT P. adametzioides CBS 313.59T = ATCC 18306 = IMI 068227 = NRRL 3405 Soil, Japan JN406578RPB2 P. aethiopicum CBS 484.84HT = FRR 2942 = IBT 21501 = IBT 5903 = IMI 285524 Grain of Hordeum vulgare, Addis Abeba, Ethiopia JN406548RPB2 P. alicantinum NRRL 35755 Unknown source EU427254RPB2 P. anatolicum CBS 479.66HT = IBT 30764 Soil, Turkey JN606593RPB2 P. angulare CBS 130293 = IBT 27051 = NRRL 28157 Old polypore, New Mexico, USA JN406554RPB2 P. angustipurcatum CBS 202.84HT = NHL 6481 Forest soil, Gandaki, near Nandanda, Nepal JN406617RPB2 P. antarcticum CBS 100492 = FRR 4989 Soil scraping, near nest site of Southern Fulmar Ardery Island, Windmill Islands, Wilkes Land, Antarctica JN406653RPB2 P. araracuarense CBS 113149T = IBT 23247 Leaf litter exposed for 6 months, 36-year old forest, Araracuara, Colombia GU981642BT P. ardesiacum CBS 497.73NT = ATCC 24719 = IMI 174719 Soil near Vitis vinifera, Alma-Ata Region, Kazakhstan JN406547RPB2 P. asperosporum CBS 324.83 = IMI 080450 Holotype of P. echinosporum; resin of Eucalyptus tereticornis, Prov. Guizhon, Guiyang, China JN406574RPB2 P. astrolabium CBS 122427T = NRRL 35611 Wine grapes, Portugal JN406634RPB2 P. atramentosum CBS 291.48NT = ATCC 10104 = IBT 6616 = IMI 039752 = IMI 039752ii = MUCL 29071 = MUCL 29126 = NRRL 795 French Camembert cheese, Storrs, Connecticut, USA JN406584RPB2 P. atrofulvum CBS 109.66T = IBT 30032 Soil, Katanga, Zaire JN606620RPB2 P. atrosanguineum CBS 380.75 Grain in silo Triticum aestivum, Praha, Czech Republic JN406557RPB2 P. aurantiogriseum CBS 324.89NT = ATCC 48920 = IBT 14016 = IMI 195050 = MUCL 29090 = NRRL 971 Unrecorded source JN406573RPB2 P. bialowiezense CBS 227.28T = IBT 23044 = IMI 092237 Soil under conifers, Bialowiezska Puszcza, Poland JN406604RPB2 P. bilaiae CBS 221.66 = ATCC 22348 = ATCC 48731 = IJFM 5025 = IMI 113677 = MUCL 31187 Soil, Kiev, Ukraine JN406610RPB2 P. boreae CBS 111717 = NRRL 31002 Petroleum contaminated soil, near Norman Wells, Northwest-Territories, Canada JN617715BT P. bovifimosum CBS 102825T = RMF 9598 Dry cow manure, Wyoming, USA JN406649RPB2 P. brasilianum CBS 253.55 = ATCC 12072 = FRR 3466 Herbarium specimen, Recife, Brazil GU981629BT P. brefeldianum CBS 235.81T = IFO 31731 = IMI 216896 = NRRL 710 Type of P. brefeldianum and P. dodgei; human alimentary tract GU981623BT P. brevicompactum CBS 257.29NT = ATCC 10418 = ATCC 9056 = IBT 23045 = IMI 040225 = MUCL 28647 = MUCL 28813 = MUCL 28935 = MUCL 30240 = MUCL 30241 = MUCL 30256 = MUCL 30257 = NRRL 2011 = NRRL 862 = NRRL 864 Unrecorded source, Belgium JN406594RPB2 P. brevissimum CBS 763.68T Mixed cereal feed for birds, Lucknow, India JN406534RPB2 P. brevistipitatum CBS 122277 = AS 3.6887 Soil, China JN406528RPB2 P. brocae CBS 116113HT = IBT 26293 = NRRL 31472 Faeces of coffee berry borer, Chiapas, Tapachula, Mexico JN406639RPB2 P. burgense CBS 325.89T Uncultivated soil, Highlands north of Burgos, Spain JN406572RPB2 P. canariense CBS 