Diaporthe: a genus of endophytic, saprobic and plant pathogenic fungi

Renata Gomes

Diaporthe caulivora is an economically important fungal pathogen and a causal agent of soybean stem canker and seed decay. Here, the genome of a Russian Far Eastern isolate of D. caulivora was sequenced, assembled, and announced. Assembly quality was enough for advanced annotation, including prediction of potential disease-related genes encoding virulence factors and molecular determinants contributing to pathogen-host selection, interactions, and adaptation. Comparative analysis of 15 Diaporthe species was conducted regarding general genome properties, collinearity, and proteomes, and included detailed investigation of interspersed repeats. A notable feature of this analysis is a high recombinant variability of Diaporthe genomes, determined by the number and distribution of interspersed repeats, which also proved to be responsible for the diversity of GC content and genome size. This variability is assumed the main determinant of the divergence of Diaporthe genomes. A Bayesian multi-gene phylogeny was inferred for the 15 Diaporthe species on the basis of twenty thousand polymorphic sites of > 100 orthologous genes using independently adjusted evolutionary models. This allowed for the most accurate determination of evolutionary relationships and species boundaries for effective reporting about these plant pathogens. The evidence, obtained by different genome analysis techniques, implies the host-independent evolution of Diaporthe species. Key points • The genome of a Far Eastern isolate of D. caulivora was announced. • A high degree of recombinant variability determines genomic divergence in Diaporthe genus. • The multi-gene phylogeny implies host-independent evolution of Diaporthe species.

Among a French collection of 150 Diaporthe helianthi / Phomopsis helianthi Munt.-Cvet. isolates collected on sunflower since 1995, 4 were chosen for their different characteristics according to their geographic origin and the part of the infected plant where they were sampled (leaf, petiole, capitulum). Phenotypic and molecular characterisation studies were conducted on these isolates. Phenotypic studies corresponded to their linear and ponderal growths, their morphology in culture on agar medium and their aggressiveness on sunflower leaf and stem through artificial contaminations in the field. Molecular characterisation concerned on one hand the whole genome (AFLP) and on the other hand the ITS sequences. The 4 isolates present phenotypic differences in their growth in vitro, their morphology (ability to differentiate perithecia) and their aggressiveness on sunflower. Similar variability was also observed in AFLP analyses of the D./P. helianthi genome. This fungus appears to have a...

Species of Diaporthe are important plant pathogens of a wide range of hosts worldwide. In the present study the species causing melanose and stem end rot diseases of Citrus spp. are revised. Three species of Diaporthe occurring on Citrus are characterised, including D. citri, D. cytosporella and D. foeniculina. Morphology and phylogenetic analyses of the complete nuclear ribosomal internal transcribed spacer regions and partial sequences of actin, beta-tubulin, calmodulin and translation elongation factor 1-alpha were used to resolve species on Citrus and related Diaporthe species. Diaporthe citri occurs on Citrus throughout the Citrus-growing regions of the world. Diaporthe cytosporella is found on Citrus in Europe and California (USA). Diaporthe foeniculina, including the synonym D. neotheicola, is recognised as a species with an extensive host range including Citrus. Diaporthe medusaea, a name widely used for D. citri, was determined to be a synonym of D. rudis, a species with a broad host range. Diaporthe citri is delimited based on molecular phylogenetic analysis with the inclusion of the conserved ex-type and additional collections from different geographic locations worldwide. D. cytosporella, D. foeniculina and D. rudis are epitypified, fully described and illustrated with a review of all synonyms based on molecular data and morphological studies. Newly designed primers are introduced to optimise the amplification and sequencing of calmodulin and actin genes in Diaporthe. A discussion is provided of the utility of genes and the need for multi-gene phylogenies when distinguishing species of Diaporthe or describing new species.

Persoonia 31, 2013: 1– 41 www.ingentaconnect.com/content/nhn/pimj RESEARCH ARTICLE http://dx.doi.org/10.3767/003158513X666844 Diaporthe: a genus of endophytic, saprobic and plant pathogenic fungi R.R. Gomes1, C. Glienke1, S.I.R. Videira 2, L. Lombard 2, J.Z. Groenewald 2, P.W. Crous 2,3,4 Key words Diaporthales Diaporthe Multi-Locus Sequence Typing (MLST) Phomopsis systematics Abstract Diaporthe (Phomopsis) species have often been reported as plant pathogens, non-pathogenic endophytes or saprobes, commonly isolated from a wide range of hosts. The primary aim of the present study was to resolve the taxonomy and phylogeny of a large collection of Diaporthe species occurring on diverse hosts, either as pathogens, saprobes, or as harmless endophytes. In the present study we investigated 243 isolates using multilocus DNA sequence data. Analyses of the rDNA internal transcribed spacer (ITS1, 5.8S, ITS2) region, and partial translation elongation factor 1-alpha (TEF1), beta-tubulin (TUB), histone H3 (HIS) and calmodulin (CAL) genes resolved 95 clades. Fifteen new species are described, namely Diaporthe arengae, D. brasiliensis, D. endophytica, D. hongkongensis, D. inconspicua, D. infecunda, D. mayteni, D. neoarctii, D. oxe, D. paranensis, D. pseudomangiferae, D. pseudophoenicicola, D. raonikayaporum, D. schini and D. terebinthifolii. A further 14 new combinations are introduced in Diaporthe, and D. anacardii is epitypiﬁed. Although species of Diaporthe have in the past chiefly been distinguished based on host association, results of this study conﬁrm several taxa to have wide host ranges, suggesting that they move freely among hosts, frequently co-colonising diseased or dead tissue. In contrast, some plant pathogenic and endophytic taxa appear to be strictly host speciﬁc. Given this diverse ecological behaviour among members of Diaporthe, future species descriptions lacking molecular data (at least ITS and HIS or TUB) should be strongly discouraged. Article info Received: 27 November 2012; Accepted: 24 February 2013; Published: 28 March 2013. INTRODUCTION Species of Diaporthe and their Phomopsis asexual states have broad host ranges and are widely distributed, occurring as plant pathogens, endophytes or saprobes, but also as pathogens of humans and other mammals (Webber & Gibbs 1984, Carroll 1986, Boddy & Grifﬁth 1989, Rehner & Uecker 1994, GarciaReyne et al. 2011, Udayanga et al. 2011). Diaporthe spp. are responsible for diseases on a wide range of plants hosts, some of which are economically important worldwide, causing root and fruit rots, dieback, cankers, leaf spots, blights, decay and wilt (Uecker 1988, Mostert et al. 2001a, van Rensburg et al. 2006, Santos et al. 2011, Thompson et al. 2011). Currently, MycoBank (accessed Sept. 2012) lists more than 1 000 names in the genus Phomopsis, while Diaporthe contains more than 860 names. In the past species have chiefly been described under the assumption they are host-speciﬁc, leading to a proliferation of names based on the hosts from which they were isolated (Uecker 1988). However, subsequent studies have found that many species are able to colonise diverse hosts as opportunists, and that several different species could even co-occur on the same host or lesion (Brayford 1990, Rehner & Uecker 1994, Mostert et al. 2001a, Farr et al. 2002, Crous & Groenewald 2005). Curiously, some species of Diaporthe can be either pathogenic or harmless endophytes depending on the 1 2 3 4 Department of Genetics, Universidade Federal do Paraná, Centro Politécnico, Box 19071, 81531-990, Curitiba, Brazil. CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands; corresponding author e-mail: p.crous@cbs.knaw.nl. Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands. Wageningen University and Research Centre (WUR), Laboratory of Phytopathology, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands. host and its health. For example, D. phaseolorum is pathogenic to soybean (Santos et al. 2011), but endophytic in mangroves (Laguncularia racemosa) (Sebastiane et al. 2011). With the deletion of Art. 59 from the International Code of Nomenclature for algae, fungi, and plants (ICN), asexual and sexual names of fungi receive equal status (Hawksworth et al. 2011, Wingﬁeld et al. 2012). Because the name Diaporthe (1870) predates Phomopsis (1905), Diaporthe is adopted in the present study for this group of fungi (Santos et al. 2010, 2011, Crous et al. 2011, Udayanga et al. 2012). Diaporthe (incl. its Phomopsis state) has been reported as one of the most frequently encountered genera of endophytic fungi in several plant hosts (Murali et al. 2006, Botella & Diez 2011). The genus has also frequently been recognised as a producer of interesting enzymes and secondary metabolites (Isaka et al. 2001, Kobayashi et al. 2003, Dai et al. 2005, Elsaesser et al. 2005) with antibiotic (Bandre & Sasek 1977, Dettrakul et al. 2003, Lin et al. 2005) or anticancer (Kumaran & Hur 2009) activity. Furthermore, species of Diaporthe have in the past been noted to deter herbivory (Brayford 1990, Weber 2009, Vesterlund et al. 2011), have lignocellulolytic activities (Jordaan et al. 2006), or have been applied as bioherbicides (Ash et al. 2010). The accurate application of accepted names of plant pathogenic fungi is essential for the development of effective biosecurity and trade policies (Crous & Groenewald 2005, Wingﬁeld et al. 2012). The taxonomy of many groups of plant pathogenic fungi has in the past been based on host association (Crous et al. 2013, Groenewald et al. 2013). Although some species of Diaporthe are host speciﬁc, a great number have been noted to occur on more than one host (Brayford 1990, Rehner & Uecker 1994, Farr et al. 2002). Similar observations led Wehmeyer © 2013 Naturalis Biodiversity Center & Centraalbureau voor Schimmelcultures 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. 2 Table 1 Host / substrate, locality, collector and GenBank accession numbers of strains included in the study. Original name Strain1 Isolation source Host family Locality Collector GenBank Accession numbers (ITS, CAL, HIS, TEF1, TUB)2 Diaporthe acaciigena D. acaciigena CBS 129521; CPC 17622 (ex-type) Acacia retinodes, leaves Mimosaceae Australia KC343005 KC343247 KC343489 KC343731 KC343973 Diaporthe acerina Diaporthe alleghaniensis Diaporthe alnea Diaporthe ambigua D. acerina D. alleghaniensis D. alnea D. alnea D. ambigua Acer saccharum Betula alleghaniensis, branches Alnus sp. Alnus sp. Pyrus communis Aceraceae Betulaceae Betulaceae Betulaceae Rosaceae – Canada – – South Africa KC343006 KC343007 KC343008 KC343009 KC343010 KC343248 KC343249 KC343250 KC343251 KC343252 KC343490 KC343491 KC343492 KC343493 KC343494 KC343732 KC343733 KC343734 KC343735 KC343736 KC343974 KC343975 KC343976 KC343977 KC343978 Diaporthe ampelina, comb. nov. D. ambigua D. ambigua D. ambigua D. scabra D. helianthi P. viticola CBS 137.27 CBS 495.72; ATCC 24097 (ex-type) CBS 146.46 CBS 159.47 CBS 114015; STE-U 2657; CPC 2657 (ex-epitype) CBS 117167; STE-U 5414; CPC 5414 CBS 123210; Di-C003/10 CBS 123211; Di-C002/9 CBS 127746; IMI 395956 CBS 187.87 CBS 111888; ATCC 48153; STE-U 2673; CPC 2673 CBS 114016; STE-U 2660; CPC 2660; PV F98-1 (ex-neotype) CBS 114867; STE-U 4708; CPC 4708 CBS 267.80; STE-U 2671; CPC 2671 CBS 111811; STE-U 2632; CPC 2632 CBS 115620; FAU 1005 CBS 120840; STE-U 5833; CPC 5833 CBS 126679 (ex-epitype) CBS 126680 CBS 720.97 (ex-epitype) CBS 100871 CBS 111591; AR 3724 CBS 111592; AR3776 (ex-epitype) CBS 123215; Ph-C133/1 CBS 344.86 CBS 501.90 CBS 136.25 CBS 161.64 (ex-isotype) CBS 535.75 CBS 114979; HKUCC 5527 (ex-type) CBS 117168; STE-U 5420; CPC 5420 CBS 117169; STE-U 5428; CPC 5428 (ex-type) CBS 117500; STE-U 5408; CPC 5408 CBS 111886; STE-U 2676; CPC 2676 (ex-type) CBS 113487; STE-U 2655; CPC 2655 CBS 122.21 CBS 138.27 CBS 133183; LGMF924; CPC 20300 (ex-type) LGMF926; CPC 20302 P.W. Crous, I.G. Pascoe & J. Edwards L.E. Wehmeyer R.H. Arnold S. Truter S. Truter S. Denman Aspalathus linearis, crown Foeniculum vulgare Foeniculum vulgare Platanus acerifolia Helianthus annuus Vitis vinifera Fabaceae Apiaceae Apiaceae Platanaceae Asteraceae Vitaceae South Africa Portugal Portugal Italy Italy USA: California J.C. Janse van Rensburg J.M. Santos J.M. Santos G. Granata A. Zazzerini J.D. Cucuzza KC343011 KC343012 KC343013 KC343014 KC343015 KC343016 KC343253 KC343254 KC343255 KC343256 KC343257 KC343258 KC343495 KC343496 KC343497 KC343498 KC343499 KC343500 KC343737 KC343738 KC343739 KC343740 KC343741 KC343742 KC343979 KC343980 KC343981 KC343982 KC343983 KC343984 Vitis vinifera Vitaceae France P. Larignon AF230751 AY745026 – AY745056 JX275452 Vitis vinifera Vitis vinifera Vitis vinifera Prunus persica, cankers Prunus salicina, wood Prunus dulcis Prunus dulcis Anacardium occidentale Foeniculum vulgare, dying twig Heracleum sphondylium, decaying stems Heracleum sphondylium, decaying stems Foeniculum vulgare Eryngium maritimum, leaf spots Heracleum sphondylium, seeds Arctium sp. Areca catechu, fruit Citrus sp., fruits Arenga engleri Aspalathus linearis, crown Aspalathus linearis, branch Vitaceae Vitaceae Vitaceae Rosaceae Rosaceae Rosaceae Rosaceae Anacardiaceae Apiaceae Apiaceae Apiaceae Apiaceae Apiaceae Apiaceae Asteraceae Arecaceae Rutaceae Arecaceae Fabaceae Fabaceae Turkey Italy South Africa USA: Georgia South Africa Portugal Portugal East Africa Italy Austria Austria Portugal France France – India Suriname Hong Kong South Africa South Africa M. Erkan A. Zazzerini L. Mostert W. Uddin U. Damm E. Diogo E. Diogo M. Puccioni L. Mugnai A.Y. Rossman A.Y. Rossman A.J.L. Phillips H.A. van der Aa H.A. van der Aa A.W. Archer H.C. Srivastava I. Block K.D. Hyde J.C. Janse van Rensburg J.C. Janse van Rensburg KC343017 KC343018 KC343019 KC343020 KC343021 KC343022 KC343023 KC343024 KC343025 KC343026 KC343027 KC343028 KC343029 KC343030 KC343031 KC343032 KC343033 KC343034 KC343035 KC343036 KC343259 KC343260 KC343261 KC343262 KC343263 KC343264 KC343265 KC343266 KC343267 KC343268 KC343269 KC343270 KC343271 KC343272 KC343273 KC343274 KC343275 KC343276 KC343277 KC343278 KC343501 KC343502 KC343503 KC343504 KC343505 KC343506 KC343507 KC343508 KC343509 KC343510 KC343511 KC343512 KC343513 KC343514 KC343515 KC343516 KC343517 KC343518 KC343519 KC343520 KC343743 KC343744 KC343745 KC343746 KC343747 KC343748 KC343749 KC343750 KC343751 KC343752 KC343753 KC343754 KC343755 KC343756 KC343757 KC343758 KC343759 KC343760 KC343761 KC343762 KC343985 KC343986 KC343987 KC343988 KC343989 KC343990 KC343991 KC343992 KC343993 KC343994 KC343995 KC343996 KC343997 KC343998 KC343999 KC344000 KC344001 KC344002 KC344003 KC344004 Aspalathus linearis Vitis vinifera Fabaceae Vitaceae South Africa Australia S. Lamprecht R.W.A. Schepers KC343037 KC343038 KC343279 KC343280 KC343521 KC343522 KC343763 KC343764 KC344005 KC344006 Vitaceae Convolvulaceae Caprifoliaceae Apocynaceae South Africa USA – Brazil L. Mostert L.L. Harter L.E. Wehmeyer K. Rodriguez KC343039 KC343040 KC343041 KC343042 KC343281 KC343282 KC343283 KC343284 KC343523 KC343524 KC343525 KC343526 KC343765 KC343766 KC343767 KC343768 KC344007 KC344008 KC344009 KC344010 Apocynaceae Brazil K. Rodriguez KC343043 KC343285 KC343527 KC343769 KC344011 CBS 114437; UPSC 2980 CBS 127268; Dpc1 (ex-neotype) CBS 178.55; ATCC 12048; Alfaro 243 Vitis vinifera Ipomoea batatas Viburnum sp. Aspidosperma tomentosum, endophytic in leaf Aspidosperma tomentosum, endophytic in leaf Carpinus betulus Glycine max, stem Glycine soja, mature stem Corylaceae Fabaceae Fabaceae Sweden Croatia Canada K. & L. Holm K. Vrandečić A.A. Hildebrand KC343044 KC343045 KC343046 KC343286 KC343287 KC343288 KC343528 KC343529 KC343530 KC343770 KC343771 KC343772 KC344012 KC344013 KC344014 CBS 139.27 CBS 454.81 CBS 753.70 CBS 719.96 CBS 199.39 CBS 230.52 Celastrus scandens Chamaerops humilis, dead part of leaf Spartium junceum, dead branch Ficus carica, branch – Citrus sinensis, decaying fruit Celastraceae Arecaceae Fabaceae Moraceae – Rutaceae – Greece Croatia Bulgaria Italy Suriname L.E. Wehmeyer H.A. van der Aa J.A. von Arx E. Ilieva G. Goidánich N.J. van Suchtelen KC343047 KC343048 KC343049 KC343050 KC343051 KC343052 KC343289 KC343290 KC343291 KC343292 KC343293 KC343294 KC343531 KC343532 KC343533 KC343534 KC343535 KC343536 KC343773 KC343774 KC343775 KC343776 KC343777 KC343778 KC344015 KC344016 KC344017 KC344018 KC344019 KC344020 P. viticola Diaporthe amygdali Diaporthe anacardii, comb. nov. Diaporthe angelicae Diaporthe arctii Diaporthe arecae, comb. nov. Diaporthe arengae, sp. nov. Diaporthe aspalathi P. viticola P. viticola P. amygdali P. amygdali P. amygdali P. amygdali 3B P. amygdali 55A P. anacardii P. foeniculi D. angelicae D. angelicae D. angelicae P. asteriscus D. angelicae D. arctii P. phoenicicola D. citri P. pittospori D. aspalathi D. aspalathi Diaporthe australafricana D. aspalathi D. australafricana Diaporthe batatas Diaporthe beckhausii Diaporthe brasiliensis, sp. nov. D. australafricana D. batatas D. beckhausii – – Diaporthe carpini Diaporthe caulivora D. carpini D. caulivora D. phaseolorum var. caulivora