111720HT = NRRL 31003 Soil, Canary Islands, Spain JN617714BT P. caperatum CBS 233.81 = IFO 31730 = IMI 216895 Neotype of E. brefeldianum fide Pitt (1979, p. 119); soil, Murrumbidgee Irrigation Area, NSW, Australia GU981659BT HT T T IsoT = FRR 1726 = IMI 197488 NT HT T www.studiesinmycology.org 51-S1 Houbraken & Samson Supplementary Information Table S1. (Continued). Name Collection no. Origin GenBank accession no. P. caperatum CBS 443.75T = ATCC 28046 Soil, Papua New Guinea GU981660BT P. capsulatum CBS 301.48NT = ATCC 10420 = IJFM 5120 = IMI 040576 = NRRL 2056 Optical instrument, Canal Zone, Panama JN406582RPB2 P. carneum CBS 112297T = IBT 6884 Mouldy rye bread, Denmark JN406642RPB2 P. chalybeum CBS 255.87 = FRR 2658 = IMI 288722 Dried fish, Decapterus sp., Indonesia JN406596RPB2 P. charlesii CBS 326.59 = ATCC 18225 = IMI 068223 Type of Penicillium decumbens var. atrovirens and P. atrovirens; soil, Japan JN406571RPB2 P. charlesii CBS 330.59 = IMI 068224 = MUCL 15638 Type of P. fellutanum var. nigrocastaneum; soil, Japan JN406570RPB2 P. ‘chermesinum’ CBS 305.48 = ATCC 10424 = IMI 040577 = NRRL 2049 Air, Panama JN406581RPB2 CBS 231.81 = IMI 191730 = NRRL 2048 Neotype of P. chermesinum sensu Pitt; deteriorating military equipment Florida, USA JN406600RPB2 P. christensenae CBS 126236T = IBT 23355 Soil in native forest, “Lowland forest” east / north east side of Costa Rica about 30 km inland from Limon and the Caribbean. JN606624RPB2 P. chrzaszczii CBS 217.28T = MUCL 29167 = NRRL 903 = NRRL 1741 = IBT 18226 = IBT 11222 = IBT 16409 Woodland soil, Puszcza Bialowieska Forest, Poland JN606628RPB2 P. ciegleri CBS 275.83T = IMI 257691 Rye grain, Spain GU981671BT P. cinereoatrum CBS 222.66 113676 Forest soil, Kiev, Ukraine JN406608RPB2 P. cinnamopurpureum CBS 847.68T = ATCC 18489 = CBS 429.65 Milled rice, Japan JN406533RPB2 P. citreonigrum NRRL 1187 = IMI 092212 = MUCL 29230 = MUCL 29783 = NRRL 1187 Type of P. citreoviride; unknown source EF198501RPB2 NRRL 2046 = CBS 308.48 = ATCC 10425 = IMI 40575 = NRRL 2046 Deteriorating military equipment, Florida, USA EF198502RPB2 P. coeruleum CBS 141.45 = NCTC 6595 As Citreomyces coeruleus; unknown source GU981655BT P. commune NRRL 35686 Unknown source EF198602RPB2 P. confertum CBS 171.87HT = IBT 21515 = IBT 3098 = IBT 5672 = IMI 296930 = NRRL 13488 = NRRL A-26904 Cheek pouch of Dipodomys spectabilis, Arizona, USA JN406622RPB2 P. coprophilum CBS 110760 = IBT 5551 Rabbit dung, Baarn, Netherlands JN406645RPB2 P. copticola CBS 127355 = IIBT 30771 Tortilla, USA JN606599RPB2 P. coralligerum CBS 123.65NT = ATCC 16968 = FRR 3465 = IMI 099159 = NRRL 3465 Seed of Hordeum vulgare (barley), France JN406632RPB2 P. corylophilum CBS 330.79 = IJFM 5147 Authentic strain of P. citreovirens Abe ex. Ramírez; air, Barcelona, Spain JN406569RPB2 P. corynephorum CBS 256.87T = FRR 2663 = IMI 288724 Dried fish, Decapterus sp., Indonesia JN406595RPB2 P. cremeogriseum CBS 223.66NT = ATCC 18323 = IJFM 5011 = IMI 197492 = NRRL 3389 Forest soil, Kiev, Ukraine GU981624BT P. crocicola CBS 745.70IsoT = ATCC 18313 Crocus sativus (Saffron), Japan JN406535RPB2 P. cyaneum CBS 315.48 = ATCC 10432 = IMI 039744 = NRRL 775 Unrecorded source, France JN406575RPB2 P. daleae CBS 211.28T = ATCC 10435 = IFO 6087 = IFO 9072 = IMI 034910 = MUCL 29234 = NRRL 2025 Soil under conifer, Poland GU981649BT P. decaturense CBS 117509T = IBT 27117 = NRRL 28152 Old resupinate fungus, Ramsey Lake State Park, Decatur, Illinois, USA JN606621RPB2 P. decumbens CBS 230.81NT = IMI 190875 = MUCL 29107 = NRRL 741 Unrecorded source, Miami, Florida, USA JN406601RPB2 P. dierckxii CBS 185.81NT = IMI 092216 = MUCL 28665 = NRRL 755 Unknown source, Belgium JN406619RPB2 P. donkii CBS 188.72HT = ATCC 48439; = IFO 31746 = IMI 197489 = MUCL 31188 Arable soil, Alaska, USA JN617718BT P. echinulonalgiovense CBS 328.59T = ATCC 18314 = IFO 6229 = IMI 068213 Soil, Japan GU981631BT P. egyptiacum CBS 244.32NT = ATCC 10441 = IBT 14684 = IMI 040580 = NRRL 2090 Soil, Cairo, Egypt JN406598RPB2 51-S2 IsoT = ATCC 22350 = IJFM 5024 = IMI T NT Phylogeny of Penicillium and its position in Trichocomaceae Supplementary Information Table S1. (Continued). Name Collection no. Origin GenBank accession no. P. ehrlichii CBS 324.48HT = ATCC 10442 = IMI 039737 = NRRL 708 Poland GU981652BT P. elleniae CBS 118135T = IBT 23229 Leaf litter exposed for 6 months, mature forest, Araracuara, Colombia GU981663BT P. fagi CBS 689.77T = CCM F-696 = IJFM 3049 = IMI 253806 Fallen leaf, on Andosol, alt. 800 m. Fagus sylvatica, Navarra, Spain JN406540RPB2 P. fellutanum IBT 15460NT = NRRL 746 = IMI 39734 = ATCC 10443 Unrecorded source, USA JN406646RPB2 P. fennelliae CBS 711.68 = ATCC 22050 = ATCC 52492 = IMI 151747 = MUCL 31322 Flour, Zaire JN406536RPB2 P. flavigenum CBS 419.89HT = IBT 21526 = IBT 3091 = IMI 293207 Rhizosphere soil of Brassica campestris var. toria, Lyngby, Denmark JN406551RPB2 P. formosanum CBS 211.92HT = IBT 19748 = IBT 21527 Soil, Hsitou, Taiwan JN406615RPB2 P. fuscum CBS 235.60 = ATCC 18483 Type of P. silvaticum; forest soil, USSR JN406599RPB2 CBS 309.63 = ATCC 18322 Type of P. macedonense; forest soil, former Yugoslavia, Macedonia JN406580RPB2 P. gallaicum CBS 167.81T = ATCC 42232 = IMI 253794 = IBT 22016 Air, Madrid, Spain JN606609RPB2 P. glabrum CBS 105.11 Type of P. frequentans, unknown substrate, former West-Germany, Germany JN406647RPB2 CBS 229.28 = IMI 092231 = MUCL 29111 = NRRL 751 Type of P. paczoskii; soil, under conifer Poland JN406602RPB2 NRRL 35684 Boiled cork, Portugal EF198601RPB2 P. gladioli CBS 332.48 = ATCC 10448 = IBT 14772 = IMI 034911 = IMI 034911ii = MUCL 29174 = NRRL 939 Gladiolus corm, imported from the Netherlands, Washington DC, District of Columbia, USA JN406567RPB2 P. glandicola CBS 498.75EpiT = IBT 21529 = IMI 154241 Corm, Portugal JN406546RPB2 P. godlewskii CBS 215.28T = ATCC 10449 = ATCC 48714 IFO 