Diaporthe celastrina D. celastrina Diaporthe chamaeropis, comb. nov. P. phoenicicola D. sarothamni Diaporthe cinerascens P. cinerascens Diaporthe citri D. conorum D. citri Persoonia – Volume 31, 2013 Species Diaporthe cynaroidis Diaporthe decedens Diaporthe detrusa Diaporthe elaeagni Diaporthe endophytica, sp. nov. Diaporthe eres Diaporthe eugeniae, comb. nov. Diaporthe fibrosa Diaporthe foeniculacea Diaporthe sp. P. convolvuli D. crataegi D. crotalariae P. cuppatea LGMF946; CPC 20322 CBS 124654; DP 0727 CBS 114435; UPSC 2938 CBS 162.33 (ex-type) CBS 117499; STE-U 5431; CPC 5431 (ex-type) D. cynaroidis CBS 122676; CMW 22190; CPC 13180 (ex-type) D. decedens CBS 109772; AR 3459 D. decedens CBS 114281; UPSC 2957 D. detrusa CBS 109770; AR 3424 D. detrusa CBS 114652; UPSC 3371 D. detrusa CBS 140.27 P. elaeagni CBS 504.72 – CBS 133811; LGMF916; CPC 20292 (ex-type) – LGMF911; CPC 20287 – LGMF919; CPC 20295 – LGMF928; CPC 20304 – LGMF934; CPC 20310 – LGMF935; CPC 20311 – LGMF937; CPC 20313 – LGMF948; CPC 20324 D. eres CBS 101742 D. medusaea CBS 102.81 D. eres CBS 109767; AR 3538; WJ 1643 D. arctii CBS 110.85 P. skimmiae CBS 122.82 Phomopsis sp. no. 23 CBS 129168 D. conorum CBS 186.37 P. controversa CBS 250.38 P. stictica CBS 267.32 P. rudis CBS 267.55 P. ranojevicii CBS 283.85 D. eres CBS 287.74 P. osmanthi CBS 297.77 P. cacti CBS 365.97 P. crustosa CBS 370.67; MUCL 9931 D. perniciosa CBS 375.61 P. phaseoli CBS 422.50 P. cotoneastri CBS 439.82; BBA P-407; IMI 162181a (isotype of Phomopsis cotoneastri) P. cruciferae CBS 445.62 P. durandiana CBS 485.96 D. seposita CBS 528.83 P. abutilonis CBS 688.97 P. crustosa CBS 694.94 P. magnoliicola CBS 791.68 P. tritici CBS 841.84 P. eugeniae CBS 444.82 D. fibrosa CBS 109751; AR 3425 D. fibrosa CBS 113830; UPSC 2117 D. foeniculacea CBS 111553 D. foeniculacea CBS 111554 Fabaceae Convolvulaceae Rosaceae Fabaceae Fabaceae Brazil Turkey Sweden USA South Africa A. Almeida D. Berner K. & L. Holm G.F. Weber J.C. Janse van Rensburg KC343053 KC343054 KC343055 KC343056 KC343057 KC343295 KC343296 KC343297 KC343298 KC343299 KC343537 KC343538 KC343539 KC343540 KC343541 KC343779 KC343780 KC343781 KC343782 KC343783 KC344021 KC344022 KC344023 KC344024 KC344025 Protea cynaroides, leaf litter Proteaceae South Africa S. Marincowitz KC343058 KC343300 KC343542 KC343784 KC344026 Corylus avellana Corylus avellana Berberis vulgaris Berberis vulgaris Berberis vulgaris Elaeagnus sp., twig Schinus terebinthifolius, endophytic in leaf Corylaceae Corylaceae Berberidaceae Berberidaceae Berberidaceae Elaeagnaceae Anacardiaceae Austria Sweden Austria Sweden – Netherlands Brazil W. Jaklitsch K. & L. Holm A.Y. Rossman K. & L. Holm L.E. Wehmeyer J. Gremmen J. Lima KC343059 KC343060 KC343061 KC343062 KC343063 KC343064 KC343065 KC343301 KC343302 KC343303 KC343304 KC343305 KC343306 KC343307 KC343543 KC343544 KC343545 KC343546 KC343547 KC343548 KC343549 KC343785 KC343786 KC343787 KC343788 KC343789 KC343790 KC343791 KC344027 KC344028 KC344029 KC344030 KC344031 KC344032 KC344033 Schinus terebinthifolius, endophytic in leaf Schinus terebinthifolius, endophytic in leaf Maytenus ilicifolia, endophytic in petiole Maytenus ilicifolia, endophytic in petiole Maytenus ilicifolia, endophytic in petiole Maytenus ilicifolia, endophytic in petiole Glycine max, seed Fraxinus sp., fallen fruit Juglans regia, twig Acer campestre Arctium sp., dead stems Skimmia japonica, dying twigs Rhododendron sp. Picea abies, seedling Fraxinus excelsior, living and dead twig – Laburnum × watereri ‘Vossii’ Allium giganteum, dead stem Sorbus aucuparia, dead branch Osmanthus aquifolium, leaf tip Opuntia sp., cladodes Ilex aquifolium, dead leaf Malus sylvestris, rotten fruit Phaseolus vulgaris Cotoneaster sp. Anacardiaceae Anacardiaceae Celastraceae Celastraceae Celastraceae Celastraceae Fabaceae Oleaceae Juglandaceae Aceraceae Asteraceae Rutaceae Ericaceae Pinaceae Oleaceae – Fabaceae Alliaceae Rosaceae Oleaceae Cactaceae Aquifoliaceae Rosaceae Fabaceae Rosaceae Brazil Brazil Brazil Brazil Brazil Brazil Brazil Netherlands Italy Austria Netherlands Netherlands Latvia UK UK: Scotland – Netherlands Netherlands Netherlands Netherlands Netherlands Netherlands – Netherlands UK: Scotland J. Lima J. Lima R.R. Gomes R.R. Gomes R.R. Gomes R.R. Gomes A. Almeida G.J.M. Verkley M. Bisiach W. Jaklitsch M. de Nooij H.A. v. Kesteren I. Apine T.R. Peace J.A. MacDonald W.G. Hutchinson I. de Boer H.A. van der Aa W.M. Loerakker H.A. van der Aa H.A. van der Aa H.A. van der Aa Geigy Goossens H. Butin KC343066 KC343067 KC343068 KC343069 KC343070 KC343071 KC343072 KC343073 KC343074 KC343075 KC343076 KC343077 KC343078 KC343079 KC343080 KC343081 KC343082 KC343083 KC343084 KC343085 KC343086 KC343087 KC343088 KC343089 KC343090 KC343308 KC343309 KC343310 KC343311 KC343312 KC343313 KC343314 KC343315 KC343316 KC343317 KC343318 KC343319 KC343320 KC343321 KC343322 KC343323 KC343324 KC343325 KC343326 KC343327 KC343328 KC343329 KC343330 KC343331 KC343332 KC343550 KC343551 KC343552 KC343553 KC343554 KC343555 KC343556 KC343557 KC343558 KC343559 KC343560 KC343561 KC343562 KC343563 KC343564 KC343565 KC343566 KC343567 KC343568 KC343569 KC343570 KC343571 KC343572 KC343573 KC343574 KC343792 KC343793 KC343794 KC343795 KC343796 KC343797 KC343798 KC343799 KC343800 KC343801 KC343802 KC343803 KC343804 KC343805 KC343806 KC343807 KC343808 KC343809 KC343810 KC343811 KC343812 KC343813 KC343814 KC343815 KC343816 KC344034 KC344035 KC344036 KC344037 KC344038 KC344039 KC344040 KC344041 KC344042 KC344043 KC344044 KC344045 KC344046 KC344047 KC344048 KC344049 KC344050 KC344051 KC344052 KC344053 KC344054 KC344055 KC344056 KC344057 KC344058 Alliaria officinalis Rumex hydrolapathum, dead stem Wisteria sinensis, dead branch Abutilon sp. Ilex aquifolium, twigs suffering from dieback Magnolia × soulangeana, withering leaf Hordeum sp., leaf spot Eugenia aromatica, leaf Rhamnus cathartica Rhamnus cathartica Foeniculum vulgare, base of senescent stem Foeniculum vulgare, base of senescent stem Pyrus pyrifolia Foeniculum vulgare Brassicaceae Polygonaceae Fabaceae Malvaceae Aquifoliaceae Magnoliaceae Poaceae Myrtaceae Rhamnaceae Rhamnaceae Apiaceae Netherlands Netherlands Netherlands Netherlands Netherlands Netherlands Germany West Sumatra Austria Sweden Spain G.H. Boerema H.A. van der Aa H.A. van der Aa A. Aptroot G.J.M. Verkley H.A. van der Aa M. Hossfeld R. Kasim A.Y. Rossman K. & L. Holm A.J.L. Phillips KC343091 KC343092 KC343093 KC343094 KC343095 KC343096 KC343097 KC343098 KC343099 KC343100 KC343101 KC343333 KC343334 KC343335 KC343336 KC343337 KC343338 KC343339 KC343340 KC343341 KC343342 KC343343 KC343575 KC343576 KC343577 KC343578 KC343579 KC343580 KC343581 KC343582 KC343583 KC343584 KC343585 KC343817 KC343818 KC343819 KC343820 KC343821 KC343822 KC343823 KC343824 KC343825 KC343826 KC343827 KC344059 KC344060 KC344061 KC344062 KC344063 KC344064 KC344065 KC344066 KC344067 KC344068 KC344069 Apiaceae Portugal A.J.L. Phillips KC343102 KC343344 KC343586 KC343828 KC344070 Rosaceae Apiaceae New Zealand Portugal W. Kandula A.J.L. Phillips KC343103 KC343104 KC343345 KC343346 KC343587 KC343588 KC343829 KC343830 KC344071 KC344072 Foeniculum vulgare Apiaceae Portugal A.J.L. Phillips KC343105 KC343347 KC343589 KC343831 KC344073 Prunus amygdalus, dried fruit Rosaceae Italy A. Ciccarone KC343106 KC343348 KC343590 KC343832 KC344074 3 CBS 116957; NZ-37 CBS 123208; Di-C004/5 (ex-type of D. neotheicola) D. neotheicola CBS 123209; Di-C004/4 (ex-type of D. neotheicola) P. mali f.sp. amygdali CBS 171.78 P. theicola D. neotheicola Glycine max, seed Convolvulus arvensis, leaves Crataegus oxyacantha Crotalaria spectabilis Aspalathus linearis R.R. Gomes et al.: Diaporthe Diaporthe convolvuli, comb. nov. Diaporthe crataegi Diaporthe crotalariae Diaporthe cuppatea Species 4 Table 1 (cont.) Strain1 Isolation source Host family Locality Collector GenBank Accession numbers (ITS, CAL, HIS, TEF1, TUB)2 P. theicola P. diospyri D. seposita P. casuarinae P. bougainvilleae CBS 187.27 (ex-type of P. theicola) CBS 287.56 CBS 357.69 CBS 400.48 CBS 603.88 Camellia sinensis, leaves and branches Diospyros kaki, twig, after frost damage Wisteria sinensis, dead twigs – Bougainvillea spectabilis, peduncles of flowers Cannabis sativa, dead leaf Gardenia florida, stem Helianthus annuus, seed Helianthus annuus, overwintering stem Hevea brasiliensis Hevea brasiliensis, leaf Carya glabra Dichroa febrífuga, fruit Theaceae Ebenaceae Fabaceae – Nyctaginaceae Italy Italy Netherlands India Portugal M. Curzi M. Ribaldi H.A. van der Aa S.R. Bose H.A. van der Aa KC343107 KC343108 KC343109 KC343110 KC343111 KC343349 KC343350 KC343351 KC343352 KC343353 KC343591 KC343592 KC343593 KC343594 KC343595 KC343833 KC343834 KC343835 KC343836 KC343837 KC344075 KC344076 KC344077 KC344078 KC344079 Cannabaceae Rubiaceae Asteraceae Asteraceae Euphorbiaceae Euphorbiaceae Juglandaceae Hydrangeaceae USA: Illinois Italy – Serbia Brazil India USA: Michigan Hong Kong J.M. McPartland M. Ribaldi – M. Muntañola-Cvetkovic D.S. Attili K. Jayarathnam L.E. Wehmeyer K.D. Hyde KC343112 KC343113 KC343114 KC343115 KC343116 KC343117 KC343118 KC343119 KC343354 KC343355 KC343356 KC343357 KC343358 KC343359 KC343360 KC343361 KC343596 KC343597 KC343598 KC343599 KC343600 KC343601 KC343602 KC343603 KC343838 KC343839 KC343840 KC343841 KC343842 KC343843 KC343844 KC343845 KC344080 KC344081 KC344082 KC344083 KC344084 KC344085 KC344086 KC344087 Hordeum vulgare, root Sorbus aucuparia Sorbus americana Maytenus ilicifolia, endophytic in petiole Poaceae Rosaceae Rosaceae Celastraceae Norway Sweden – Brazil L. Sundheim K. & L. Holm L.E. Wehmeyer R.R. Gomes KC343120 KC343121 KC343122 KC343123 KC343362 KC343363 KC343364 KC343365 KC343604 KC343605 KC343606 KC343607 KC343846 KC343847 KC343848 KC343849 KC344088 KC344089 KC344090 KC344091 Spondias mombin Maytenus ilicifolia, endophytic in petiole Schinus terebinthifolius, endophytic in leaf Anacardiaceae Celastraceae Anacardiaceae Brazil Brazil Brazil K. Rodriguez R.R. Gomes J. Lima KC343124 KC343125 KC343126 KC343366 KC343367 KC343368 KC343608 KC343609 KC343610 KC343850 KC343851 KC343852 KC344092 KC344093 KC344094 Schinus terebinthifolius, endophytic in leaf Schinus terebinthifolius, endophytic in leaf Schinus terebinthifolius, endophytic in leaf Schinus terebinthifolius, endophytic in leaf Schinus terebinthifolius, endophytic in leaf Maytenus ilicifolia, endophytic in petiole Maytenus ilicifolia, endophytic in petiole Juglans sp., dead wood Ribes sp. Anacardiaceae Anacardiaceae Anacardiaceae Anacardiaceae Anacardiaceae Celastraceae Celastraceae Juglandaceae Grossulariaceae Brazil Brazil Brazil Brazil Brazil Brazil Brazil USA: Tennessee Canada J. Lima J. Lima J. Lima J. Lima J. Lima R.R. Gomes R.R. Gomes L. Vasilyeva L.E. Wehmeyer KC343127 KC343128 KC343129 KC343130 KC343131 KC343132 KC343133 KC343134 KC343135 KC343369 KC343370 KC343371 KC343372 KC343373 KC343374 KC343375 KC343376 KC343377 KC343611 KC343612 KC343613 KC343614 KC343615 KC343616 KC343617 KC343618 KC343619 KC343853 KC343854 KC343855 KC343856 KC343857 KC343858 KC343859 KC343860 KC343861 KC344095 KC344096 KC344097 KC344098 KC344099 KC344100 KC344101 KC344102 KC344103 CBS 123212; Di-C001/5 (ex-type) CBS 123213; Di-C001/3 CBS 505.76 CBS 133185; LGMF938; CPC 20314 (ex-type) CBS 143.27 CBS 435.87 Foeniculum vulgare, stem Foeniculum vulgare, stem Manihot utilissima, leaves Maytenus ilicifolia, endophytic in petiole Apiaceae Apiaceae Euphorbiaceae Celastraceae Portugal Portugal Rwanda Brazil J.M. Santos J.M. Santos J. Semal R.R. Gomes KC343136 KC343137 KC343138 KC343139 KC343378 KC343379 KC343380 KC343381 KC343620 KC343621 KC343622 KC343623 KC343862 KC343863 KC343864 KC343865 KC344104 KC344105 KC344106 KC344107 Sambucus canadensis Glycine soja Caprifoliaceae Fabaceae – Indonesia L.E. Wehmeyer H. Vermeulen KC343140 KC343141 KC343382 KC343383 KC343624 KC343625 KC343866 KC343867 KC344108 KC344109 CBS 507.78 (ex-isotype) CBS 129519; CPC 17026 (ex-type) CBS 144.27 CBS 109490; GB 6421; AR 3450 (ex-type) Cucumis melo Musa sp., leaves Spiraea sp. Ambrosia trifida Cucurbitaceae Musaceae Rosaceae Asteraceae L. Beraha & M.J. O’Brien KC343142 P.W. Crous & R.G. Shivas KC343143 L.E. Wehmeyer KC343144 G. Bills KC343145 KC343384 KC343385 KC343386 KC343387 KC343626 KC343627 KC343628 KC343629 KC343868 KC343869 KC343870 KC343871 KC344110 KC344111 KC344112 KC344113 Fagaceae USA: Texas Australia – USA: New Jersey Korea K.A. Seifert KC343146 KC343388 KC343630 KC343872 KC344114 Rosaceae New Zealand W. Kandula & L. Castlebury W. Kandula & L. Castlebury G.J. Samuels I. Apine Kotthoff M. Muntañola-Cvetkovic KC343147 KC343389 KC343631 KC343873 KC344115 KC343148 KC343390 KC343632 KC343874 KC344116 KC343149 KC343150 KC343151 KC343152 KC343391 KC343392 KC343393 KC343394 KC343633 KC343634 KC343635 KC343636 KC343875 KC343876 KC343877 KC343878 KC344117 KC344118 KC344119 KC344120 Diaporthe ganjae, comb. nov. Diaporthe gardeniae, comb. nov. Diaporthe helianthi P. ganjae P. gardeniae D. helianthi D. helianthi Diaporthe cf. heveae 1 P. heveae Diaporthe cf. heveae 2 P. heveae Diaporthe hickoriae D. hickoriae Diaporthe hongkongensis, sp. nov. P. pittospori Diaporthe hordei, comb. nov. Diaporthe impulsa Diaporthe inconspicua, sp. nov. P. hordei D. impulsa D. impulsa Diaporthe sp. Diaporthe infecunda, sp. nov. Diaporthe sp. Diaporthe sp. Diaporthe sp. Diaporthe juglandina Diaporthe longispora, comb. nov. Diaporthe lusitanicae Diaporthe manihotia Diaporthe mayteni, sp. nov. Diaporthe megalospora Diaporthe melonis Diaporthe sp. Diaporthe sp. Diaporthe sp. Diaporthe sp. Diaporthe sp. Diaporthe sp. Diaporthe sp. D. juglandina D. strumella var. longispora D. lusitanicae D. lusitanicae P. manihot – CBS 180.91; ILLS 43621 (ex-type) CBS 288.56 CBS 344.94 CBS 592.81 (ex-type) CBS 852.97 CBS 681.84 CBS 145.26 (ex-type) CBS 115448; HKUCC 9104; AT 646 DF 24 (ex-type) CBS 481.92 CBS 114434; UPSC 3052 CBS 141.27 CBS 133813; LGMF930; CPC 20306 (ex-type) LGMF922; CPC 20298 LGMF931; CPC 20307 CBS 133812; LGMF906; CPC 20282 (ex-type) LGMF908; CPC 20284 LGMF912; CPC 20288 LGMF917; CPC 20293 LGMF918; CPC 20294 LGMF920; CPC 20296 LGMF933; CPC 20309 LGMF940; CPC 20316 CBS 121004; DP 0659 CBS 194.36 (ex-type) Diaporthe musigena Diaporthe neilliae Diaporthe neoarctii, sp. nov. D. megalospora D. phaseolorum var. sojae D. melonis D. musigena D. neilliae D. arctii Diaporthe nobilis P. castanea CBS 113470; DAOM 226800 P. fukushii CBS 116953; NZ-26 Castanea sativa, chestnuts collected in grocery store Pyrus pyrifolia P. fukushii CBS 116954; NZ-27 Pyrus pyrifolia Rosaceae New Zealand D. perniciosa Phomopsis sp. no. 22 D. nobilis D. pulla CBS 124030; GJS 77-49 CBS 129167 CBS 200.39 CBS 338.89 Malus pumila, bark Rhododendron sp. Laurus nobilis, stem Hedera helix Rosaceae Ericaceae Lauraceae Araliaceae New Zealand Latvia Germany Yugoslavia Persoonia – Volume 31, 2013 Original name CBS 587.79 D. nomurai D. novem D. novem D. novem D. pardalota Diaporthe sp. D. oncostoma D. oncostoma D. oncostoma P. crustosa – Pinus pentaphylla, bonzai imported from Japan into Netherlands Morus sp. Glycine max, seed Glycine max, seed Glycine max, seed Polygonatum odoratum, leaves Maytenus ilicifolia, endophytic in petiole Robinia pseudoacacia, leaf spot Robinia pseudoacacia Robinia pseudoacacia, dead branches Ilex aquifolium, leaf Maytenus ilicifolia, endophytic in petiole Pinaceae Japan G.H. Boerema KC343153 KC343395 KC343637 KC343879 KC344121 Moraceae Fabaceae Fabaceae Fabaceae Convallariaceae Celastraceae Fabaceae Fabaceae Fabaceae Aquifoliaceae Celastraceae Japan Croatia Croatia Croatia Romania Brazil Germany Russia France Germany Brazil K. Togashi T. Duvnjak T. Duvnjak T. Duvnjak O. Constantinescu R.R. Gomes H. Butin L. Vasilyeva H.A. van der Aa M. Hesse R.R. Gomes KC343154 KC343155 KC343156 KC343157 KC343158 KC343159 KC343160 KC343161 KC343162 KC343163 KC343164 KC343396 KC343397 KC343398 KC343399 KC343400 KC343401 KC343402 KC343403 KC343404 KC343405 KC343406 KC343638 KC343639 KC343640 KC343641 KC343642 KC343643 KC343644 KC343645 KC343646 KC343647 KC343648 KC343880 KC343881 KC343882 KC343883 KC343884 KC343885 KC343886 KC343887 KC343888 KC343889 KC343890 KC344122 KC344123 KC344124 KC344125 KC344126 KC344127 KC344128 KC344129 KC344130 KC344131 KC344132 Maytenus ilicifolia, endophytic in petiole Schinus terebinthifolius, endophytic in leaf Maytenus ilicifolia, endophytic in petiole Maytenus ilicifolia, endophytic in petiole Prunus padus Alnus glutinosa Maytenus ilicifolia, endophytic in petiole Celastraceae Anacardiaceae Celastraceae Celastraceae Rosaceae Betulaceae Celastraceae Brazil Brazil Brazil Brazil Sweden Sweden Brazil R.R. Gomes J. Lima S.A.V. Pileggi R.R. Gomes K. & L. Holm K. & L. Holm R.R. Gomes KC343165 KC343166 KC343167 KC343168 KC343169 KC343170 KC343171 KC343407 KC343408 KC343409 KC343410 KC343411 KC343412 KC343413 KC343649 KC343650 KC343651 KC343652 KC343653 KC343654 KC343655 KC343891 KC343892 KC343893 KC343894 KC343895 KC343896 KC343897 KC344133 KC344134 KC344135 KC344136 KC344137 KC344138 KC344139 Ulmus glabra Ulmaceae Austria A.Y. Rossman KC343172 KC343414 KC343656 KC343898 KC344140 Persea gratissima, young fruit Lauraceae E. Laville KC343173 KC343415 KC343657 KC343899 KC344141 G.J.M. Verkley A. Mengistu A. Mengistu S.R. Pennycook L. Beraha R.R. Gomes R.R. Gomes P. de Leeuw KC343174 KC343175 KC343176 KC343177 KC343178 KC343179 KC343180 KC343181 KC343416 KC343417 KC343418 KC343419 KC343420 KC343421 KC343422 KC343423 KC343658 KC343659 KC343660 KC343661 KC343662 KC343663 KC343664 KC343665 KC343900 KC343901 KC343902 KC343903 KC343904 