7724 = IMI 040591 = MUCL 29243 = NRRL 2111 Soil under pine, Bialowieska, Poland JN606626RPB2 P. gorlenkoanum CBS 408.69IsoT = IMI 140339 Soil, Syria JN606601RPB2 P. heteromorphum CBS 226.89NT Soil, Hubei Province, Shennongjia, China JN406605RPB2 P. hetheringtonii CBS 122392 Soil, Treasure Island, Florida, USA JN606606RPB2 P. hirayamae NRRL 143NT = CBS 527.65 = 229.60 = ATCC 18312 = IMI 078255 = IMI 078255ii = NRRL 143 Milled rice, Thailand EU021625RPB2 P. hirsutum CBS 135.41T = ATCC 10429 = IBT 21531 = IMI 040213 = MUCL 15622 = NRRL 2032 Aphid, green fly, Baarn, Netherlands JN406629RPB2 P. hispanicum CBS 184.81 = FRR 2061 = IMI 190235 = NRRL 2061 Neotype of P. implicatum sensu Pitt; soil, New Delhi, India JN406620RPB2 CBS 691.77T = ATCC 38667 = IJFM 3223 = IMI 253785 Citrus limonium, Madrid, Spain JN406539RPB2 P. incoloratum CBS 101753HT = AS 3.4672 Seed of Phaseolus angularis, Beijing, China JN406651RPB2 P. indicum CBS 115.63IsoT = ATCC 18324 = FRR 3387 = IMI 166620 Sputum, man, Delhi, India JN406640RPB2 P. jamesonlandense CBS 102888T = DAOM 234087 = IBT 21984 = IBT 24411 Soil near Cassiope tetragona and Phyllodoce coerulea, East Greenland, Jameson Land near Hugin Lake, Greenland JN406648RPB2 P. janczewskii CBS 221.28NT = IMI 191499 = NRRL 919 Soil under Pinus sp., Poland JN406612RPB2 P. janthinellum CBS 340.48 = ATCC 10455 = IMI 040238 = NRRL 2016 Soil, Nicaragua GU981625BT P. javanicum CBS 341.48HT = ATCC 9099 = IFO 31735 = IMI 039733 = MUCL 29099 = NRRL 707 Root of Camellia sinensis, Indonesia, Java GU981657BT P. jensenii CBS 216.28T = ATCC 10456 = IMI 068233 = NRRL 3431 Forest soil, Poland JN406614RPB2 P. jugoslavicum CBS 192.87NT = IJFM 7785 = IMI 314508 Seed of Helianthus annuus (sunflower), former Yugoslavia JN406618RPB2 P. kojigenum CBS 345.61T = ATCC 18227 = IMI 086562 = MUCL 2457 = NRRL 3442 Roadside soil, Kirkcudbrightshire, Gelston, Scotland JN406564RPB2 HT NT T NT www.studiesinmycology.org 51-S3 Houbraken & Samson Supplementary Information Table S1. (Continued). Name Collection no. Origin GenBank accession no. P. levitum CBS 345.48NT = ATCC 10464 = IFO 6101 = IMI 039735 = NRRL 705 Modeling clay, USA GU981654BT P. limosum CBS 339.97 Marine sediment, Nagasaki prefecture, Japan GU981621BT P. lineolatum CBS 188.77 = NHL 2776 Soil from copse, Japan GU981620BT P. lividum CBS 347.48NT = ATCC 10102 = IMI 039736 = NRRL 754 Soil, Scotland JN406563RPB2 P. luteocoeruleum CBS 347.51T = ATCC 18237 = IMI 107651 = NRRL 3450 Wakamoto corn and rice cake, Nehira, Osaka Univ. Fac. Techn., Japan JN406562RPB2 P. luzoniacum CBS 622.72IsoT = DSM 2418 = NHL 6128 Soil from pine forest, Luzon Island, Sinipsip near Baguio, Philippines JN406543RPB2 P. madriti CBS 347.61HT = ATCC 18233 = IMI 086563 = MUCL 2456 = MUCL 31193 = NRRL 3452 Garden soil, Madrid, Spain JN406561RPB2 CBS 170.81 = ATCC 42229 = IJFM 5144 = IMI 253791 Type of P. castellonense; air, Madrid, Spain JN406623RPB2 CBS 160.81T = ATCC 