KC343905 KC343906 KC343907 KC344142 KC344143 KC344144 KC344145 KC344146 KC344147 KC344148 KC344149 – M.S.A. Al-Momen KC343182 KC343183 KC343424 KC343425 KC343666 KC343667 KC343908 KC343909 KC344150 KC344151 Diaporthe paranensis, sp. nov. – – – – D. decorticans D. valsiformis – Diaporthe perjuncta D. perjuncta Diaporthe perseae, comb. nov. P. perseae CBS 157.29 CBS 127269; 5-27/3-1 CBS 127270; 4-27/3-1 (ex-type) CBS 127271; 5/27/3-3 CBS 354.71 LGMF943; CPC 20319 CBS 100454 CBS 109741; AR 3445 CBS 589.78 CBS 809.85 CBS 133186; LGMF942; CPC 20318 (ex-type) CBS 133187; LGMF936; CPC 20312 LGMF915; CPC 20291 LGMF939; CPC 20315 LGMF945; CPC 20321 CBS 114200; UPSC 2569 CBS 114649; UPSC 3496 CBS 133184; LGMF929; CPC 20305 (ex-type) CBS 109745; ARSEF 3461; AR 3461 (ex-epitype) CBS 151.73 Diaporthe phaseolorum P. oleariae D. phaseolorum D. phaseolorum Diaporthe sp. D. melonis Diaporthe sp. Diaporthe sp. P. mangiferae CBS 113425 CBS 116019; STAM 30 CBS 116020; STAM 31 CBS 127465; GJS 83-379 CBS 257.80 LGMF927; CPC 20303 LGMF941; CPC 20317 CBS 101339 (ex-type) Olearia cf. rani Caperonia palustris Aster exilis Actinidia chinensis, rotting fruit – Maytenus ilicifolia, endophytic in petiole Maytenus ilicifolia, endophytic in petiole Mangifera indica Asteraceae Euphorbiaceae Asteraceae Actinidiaceae – Celastraceae Celastraceae Anacardiaceae P. mangiferae P. mangiferae CBS 388.89 CBS 176.77 Mangifera indica, peel of fruit Mangifera indica, showing dieback Anacardiaceae Anacardiaceae Netherlands Antilles New Zealand USA: Mississippi USA: Mississippi New Zealand – Brazil Brazil Dominican Republic Mexico Iraq P. phoenicicola CBS 462.69 (ex-type) Phoenix dactylifera, dead tops of green leaves Acer pseudoplatanus Acer pseudoplatanus Prunus padus Spondias mombin, endophytic in leaf Arecaceae Spain H.A. van der Aa KC343184 KC343426 KC343668 KC343910 KC344152 Aceraceae Aceraceae Rosaceae Anacardiaceae Austria Austria Austria Brazil A.Y. Rossman A.Y. Rossman A.Y. Rossman K. Rodriguez KC343185 KC343186 KC343187 KC343188 KC343427 KC343428 KC343429 KC343430 KC343669 KC343670 KC343671 KC343672 KC343911 KC343912 KC343913 KC343914 KC344153 KC344154 KC344155 KC344156 Rhus toxicodendron Protea repens, cankers Anacardiaceae Proteaceae – South Africa L.E. Wehmeyer S. Denman KC343189 KC343190 KC343431 KC343432 KC343673 KC343674 KC343915 KC343916 KC344157 KC344158 Schinus terebinthifolius, endophytic in leaf Anacardiaceae Brazil J. Lima KC343191 KC343433 KC343675 KC343917 KC344159 Schinus terebinthifolius, endophytic in leaf Cucumis sativus, root Anacardiaceae Cucurbitaceae Brazil Netherlands J. Lima H.A. van der Kesteren KC343192 KC343193 KC343434 KC343435 KC343676 KC343677 KC343918 KC343919 KC344160 KC344161 Cucumis sativus, root Fraxinus excelsior, living and dead twig Glycine soja Euphorbia nutans Glycine max Glycine max, stem Glycine soja, mature stem Cucurbitaceae Oleaceae Fabaceae Euphorbiaceae Fabaceae Fabaceae Fabaceae Netherlands UK: Scotland Italy USA: Mississippi USA: Mississippi Croatia – – J.A. MacDonald P. Giunchi A. Mengistu A. Mengistu K. Vrandečić A.A. Hildebrand KC343194 KC343195 KC343196 KC343197 KC343198 KC343199 KC343200 KC343436 KC343437 KC343438 KC343439 KC343440 KC343441 KC343442 KC343678 KC343679 KC343680 KC343681 KC343682 KC343683 KC343684 KC343920 KC343921 KC343922 KC343923 KC343924 KC343925 KC343926 KC344162 KC344163 KC344164 KC344165 KC344166 KC344167 KC344168 Glycine soja, seedling Fabaceae USA J. Marcinkowska KC343201 KC343443 KC343685 KC343927 KC344169 Diaporthe nomurai Diaporthe novem Diaporthe oncostoma Diaporthe oxe, sp. nov. Diaporthe padi var. padi Diaporthe pseudomangiferae, sp. nov. Diaporthe pseudophoenicicola, sp. nov. Diaporthe pustulata D. pustulata D. pustulata D. padi Diaporthe raonikayaporum, sp. nov. – Diaporthe rhoina Diaporthe saccarata, comb. nov. D. rhoina P. saccarata Diaporthe schini, sp. nov. – Diaporthe sclerotioides – P. sclerotioides Diaporthe scobina Diaporthe sojae 5 P. sclerotioides P. scobina P. longicolla P. longicolla P. longicolla P. longicolla D. phaseolorum var. sojae D. phaseolorum var. sojae CBS 109742; AR 3430 CBS 109760; AR 3535 CBS 109784; AR 3419 CBS 133182; LGMF923; CPC 20299 (ex-type) CBS 146.27 CBS 116311; STE-U 3743; CPC 3743 (ex-type) CBS 133181; LGMF921; CPC 20297 (ex-type) LGMF910; CPC 20286 CBS 296.67; ATCC 18585; IMI 151828 (ex-type) CBS 710.76; PD 76/674 CBS 251.38 CBS 100.87 CBS 116017; DP 0508; STAM 28 CBS 116023; STAM 35 CBS 127267; PL4 CBS 180.55; ATCC 12050; CECT 2024; Alfaro 245 CBS 659.78; NRRL 13656 R.R. Gomes et al.: Diaporthe P. conorum 6 Table 1 (cont.) Isolation source Host family Locality Collector GenBank Accession numbers (ITS, CAL, HIS, TEF1, TUB)2 D. phaseolorum Diaporthe sp. Diaporthe sp. 2 Diaporthe sp. Diaporthe sp. 3 P. conorum Diaporthe sp. 4 Diaporthe sp. Diaporthe sp. 5 – Diaporthe sp. 6 P. pittospori P. pittospori Diaporthe sp. 7 P. anacardii Diaporthe sp. 8 Diaporthe sp. Diaporthe stictica, comb. nov. P. stictica Diaporthe subordinaria, comb. nov. P. subordinaria P. subordinaria Diaporthe tecomae P. tecomae CBS 119639; B 11861 LGMF947; CPC 20323 LGMF932; CPC 20308 CBS 287.29 LGMF944; CPC 20320 CBS 125575 CBS 115584; HKUCC 7784; AT 7 CBS 115595; HKUCC 10129 CBS 458.78 LGMF925; CPC 20301 CBS 370.54 CBS 101711 CBS 464.90 CBS 100547 – Fabaceae Celastraceae Pinaceae Celastraceae Aceraceae Myrsinaceae Myrsinaceae Anacardiaceae Apocynaceae Buxaceae Plantaginaceae Plantaginaceae Bignoniaceae Germany Brazil Brazil UK: Scotland Brazil Italy Hong Kong Hong Kong India Brazil Italy New Zealand South Africa Brazil K. Plechulla A. Almeida R.R. Gomes G.G. Hahn R.R. Gomes W. Jaklitsch K.D. Hyde K.D. Hyde H.C. Govindu K. Rodriguez M. Ribaldi B. Alexander R. Shivas A. Aptroot KC343202 KC343203 KC343204 KC343205 KC343206 KC343207 KC343208 KC343209 KC343210 KC343211 KC343212 KC343213 KC343214 KC343215 KC343444 KC343445 KC343446 KC343447 KC343448 KC343449 KC343450 KC343451 KC343452 KC343453 KC343454 KC343455 KC343456 KC343457 KC343686 KC343687 KC343688 KC343689 KC343690 KC343691 KC343692 KC343693 KC343694 KC343695 KC343696 KC343697 KC343698 KC343699 KC343928 KC343929 KC343930 KC343931 KC343932 KC343933 KC343934 KC343935 KC343936 KC343937 KC343938 KC343939 KC343940 KC343941 KC344170 KC344171 KC344172 KC344173 KC344174 KC344175 KC344176 KC344177 KC344178 KC344179 KC344180 KC344181 KC344182 KC344183 Diaporthe terebinthifolii, sp. nov. Anacardiaceae Brazil J. Lima KC343216 KC343458 KC343700 KC343942 KC344184 – – – D. toxica D. toxica D. toxica D. vaccinii P. vaccinii P. vaccinii P. vaccinii P. vaccinii CBS 133180; LGMF914; CPC 20290 (ex-type) LGMF907; CPC 20283 LGMF909; CPC 20285 LGMF913; CPC 20289 CBS 534.93; ATCC 96741 (ex-type) CBS 535.93 CBS 546.93 CBS 118571; G.C.A.Dvacc CBS 122112; FAU 474 CBS 122114; FAU 634 CBS 122115; FAU 590 CBS 122116; DF 5022 Man, abscess Glycine max, seed Maytenus ilicifolia, endophytic in petiole Pseudotsuga menziesii Maytenus ilicifolia, endophytic in petiole Acer opalus Maesa perlarius, fruit Maesa perlarius, fruit Anacardium occidentale Aspidosperma tomentosum Buxus sempervirens, dead twig Plantago lanceolata, blackened seed Plantago lanceolata, stalk Tabebuia sp., mycocecidium caused by Prosopodium tecomicola Schinus terebinthifolius, endophytic in leaf Schinus terebinthifolius, endophytic in leaf Schinus terebinthifolius, endophytic in leaf Schinus terebinthifolius, endophytic in leaf Lupinus angustifolius, stem Lupinus sp. Lupinus sp., stem Vaccinium corymbosum Vaccinium macrocarpon Vaccinium corymbosum Vaccinium corymbosum Vaccinium corymbosum Anacardiaceae Anacardiaceae Anacardiaceae Fabaceae Fabaceae Fabaceae Ericaceae Ericaceae Ericaceae Ericaceae Ericaceae J. Lima J. Lima J. Lima J.B. Nunn P.M. Williamson P.M. Williamson G.C. Adams L. Carris D.C. Ramsdell D.C. Ramsdell D.F. Farr KC343217 KC343218 KC343219 KC343220 KC343221 KC343222 KC343223 KC343224 KC343225 KC343226 KC343227 KC343459 KC343460 KC343461 KC343462 KC343463 KC343464 KC343465 KC343466 KC343467 KC343468 KC343469 KC343701 KC343702 KC343703 KC343704 KC343705 KC343706 KC343707 KC343708 KC343709 KC343710 KC343711 KC343943 KC343944 KC343945 KC343946 KC343947 KC343948 KC343949 KC343950 KC343951 KC343952 KC343953 KC344185 KC344186 KC344187 KC344188 KC344189 KC344190 KC344191 KC344192 KC344193 KC344194 KC344195 D. vaccinii CBS 160.32; IFO 32646 (ex-type) Oxycoccus macrocarpos Ericaceae C.L. Shear KC343228 KC343470 KC343712 KC343954 KC344196 P. vexans P. controversa D. aucubae D. medusaea D. pardalota D. viticola Solanum melongena Fraxinus excelsior, leaf spot Aucuba japonica, branches and twigs Laburnum anagyroides Epilobium angustifolium Vitis vinifera Solanaceae Oleaceae Aucubaceae Fabaceae Onagraceae Vitaceae L.L. Harter H.A. van der Aa G.J.M. Verkley A.Y. Rossman M. Barr A.J.L. Phillips KC343229 KC343230 KC343231 KC343232 KC343233 KC343234 KC343471 KC343472 KC343473 KC343474 KC343475 KC343476 KC343713 KC343714 KC343715 KC343716 KC343717 KC343718 KC343955 KC343956 KC343957 KC343958 KC343959 KC343960 KC344197 KC344198 KC344199 KC344200 KC344201 KC344202 D. viticola D. circumscripta D. medusaea D. woodii CBS 127.14 CBS 100170 CBS 106.95 CBS 109492 CBS 109768; AR 3478 CBS 113201; STE-U 5683; CPC 5683 (ex-epitype) CBS 114011; CPC 2677 CBS 114436; UPSC 2960 CBS 266.85; PD 85/25 CBS 312.91 Brazil Brazil Brazil Western Australia Western Australia Western Australia USA: Michigan USA: New Jersey USA: Michigan USA: Michigan USA: North Carolina USA: Massachusetts USA Netherlands Netherlands Austria Canada Portugal Vitis vinifera Sambucus cf. racemosa Rosa rugosa Lupinus arboreus, dead stem Vitaceae Caprifoliaceae Rosaceae Fabaceae Portugal Sweden Netherlands Netherlands KC343235 KC343236 KC343237 KC343238 KC343477 KC343478 KC343479 KC343480 KC343719 KC343720 KC343721 KC343722 KC343961 KC343962 KC343963 KC343964 KC344203 KC344204 KC344205 KC344206 P. salicina D. woodii P. dipsaci P. asphodelina D. aucubae D. woodii D. woolworthii – CBS 446.62 CBS 449.82 CBS 502.85 CBS 759.95 CBS 794.96 CBS 558.93 CBS 148.27 CBS 121124; AR 4131 Salix sp., twig Lupinus sp., dead stem Dipsacus fullonum, dead stem Asphodelus albus, 1-yr-old stems Aucuba japonica Lupinus sp., stem Ulmus americana Corylus sp., dying stems Salicaceae Fabaceae Dipsacaceae Asphodelaceae Aucubaceae Fabaceae Ulmaceae Corylaceae KC343239 KC343240 KC343241 KC343242 KC343243 KC343244 KC343245 KC343004 KC343481 KC343482 KC343483 KC343484 KC343485 KC343486 KC343487 KC343246 KC343723 KC343724 KC343725 KC343726 KC343727 KC343728 KC343729 KC343488 KC343965 KC343966 KC343967 KC343968 KC343969 KC343970 KC343971 KC343730 KC344207 KC344208 KC344209 KC344210 KC344211 KC344212 KC344213 KC343972 Original name Diaporthe sp. 1 Diaporthe toxica Diaporthe vaccinii Diaporthe vexans Diaporthe viticola Diaporthe woodii Diaporthe woolworthii Diaporthella corylina 1 2 – A.J.L. Phillips K. & L. Holm G.H. Boerema H.A. van der Aa & F. Meurs Netherlands G.H. Boerema Netherlands H.A. van der Aa Netherlands H.A. van der Aa France G.J.M. Verkley UK G.J.M. Verkley Western Australia P.M. Williamson – L.E. Wehmeyer China: Fuyuan L.N. Vassiljeva AR: Collection of A.Y. Rossman; ATCC: American type culture collection; CBS: CBS Fungal Biodiversity Centre, Utrecht, The Netherlands; CECT: Coleccion Española de Cultivos Tipo, University of Valencia, Valencia, Spain; CPC: Collection Pedro Crous, housed at CBS; DAOM: Plant Research Institute, Department of Agriculture (Mycology), Ottawa, Canada; HKUCC: University of Hong Kong Culture Collection, Department of Ecology and Biodiversity, Hong Kong, China; IFO: Institute for Fermentation, Osaka, Japan; IMI: International Mycological Institute, CABI-Bioscience, Egham, Bakeham Lane, U.K.; LGMF: Culture collection of Laboratory of Genetics of Microorganisms, Federal University of Parana, Curitiba, Brazil; MUCL: Université Catholique de Louvain, Louvain-la-Neuve, Belgium; NRRL: National Center for Agricultural Utilization Research, Peoria, Illinois, U.S.A.; PD: Plant Protection Service, Wageningen, The Netherlands; STE-U: Stellenbosch University culture collections, South Africa; UPSC: Fungal Culture Collection at the Botanical Museum, Uppsala University, Uppsala, Sweden TUB: partial beta-tubulin gene; CAL: partial calmodulin gene; HIS: partial histone H3 gene; ITS: internal transcribed spacer regions of the nrDNA and intervening 5.8S nrDNA; TEF1: partial translation elongation factor 1-alpha gene. Persoonia – Volume 31, 2013 Strain1 Species 7 R.R. Gomes et al.: Diaporthe (1933) to the conclusion that host-association was not informative enough in Diaporthe, thereby reducing the number of species from 650 to only 70 in the genus. However, this revision was based strictly on morphological characters of the Diaporthe sexual state, and connections to the Phomopsis asexual states (prior to molecular analyses) had been identiﬁed only in 20 % of the species (Wehmeyer 1933). Although the classiﬁcation of Diaporthe has been on-going, species are presently being redeﬁned based on a combination of morphological, cultural, phytopathological, mating type and DNA sequence data (Rehner & Uecker 1994, Zhang et al. 1998, Mostert et al. 2001a, Farr et al. 2002, Santos et al. 2010). However, even when using a combination of morphological and molecular data, the delimitation of species within the genus Diaporthe only proved satisfactory once multi-gene DNA sequence data were generated (Castlebury & Mengistu 2006, van Rensburg et al. 2006, Santos et al. 2010, Udayanga et al. 2012), since this adds valuable information in the resolution of complex evolutionary relationships. The aims of the present study were thus to: 1) provide a multi-gene phylogeny for the genus Diaporthe based on a large set of well-identiﬁed cultures deposited in the CBS culture collection; 2) to identify potential isolates for epitypiﬁcation, thereby ﬁxing the application of previously established names; 3) to link Diaporthe names to their Phomopsis asexual states; and 4) to identify a collection of mostly sterile endophytic Diaporthe strains isolated from several medicinal hosts in Brazil. MATERIALS AND METHODS Isolates In the present study we analysed 243 Diaporthe isolates (Table 1), as well as the outgroup Diaporthella corylina. Isolates were obtained from several sources, including 40 endophytic strains isolated from medicinal plants in Brazil (LabGeM/UFPR collection, Curitiba, Brazil), and three isolates from the EMBRAPASOJA collection, Londrina, Brazil. A further 199 isolates were obtained from the CBS-KNAW Fungal Biodiversity Centre (CBS), or the working collection of P.W. Crous (CPC) housed at CBS. DNA isolation, amplification and phylogenetic analysis Colonies were cultivated on 2 % potato-dextrose agar (PDA), and genomic DNA extraction was undertaken using the UltraClean™ Microbial DNA Kit (MO Bio, Carlsbad, CA, USA) according to manufacturer’s instructions. Using 20 isolates, we screened nine loci, of which the ﬁve more informative loci were selected for multi-gene analyses. The primers ITS5 and ITS4 (White et al. 1990) were used to amplify the internal transcribed spacer region (ITS) of the nuclear ribosomal RNA gene operon, including the 3’ end of the 18S nrRNA, the ﬁrst internal transcribed spacer region, the 5.8S nrRNA gene; the second internal transcribed spacer region and the 5’ end of the 28S nrRNA gene. The primers EF1-728F and EF1-986R (Carbone & Kohn 1999) were used to amplify part of the translation elongation factor 1-α gene (TEF1) and the primers ACT-512F and ACT-783R (Carbone & Kohn 1999) were used to amplify part of the actin gene (ACT). The primers Gpd1-LM and Gpd2-LM (Myllys et al. 2002) were used to amplify part of the glyceraldehyde-3-phosphate dehydrogenase (GPDH) gene, and part of the calmodulin (CAL) gene was sequenced using the primers CAL-228F and CAL-737R (Carbone & Kohn 1999). The primers CYLH3F (Crous et al. 2004b) and H3-1b (Glass & Donaldson 1995) were used to amplify part of the histone H3 (HIS) gene, and the primers T1 (O’Donnell & Cigelnik 1997) and Bt-2b (Glass & Donaldson 1995) to amplify part of the β-tubulin gene (TUB). The primers NMS1 and NMS2 (Li et al. 1994) were used to amplify an internal region of the mitochondrial SSU (mtSSU). The partial large subunit nrDNA (LSU) was sequenced using the primers LSU1Fd (Crous et al. 2009a) and LR5 (Vilgalys & Hester 1990). Ampliﬁcation reactions had a total reaction volume of 12.5 μL which was composed of 1× PCR buffer (Bioline GmbH, Luckenwalde, Germany), 5.6 % DMSO (v/v), 20 μM dNTPs, 0.2 μM of each forward and reverse primers, 0.25 U of BioTaq Taq DNA polymerase (Bioline GmbH, Luckenwalde, Germany), and 10 ng of genomic DNA. PCR conditions were the same for all loci, except for the MgCl2 concentration: 2 mM MgCl2 for the genes LSU and TEF1, 1.5 mM MgCl2 for the genes ACT, GPDH, mtSSU, ITS and TUB, and 1 mM MgCl2 for CAL and HIS genes. The PCR conditions were: start step of 2 min at 94 °C, followed by 40 cycles of 30 s at 94 °C, 1 min at adequate annealing temperature, and 1 min at 72 °C, followed by a ﬁnishing step of 3 min at 72 °C and a cool down step to 4 °C. The annealing temperature varied for each gene: 61 °C (ACT, GPDH, mtSSU); 58 °C (CAL, ITS, HIS); 55 °C (TEF1, TUB) and 48 °C (LSU). However, some of these primer pairs failed to amplify with some isolates included in this study, and therefore additional combinations were used. The ampliﬁcation reaction and cycle conditions were the same except the annealing temperature and MgCl2 concentration. For the ampliﬁcation of TEF1 with primers EF1-728F and EF2 (O’Donnell et al. 1998), 52 °C and 2 mM MgCl2; TUB with primers T1 (O’Donnell & Cigelnik 1997) and CYLTUB1R (Crous et al. 2004b), 50 °C and 1 mM MgCl2; CAL with primers CAL-228F and CAL2Rd (Quaedvlieg et al. 2011, Groenewald et al. 2013), 58 °C and 1 mM MgCl2. Amplicons were sequenced using both PCR primers with a BigDye Terminator Cycle Sequencing Kit v. 3.1 (Applied Biosystems, Foster City, CA, USA) according to the manufacturer’s instructions, and sequences were analysed on an ABI Prism 3700 DNA Sequencer (Perkin-Elmer, Norwalk, Foster City, CA, USA). The consensus sequences were visually inspected using MEGA v. 5 software (Tamura et al. 2011). The alignment of obtained sequences was performed using the online MAFFT interface (Katoh & Toh 2008; http://mafft.cbrc.jp/alignment/server). For the phylogenetic analyses based on Maximum Likelihood and Bayesian inference, we chose the best evolutionary models for each data partition using the software MrModelTest v. 2.3 (Nylander 2004). MrBayes v. 3.1.1 (Ronquist & Huelsenbeck 2003) was used to generate the phylogenetic trees under optimal criteria per data partition. The heating parameter was set at 0.3 and the Markov Chain Monte Carlo (MCMC) analysis of four chains was started in parallel from a random tree topology and lasted until the average standard deviation of split frequencies came below 0.01. Trees were saved each 10 000 generations and the resulting phylogenetic tree (Fig. 1) was printed with Geneious v. 5.5.4 (Drummond et al. 2011) and the layout of the tree was done in Adobe Illustrator v. CS5.1. Diaporthella corylina (CBS 121124) was used as outgroup in the phylogenetic analyses based on its position as sister family in Diaporthales (Vasilyeva et al. 2007). New sequences generated in this study were deposited in NCBIs GenBank nucleotide database (www. ncbi.nlm.nih.gov; Table 1) and the alignment and phylogenetic tree in TreeBASE (study S13943; www.treebase.org). Locus resolution and SNP detection Neighbour-joining analyses using the general time-reversible substitution model were applied to each data partition individually to check the stability and robustness of each species clade under each dataset using PAUP v. 4.0b10 (Swofford 2003) (TreeBASE study S13943). Alignment gaps were treated as missing data and all characters were unordered and of equal 8 Persoonia – Volume 31, 2013 100 100 100 CBS 116023 CBS 659.78 CBS 116017 CBS 100.87 CBS 127267 CBS 180.55 Phomopsis longicolla Glycine max USA D. phaseolorum var. sojae Glycine soja USA Phomopsis longicolla Euphorbia nutans USA Phomopsis longicolla Glycine soja Italy Phomopsis longicolla Glycine max Croatia D. phaseolorum var. sojae Glycine soja Unknown Diaporthe sojae CBS 119639 “Diaporthe phaseolorum” Man, abscess Germany Diaporthe sp. 1 LGMF947 Glycine max Brazil CBS 124654 Phomopsis convolvuli Convolvulus arvensis Turkey D. convolvuli 99 LGMF941 Maytenus ilicifolia Brazil 100 LGMF927 Maytenus ilicifolia Brazil CBS 257.80 “Diaporthe melonis” Unknown Unknown 100 CBS 116019 Diaporthe phaseolorum Caperonia palustris USA D. phaseolorum CBS 127465 Diaporthe sp. Actinidia chinensis New Zealand CBS 113425 Phomopsis oleariae Olearia cf. rani New Zealand CBS 116020 Diaporthe phaseolorum Aster exilis USA 100 LGMF935 Maytenus ilicifolia Brazil 63 99 LGMF928 Maytenus ilicifolia Brazil LGMF919 Schinus terebinthifolius Brazil LGMF934 Maytenus ilicifolia Brazil 94 100 Diaporthe endophytica LGMF937 Maytenus ilicifolia Brazil LGMF911 Schinus terebinthifolius Brazil 100 CBS 133811 = LGMF916 Schinus terebinthifolius Brazil 58 LGMF948 Glycine max Brazil CBS 199.39 Diaporthe conorum Unknown Italy 100 100 CBS 230.52 Diaporthe citri Citrus sinensis Suriname Diaporthe citri 100 LGMF946 Glycine max Brazil 100 CBS 507.78 Diaporthe melonis Cucumis melo USA Diaporthe melonis CBS 435.87 D. phaseolorum var. sojae Glycine soja Indonesia CBS 122.21 Diaporthe batatas Ipomoea batatas USA Diaporthe batatas 97 100 LGMF909 Schinus terebinthifolius Brazil 81 LGMF907 Schinus terebinthifolius Brazil 100 100 Diaporthe terebinthifolii CBS 133180 = LGMF914 Schinus terebinthifolius Brazil 100 LGMF913 Schinus terebinthifolius Brazil 71 CBS 100547 “Phomopsis tecomae” Tabebuia sp. Brazil Diaporthe tecomae 100 LGMF910 Schinus terebinthifolius Brazil Diaporthe schini 100 CBS 133181 = LGMF921 Schinus terebinthifolius Brazil 98 CBS 127.14 Phomopsis vexans Solanum melongena Unknown Diaporthe vexans 100 CBS 481.92 Phomopsis hordei Hordeum vulgare Norway Diaporthe hordei CBS 592.81 Diaporthe helianthi Helianthus annuus Serbia 100 Diaporthe helianthi 100 CBS 344.94 Diaporthe helianthi Helianthus annuus Unknown CBS 143.27 Diaporthe megalospora Sambucus canadensis Unknown D. megalospora 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 0.2 Fig. 1 Consensus phylogram of 22 104 trees resulting from a Bayesian analysis of the combined 5-gene sequence alignment. Clades are numbered on the right of the boxes and Diaporthe species names in purple reflect new combinations and in red new species. Strain accession numbers are followed by the original species name (black, when applicable), the isolation source (green) and country of origin (blue). Accession numbers and names in bold represent strains known to be ex-type strains or are considered to be authentic for the species. Red dots indicate strains from medicinal plants and yellow dots from humans. Bayesian posterior probabilities are shown at the nodes and the scale bar represents the expected changes per site. The tree was rooted to Diaporthella corylina (strain CBS 121124). weight. Any ties were broken randomly when encountered. The robustness of the trees obtained was evaluated by 1 000 bootstrap replications (Hillis & Bull 1993). In the present study, both the analysis of the combined alignment (Fig. 1) and of the individual loci were used to determine the species boundaries. For each clade in the combined analysis, the position of the members of that clade was determined in the phylogenetic tree obtained from each of the individual loci to check whether these members still represent a single clade in the individual gene tree. In this way the robustness of a given clade could be evaluated together with the posterior probability value of that clade. A species was only counted if it was distinct from its closest relatives and the species clade contained all the associated strains. Unique ﬁxed nucleotide positions are used to characterise and describe several sterile species (see applicable species notes). For each sterile species that was described, the closest phylogenetic neighbour(s) were selected from Fig. 1 and this focused dataset was subjected to SNP analyses. These single nucleotide polymorphisms (SNPs) were determined for 9 R.R. Gomes et al.: Diaporthe Fig. 1 (cont.) Diaporthe neoarctii CBS 109490 “Diaporthe arctii” Ambrosia trifida USA CBS 501.90 Diaporthe angelicae Heracleum sphondylium France CBS 111591 Diaporthe angelicae Heracleum sphondylium Austria 100 CBS 111592 Diaporthe angelicae Heracleum sphondylium Austria D. angelicae 100 86 CBS 123215 Diaporthe angelicae Foeniculum vulgare Portugal 100 CBS 344.86 Phomopsis asteriscus Eryngium maritimum France 96 CBS 100871 Phomopsis foeniculi Foeniculum vulgare Italy 100 CBS 101711 Phomopsis subordinaria Plantago lanceolata New Zealand 100 D. subordinaria CBS 464.90 Phomopsis subordinaria Plantago lanceolata South Africa Diaporthe arctii CBS 136.25 Diaporthe arctii Arctium sp. Unknown 100 Diaporthe cuppatea CBS 117499 Phomopsis cuppatea Aspalathus linearis South Africa 100 95 CBS 123213 Diaporthe lusitanicae Foeniculum vulgare Portugal 100 Diaporthe lusitanicae CBS 123212 Diaporthe lusitanicae Foeniculum vulgare Portugal LGMF943 Maytenus ilicifolia Brazil CBS 127271 Diaporthe novem Glycine max Croatia 100 100 100 Diaporthe novem CBS 354.71 Diaporthe pardalota Polygonatum odoratum Romania 100 100 CBS 127269 Diaporthe novem Glycine max Croatia 100 CBS 127270 Diaporthe novem Glycine max Croatia CBS 133812 = LGMF906 Schinus terebinthifolius Brazil LGMF912 Schinus terebinthifolius Brazil 100 LGMF920 Schinus terebinthifolius Brazil 100 LGMF933 Maytenus ilicifolia Brazil Diaporthe infecunda LGMF918 Schinus terebinthifolius Brazil LGMF940 Maytenus ilicifolia Brazil 100 93 LGMF908 Schinus terebinthifolius Brazil LGMF917 Schinus terebinthifolius Brazil Diaporthe ganjae CBS 180.91 Phomopsis ganjae Cannabis sativa USA 100 Diaporthe manihotia CBS 505.76 Phomopsis manihot Manihot utilissima Rwanda CBS 114015 Diaporthe ambigua Pyrus communis South Africa CBS 117167 Diaporthe ambigua Aspalathus linearis South Africa CBS 123211 Diaporthe ambigua Foeniculum vulgare Portugal Diaporthe ambigua 100 100 CBS 123210 Diaporthe ambigua Foeniculum vulgare Portugal CBS 127746 Diaporthe scabra