42241 = IJFM 7093 = IMI 253801 Air, Madrid, Spain JN406626RPB2 CBS 163.81 = ATCC 42237 = IJFM 7029 Type of P. ovetense; sandy soil, Madrid, Spain JN406624RPB2 P. manginii CBS 253.31NT = NRRL 2134 = IMI 191732 = IBT 18224 Soil, unknown source JN606618RPB2 P. mariaecrucis CBS 271.83T = IMI 256075 Secale cereale, Spain GU981630BT P. melanoconidium CBS 641.95 = IBT 11406 = IBT 21534 Soil, Denmark JN406529RPB2 P. melinii CBS 218.30 = ATCC 10469 = IMI 040216 = MUCL 29235 = NRRL 2041 Forest soil, USA JN406613RPB2 CBS 280.58 = ATCC 18383 = IMI 071624 = NRRL 2672 Type of P. radulatum; Calluna heathland soil, England JN406586RPB2 P. meloforme CBS 445.74HT = ATCC 28049 = IMI 216903 = NHL 6468 Soil, Papua New Guinea GU981656BT P. meridianum CBS 314.67HT = ATCC 18545 = IMI 136209 Grassland soil, Pretoria, South Africa JN406576RPB2 P. miczynskii CBS 220.28 = ATCC 10470 = DSM 2437 = IFO 7730 = IMI 040030 = MUCL 29228 = NRRL 1077 = IBT 5491 Soil under conifer, Tatry mountains, Poland JN606623RPB2 P. molle CBS 456.72HT = ATCC 24075 = IMI 084589 Soil, Pakistan JN406550RPB2 P. montanense CBS 310.63 = ATCC 14941 = IMI 099468 = MUCL 31326 = NRRL 3407 Coniferous forest soil, Ravalli Co., Montana, USA JN406579RPB2 P. multicolor NRRL 2060 = IMI 092040 = NRRL 2060 Weathering treated cellophane, Florida, USA EU427262RPB2 P. murcianum CBS 161.81 = ATCC 42239 = IJFM 7031 = IMI 253800 Sandy soil, Madrid, Spain JN406625RPB2 P. nalgiovense CBS 352.48NT = ATCC 10472 = IBT 21536 = IMI 039804 = MUCL 31194 = NRRL 911 Ellischauer cheese, fomer Czechoslovakia JN406560RPB2 P. neocrassum CBS 122428T = NRRL 35639 Wine grapes, Madeira Island, Portugal JN406633RPB2 P. nodositatum CBS 330.90T Soil, Alberta, Canada JN406568RPB2 P. nodulum CBS 227.89 Mouldy pork, Hubei Province, Shennongjia, China JN406603RPB2 P. novae-zeelandiae CBS 137.41 = ATCC 10473 = IMI 040584ii = NRRL 2128 Apothecium of Sclerotinia, Palmerston North, New Zealand JN406628RPB2 P. ochrochloron CBS 357.48NT = ATCC 10540 = IMI 039806 = NRRL 926 Copper sulphate solution, Washington, USA GU981672BT P. ochrosalmoneum CBS 489.66HT = ATCC 18338 = IMI 116248ii Cornmeal, South Africa JN606631RPB2 P. odoratum CBS 294.62T = ATCC 14769 = CBS 296.62 = IMI 094208ii = NRRL 3007 Peaty soil in Picea-Larix bog, Taylor Co., Wisconsin, USA JN406583RPB2 P. oligosporum CBS 349.51T Japan GU981658BT P. onobense CBS 174.81T = ATCC 42225 = IJFM 3026 Soil, Navarra, Spain GU981627BT P. palmense CBS 336.79 = ATCC 38669 = IJFM 3840 Gran Canaria, Las Palmas, Spain JN406566RPB2 P. paneum CBS 465.95 = IBT 13929 Mouldy baker’s yeast, Vangede, Denmark JN406549RPB2 P. malacaense 51-S4 HT NT T HT T NT T T Phylogeny of Penicillium and its position in Trichocomaceae Supplementary Information Table S1. (Continued). Name Collection no. Origin GenBank accession no. P. papuaneum CBS 570.73IsoT = ATCC 28050 = ATCC 48363 Forest soil under Pinus sp. Central Dist., Port Moresby, Papua New Guinea JN406545RPB2 P. paraherquei CBS 430.65AUT = FAT 824 Soil, Japan GU981628BT P. parvum CBS 359.48 = ATCC 10479 = IFO 7732 = IMI 040587 = NRRL 2095 = QM 1878 Soil, Nicaragua JN406559RPB2 P. pasqualense CBS 122402 = IBT 29047 Air in bakery, Averhorn, the Netherlands JN606617RPB2 P. patens CBS 260.87HT = FRR 2662 Dried fish, Rastrelliger kanagurta, Indonesia JN406593RPB2 P. paxilli CBS 360.48 = ATCC 10480 = IMI 040226 = NRRL 2008 = IBT 16202 Ex-type; optical instrument, Barro Colorado Island, Panama JN606610RPB2 P. penarojense CBS 113178T = IBT 23262 Leaf litter exposed 6 months, mature forest, Peña Roja, Colombia GU981646BT P. percisinum CBS 111235T = AS 3.5891 = IBT 24565 Soil, Qinghai prov., China JN406644RPB2 P. philippinense CBS 623.72 Twig peduncle and fruit, Luzon Island, Sinipsip near Baguio, Philippines JN406542RPB2 P. phoeniceum CBS 249.32NT = ATCC 10481 = IJFM 5122 = IMI 040585 = NRRL 2070 Sooty mould on Phoenix sp. (palm) JN406597RPB2 P. pimiteoiense CBS 102479T = NRRL 25542 Kidney epithelial cell culture flask, Peoria, Illinois, USA JN406650RPB2 P. piscarium CBS 362.48T = ATCC 10482 = IMI 040032 = NRRL 1075 Cod-liver oil emulsion, Norway GU981668BT P. polonicum CBS 222.28T = IBT 12821 = IMI 291194 = MUCL 29204 = NRRL 995 Soil, Puszcza Bialowieska Forest, Poland JN406609RPB2 P. psychrosexualis CBS 128036HT Wooden crate in cold-store of apples, Netherlands JN406537RPB2 P. pullum CBS 331.48 = ATCC 10447 = IFO 6097 = IMI 039747 = NRRL 721 Soil, Tennessee, USA JN617719BT P. pulvillorum CBS 280.39NT = IFO 7763 = NRRL 2026 Acidic soil, UK GU981670BT P. quebecense CBS 101623 = IBT 29050 Air in sawmill, Quebec, Canada JN606622RPB2 P. quercetorum CBS 417.69IsoT = ATCC 48727 = IMI 140342 = MUCL 31203 Soil, Syria JN406552RPB2 P. raciborskii CBS 224.28T = ATCC 10488 = IMI 040568 = MUCL 29246 = NRRL 2150 Soil, under conifer Poznan area, “Dluga Goslina”, Poland JN406607RPB2 P. raistrickii CBS 261.33T = ATCC 10490 = IMI 040221 = NRRL 1044 = NRRL 2039 Cotton yarn, UK JN406592RPB2 P. ramusculum NRRL 2279 Unknown source EU427260RPB2 P. raperi CBS 281.58NT = ATCC 22355 = IFO 8179 = IMI 071625 = NRRL 2674 Soil, Bedford, UK GU981622BT P. raphiae CBS 126234T = IBT 22407 Soil under Raphia (?) palm in primary forest, Las Alturas, elev. 1530 m, Costa Rica JN606619RPB2 P. reticulisporum CBS 513.74 = DSM 2207 = IFO 9712 Type of P. arvense and E. arvense; soil, Japan GU981666BT CBS 121.68AUT = ATCC 18565 = IMI 136699 = NHL 6102 = NRRL 3446 Soil, Japan GU981665BT P. ribeum CBS 127809T = IBT 16537 = IBT 24431 = DAOM 234091 Red currant, Wyoming, USA JN406631RPB2 P. rolfsii CBS 368.48T = ATCC 10491 = IFO 7735 = IMI 040029 = MUCL 29229 = NRRL 1078 Pineapple, Florida, USA GU981667BT P. roqueforti CBS 221.30NT = ATCC 10110 = ATCC 1129 = IBT 6754 = IMI 024313 = NRRL 849 French Roquefort cheese, USA JN406611RPB2 P. roseopurpureum CBS 266.29NT = ATCC 10492 = IMI 040573 = MUCL 28654 = MUCL 29237 = NRRL 2064 = NRRL 2064A Unrecorded source JN606613RPB2 P. rubefaciens CBS 145.83HT Sandy soil under pine tree, Valladolid, Spain JN406627RPB2 P. rubens CBS 205.57 = ATCC 8537 = ATCC 9478 = IBT 23019 = IMI 015378 = NRRL 1209 = NRRL 824 Contaminant of bacterial culture (Fleming’s strain), UK JN406616RPB2 P. rubidurum CBS 609.73HT = ATCC 28051 = ATCC 48238 = IMI 228551 Soil, East Sepik Dist., Wewak, Papua New Guinea JN406544RPB2 P. sabulosum CBS 261.87HT = FRR 2743 Spoiled pasteurized fruit juice, Sydney, New South Wales, Australia JN406591RPB2 NT T AUT = DSM 2420 = NHL 6130 T www.studiesinmycology.org 51-S5 Houbraken & Samson Supplementary Information Table S1. (Continued). Name Collection no. Origin GenBank accession no. P. sajarovii CBS 277.83NT = CECT 2751 = IMI 259992 Secale cereale (rye) Zamora, Castrocontrigo, Spain JN406588RPB2 P. sanguifluum CBS 148.83 = CECT 2753 Sandy soil under pine tree, Valladolid, Spain JN606614RPB2 CBS 685.85 = IJFM 19078 = IBT 4904 = IBT 10578 = IBT 10579 Ex-type of P. lacussarmientei, sandy soil, National Park of Torres del Paine, near Lake Sarmiento, Tierra del Fuego, Chile JN606615RPB2 P. scabrosum CBS 683.89HT = FRR 2950 = IBT 3736 = IMI 285533 Zea mays, Denmark JN406541RPB2 P. sclerotigenum CBS 101033T = ATCC 18488 = CBS 343.59 = IBT 14346 = IBT 21544 = IMI 68616 = NRRL 3461 Rotting tuber, Dioscorea batatas, Myogo Pref., Tamba Prov., Sasayama, Japan JN406652RPB2 P. sclerotiorum CBS 287.36NT = ATCC 10494 = IMI 040569 = NRRL 2074 Air, Buitenzorg, Java, Indonesia JN406585RPB2 P. simplicissimum CBS 372.48NT = ATCC 10495 = IFO 5762 = IMI 039816 Flannel bag, South Africa GU981632BT P. sinaicum CBS 279.82HT = NHL 2894 Secale cereale (rye) Suez Canal, 30 km N of Port Said, Sinai Peninsula, Egypt JN406587RPB2 P. sizovae CBS 413.69NT = IMI 140344 Soil, Syria JN606603RPB2 P. skrjabinii CBS 439.75NT = IMI 196528 Soil, Russia (far East) GU981626BT P. smithii CBS 276.83 = CECT 2744 = IMI 259693 Secale cereale (rye), Zamora, Torneros, Spain JN406589RPB2 P. soppii CBS 226.28NT = ATCC 10496 = IMI 040217 = MUCL 29233 = NRRL 2023 Soil, Puszcza Bialowieska Forest, square “652”, Poland JN406606RPB2 P. spinulosum CBS 374.48NT = ATCC 10498 = IMI 024316 = MUCL 13910 = MUCL 13911 = NRRL 1750 Culture contaminant, Hannover, Germany JN406558RPB2 P. steckii CBS 260.55NT = ATCC 10499 = DSM 1252 = IMI 040583 = NRRL 2140 Cotton fabric treated with copper naphthenate; Panama JN606602RPB2 P. stolkiae CBS 315.67HT = IMI 136210 = ATCC 18546 Peaty forest soil, Eastern Transvaal, South-Africa JN617717BT P. striatisporum CBS 705.68HT = ATCC 22052 = IMI 151749 = MUCL 31202 Leaf litter, Acacia karroo (Sweet Thorn), Potchefstroom, South Africa JN406538RPB2 P. subarcticum CBS 111719HT = NRRL 31108 Petroleum contaminated soil, near Norman Wells, Northwest-Territories, Canada JN617716BT P. subericola CBS 125096T Non-boiled cork, Coruche, Portugal JN406621RPB2 P. sublateritium CBS 267.29NT = ATCC 10502 = IMI 040594 = MUCL 28655 = NRRL 2071 Unrecorded source, Belgium JN406590RPB2 P. sumatrense NRRL 6181 Unknown source EF198540RPB2 NRRL 779 = CBS 281.36 = NRRL 779 = ATCC 48669 = IBT 29658 = IBT 4978 Soil, Toba Heath, Sumatra, Indonesia EF198541RPB2 CBS 416.69 = IMI 140336 = IBT 29648 Isotype of P. baradicum; soil under cornel, Damascus, Syria JN606612RPB2 P. svalbardense CBS 122416T = IBT 23856 = EX-F 1307 Glacial ice, Svalbard, Greenland GU981669BT P. swiecickii CBS 119391 = FRR 918 = IBT 27865 = IMI 191500 = NRRL 918 Pine forest soil, Poland JN406635RPB2 P. terrenum CBS 313.67HT = ATCC 18547 = IMI 136208 Soil in subtropical forest, Eastern Transvaal, South Africa JN406577RPB2 P. terrigenum CBS 127354T = IBT 30769 Soil, Hawaii, USA JN606600RPB2 P. toxicarium NRRL 31271 Unknown source EF198486RPB2 NRRL 6172 Unknown source EF198499RPB2 NT T T P. tropicoides CBS 122410 Soil rainforest, near Hua-Hin, Thailand JN606608RPB2 P. tropicum CBS 112584T = IBT 24580 Soil between Coffea arabica, Karnataka, India JN606607RPB2 P. turbatum CBS 134.41 = ATCC 10415 = IMI 040590 = NRRL 2086 Neotype of P. baarnense; soil , Baarn, Netherlands JN406630RPB2 CBS 339.61 = NRRL 2087 Contaminant of P. euglaucum culture, see also Stolk Scott (1967); leaf litter of Acacia mollissima, Natal, South Africa JN406565RPB2 CBS 383.48NT = ATCC 9782 = CBS 237.60 = IMI 039738 = MUCL 29115 = NRRL 757 = NRRL 758 Rotten twig Taxus baccata JN406556RPB2 CBS 126216T = DTO 97A3 = IBT 23203 Leaf litter exposed for 6 months, mature forest, Araracuara, Colombia GU981647BT P. vanderhammenii 51-S6 T Phylogeny of Penicillium and its position in Trichocomaceae Supplementary Information Table S1. (Continued). Name Collection no. Origin GenBank accession no. P. vasconiae CBS 339.79T = CBS 175.81, IJFM 3008 Acid washed brown soil, Spain GU981653BT P. vinaceum CBS 389.48NT = ATCC 10514 = IMI 029189 = NRRL 739 Soil, Utah, USA JN406555RPB2 P. virgatum CBS 114838IsoT = BBA 65745 Soil near soy bean plant North of Noumea, Port Laguerre, New Caledonia JN406641RPB2 P. waksmanii CBS 230.28NT = ATCC 10516 = IFO 7737 = IMI 039746 = IMI 039746i = MUCL 29120 = NRRL 777 = IBT 5003 = IBT 6994 Woodland soil, Puszcza Bialowieska Forest, Poland JN606627RPB2 P. wellingtonense CBS 130375 = IBT 23557 Soil, New Zealand JN606616RPB2 P. westlingii CBS 231.28 = IMI 092272 = IBT 15088 Soil under conifer, Denga Goolina, Poznan, Poland JN606625RPB2 P. wotroi CBS 118171T = IBT 23253 Leaf litter exposed for 6 months, mature forest, Araracuara, Colombia GU981637BT P. yarmokense CBS 410.69IsoT = FRR 520 = IMI 140346 Soil, Syria JN406553RPB2 P. zonatum CBS 992.72HT = ATCC 24353 Coastal marsh soil, USA, North Carolina GU981651BT Penicillium sp. CBS 116986 = IBT 3265 Soil, Wales JN406638RPB2 CBS 117181 = IBT 6005 = IMI 304286 Barley, Denmark JN406637RPB2 CBS 117192 = IBT 22220 = IBT 24432 Chestnut, France JN406636RPB2 T www.studiesinmycology.org View publication stats 51-S7