Platanus acerifolia Italy CBS 187.87 “Diaporthe helianthi” Helianthus annuus Italy 100 Diaporthe longispora CBS 194.36 Diaporthe strumella var. longispora Ribes sp. Canada CBS 296.67 Phomopsis sclerotioides Cucumis sativus Netherlands Diaporthe sclerotioides 100 CBS 710.76 Phomopsis sclerotioides Cucumis sativus Netherlands 100 100 Diaporthe sp. 2 LGMF932 Maytenus ilicifolia Brazil 100 Diaporthe mayteni CBS 133185 = LGMF938 Maytenus ilicifolia Brazil Diaporthe raonikayaporum CBS 133182 = LGMF923 Spondias mombin Brazil 100 Diaporthe sp. 3 CBS 287.29 Phomopsis conorum Pseudotsuga menziesii UK 100 Diaporthe sp. 4 LGMF944 Maytenus ilicifolia Brazil 100 LGMF915 Schinus terebinthifolius Brazil CBS 133186 = LGMF942 Maytenus ilicifolia Brazil 100 100 99LGMF939 Maytenus ilicifolia Brazil Diaporthe oxe 100 LGMF945 Maytenus ilicifolia Brazil 100 LGMF936 Maytenus ilicifolia Brazil Diaporthe paranensis CBS 133184 = LGMF929 Maytenus ilicifolia Brazil CBS 133183 = LGMF924 Aspidosperma tomentosum Brazil 100 Diaporthe brasiliensis 100 LGMF926 Aspidosperma tomentosum Brazil Diaporthe sp. 5 CBS 125575 Acer opalus Italy 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 0.2 each aligned data partition using DnaSP v. 5.00.07 (Librado & Rozas 2009). Taxonomy All descriptions provided are based on colonies sporulating in culture, which for the most part only formed the asexual morph. Colonies were subcultured onto 2 % tap water agar supplemented with sterile pine needles (PNA; Smith et al. 1996), or autoclaved leaf pieces of Ilex aquifolium, Maytenus ilicifolia or Schinus terebinthifolius, PDA, oatmeal agar (OA), and 2 % malt extract agar (MEA) (according to Crous et al. 2009b), and incubated at 20 °C under a 12 h near-ultraviolet light (400–315 nm) (Sylvania Blacklight-Blue, Osram Nederland B.V., Alphen aan den Rijn, The Netherlands), 12 h dark cycle to promote sporulation. Structures were mounted in clear lactic acid, and 50 measurements determined for conidia, and 30 for other Persoonia – Volume 31, 2013 10 Fig. 1 (cont.) CBS 251.38 Phomopsis scobina Fraxinus excelsior UK Diaporthe scobina CBS 137.27 Diaporthe acerina Acer saccharum Unknown Diaporthe acerina 98 CBS 109745 Diaporthe perjuncta Ulmus glabra Austria Diaporthe perjuncta CBS 114435 Diaporthe crataegi Crataegus oxyacantha Sweden Diaporthe crataegi 89 CBS 126679 Phomopsis amygdali 3B Prunus dulcis Portugal 100 CBS 115620 Phomopsis amygdali Prunus persica USA 89 100 CBS 120840 Phomopsis amygdali Prunus salicina South Africa Diaporthe amygdali CBS 126680 Phomopsis amygdali 55A Prunus dulcis Portugal 74 100 100 CBS 111811 Phomopsis amygdali Vitis vinifera South Africa 100 CBS 129521 Diaporthe acaciigena Acacia retinodes Australia Diaporthe acaciigena CBS 109742 Diaporthe pustulata Acer pseudoplatanus Austria 100 CBS 109784 Diaporthe padi Prunus padus Austria Diaporthe pustulata 100 CBS 109760 Diaporthe pustulata Acer pseudoplatanus Austria CBS 534.93 Diaporthe toxica Lupinus angustifolius Western Australia 100 CBS 546.93 Diaporthe toxica Lupinus sp. Western Australia Diaporthe toxica CBS 535.93 Diaporthe toxica Lupinus sp. Western Australia CBS 852.97 “Phomopsis heveae” Hevea brasiliensis Brazil Diaporthe cf. heveae 1 100 CBS 138.27 Diaporthe beckhausii Viburnum sp. Unknown Diaporthe beckhausii 100 CBS 122676 Diaporthe cynaroidis Protea cynaroides South Africa Diaporthe cynaroidis CBS 111886 Diaporthe australafricana Vitis vinifera Australia 100 100 Diaporthe australafricana CBS 113487 Diaporthe australafricana Vitis vinifera South Africa 89 100 CBS 446.62 Phomopsis salicina Salix sp. Netherlands CBS 449.82 “Diaporthe woodii” Lupinus sp. Netherlands 100 CBS 113201 Diaporthe viticola Vitis vinifera Portugal CBS 100170 Phomopsis controversa Fraxinus excelsior Netherlands CBS 759.95 Phomopsis asphodelina Asphodelus albus France 100 CBS 109492 Diaporthe medusaea Laburnum anagyroides Austria CBS 266.85 Diaporthe medusaea Rosa rugosa Netherlands Diaporthe viticola CBS 114011 Diaporthe viticola Vitis vinifera Portugal CBS 114436 Diaporthe circumscripta Sambucus cf. racemosa Sweden CBS 106.95 Diaporthe aucubae Aucuba japonica Netherlands CBS 109768 Diaporthe pardalota Epilobium angustifolium Canada CBS 794.96 Diaporthe aucubae Aucuba japonica UK CBS 502.85 Phomopsis dipsaci Dipsacus fullonum Netherlands CBS 312.91 “Diaporthe woodii” Lupinus arboreus Netherlands CBS 114434 Diaporthe impulsa Sorbus aucuparia Sweden 100 Diaporthe impulsa CBS 141.27 Diaporthe impulsa Sorbus americana Unknown 100 CBS 113830 Diaporthe fibrosa Rhamnus cathartica Sweden 100 Diaporthe fibrosa CBS 109751 Diaporthe fibrosa Rhamnus cathartica Austria 97 CBS 267.80 Phomopsis viticola Vitis vinifera Italy 100 100 CBS 114867 Phomopsis viticola Vitis vinifera Turkey Diaporthe ampelina CBS 111888 Phomopsis viticola Vitis vinifera USA CBS 140.27 Diaporthe detrusa Berberis vulgaris Unknown 100 CBS 109770 Diaporthe detrusa Berberis vulgaris Austria Diaporthe detrusa 100 CBS 114652 Diaporthe detrusa Berberis vulgaris Sweden CBS 114437 Diaporthe carpini Carpinus betulus Sweden Diaporthe carpini 95 CBS 114649 Diaporthe valsiformis Alnus glutinosa Sweden 100 Diaporthe padi var. padi CBS 114200 Diaporthe decorticans Prunus padus Sweden 100 CBS 148.27 Diaporthe woolworthii Ulmus americana Unknown Diaporthe woolworthii 89 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 0.2 structures. The 95 % conﬁdence levels were determined, and the extremes given in parentheses. Colony diameters were determined at 25 °C in darkness on PDA, OA and MEA. Colony colours (surface and reverse) were described after 14 d using the colour charts of Rayner (1970). Nomenclatural novelties and descriptions were deposited in MycoBank (www.MycoBank. org; Crous et al. 2004a). RESULTS DNA sequencing and phylogenetic analysis The most suitable genes for Diaporthe species delimitation in this study were found to be CAL, HIS, ITS, TEF1 and TUB. The ampliﬁed genomic regions of these genes were more informative, and the combined analysis provided a more robust species identiﬁcation, from which phylogenetic relationships could be inferred. R.R. Gomes et al.: Diaporthe Fig. 1 (cont.) 61 98 11 CBS 157.29 Diaporthe nomurai Morus sp. Japan CBS 288.56 Phomopsis gardeniae Gardenia florida Italy CBS 144.27 Diaporthe neilliae Spiraea sp. Unknown Diaporthe nomurai 58 Diaporthe gardeniae 59 Diaporthe neilliae 60 100 CBS 159.47 Diaporthe alnea Alnus sp. Unknown Diaporthe alnea 61 CBS 146.46 Diaporthe alnea Alnus sp. Unknown 99 CBS 587.79 Phomopsis conorum Pinus pentaphylla Japan 99 CBS 338.89 Diaporthe pulla Hedera helix Yugoslavia CBS 116953 Phomopsis fukushii Pyrus pyrifolia New Zealand 100 CBS 129167 Phomopsis sp. 22 Rhododendron sp. Latvia 100 Diaporthe nobilis complex 62 CBS 200.39 Diaporthe nobilis Laurus nobilis Germany CBS 124030 Diaporthe perniciosa Malus pumila New Zealand 79 CBS 113470 Phomopsis castanea Castanea sativa Korea 100 100 CBS 116954 Phomopsis fukushii Pyrus pyrifolia New Zealand CBS 160.32 Diaporthe vaccinii Oxycoccus macrocarpos USA 92 CBS 122114 Phomopsis vaccinii Vaccinium corymbosum USA CBS 122115 Phomopsis vaccinii Vaccinium corymbosum USA 100 Diaporthe vaccinii 63 CBS 122116 Phomopsis vaccinii Vaccinium corymbosum USA CBS 122112 Phomopsis vaccinii Vaccinium macrocarpon USA 71 CBS 118571 Diaporthe vaccinii Vaccinium corymbosum USA Diaporthe alleghaniensis 64 CBS 495.72 Diaporthe alleghaniensis Betula alleghaniensis Canada 99 Diaporthe juglandina 65 CBS 121004 Diaporthe juglandina Juglans sp. USA Diaporthe celastrina 66 CBS 139.27 Diaporthe celastrina Celastrus scandens Unknown CBS 267.32 Phomopsis stictica Unknown Unknown CBS 375.61 Diaporthe perniciosa Malus sylvestris Unknown CBS 445.62 Phomopsis cruciferae Alliaria officinalis Netherlands 100 CBS 283.85 Phomopsis ranojevicii Allium giganteum Netherlands 100 CBS 365.97 Phomopsis cacti Opuntia sp. Netherlands CBS 129168 Phomopsis sp. 23 Rhododendron sp. Latvia CBS 370.67 Phomopsis crustosa Ilex aquifolium Netherlands CBS 287.74 Diaporthe eres Sorbus aucuparia Netherlands CBS 439.82 Phomopsis cotoneastri Cotoneaster sp. UK CBS 110.85 ”Diaporthe arctii” Arctium sp. Netherlands CBS 122.82 Phomopsis skimmiae Skimmia japonica Netherlands 100 CBS 267.55 Phomopsis rudis Laburnum x watereri 'Vossii' Netherlands Diaporthe eres 67 CBS 250.38 Phomopsis controversa Fraxinus excelsior UK CBS 528.83 Diaporthe seposita Wisteria sinensis Netherlands CBS 841.84 Phomopsis tritici Hordeum sp. Germany CBS 109767 Diaporthe eres Acer campestre Austria CBS 102.81 Diaporthe medusaea Juglans regia Italy 100 CBS 485.96 Phomopsis durandiana Rumex hydrolapathum Netherlands CBS 297.77 Phomopsis osmanthi Osmanthus aquifolium Netherlands CBS 186.37 Diaporthe conorum Picea abies UK CBS 422.50 Phomopsis phaseoli Phaseolus vulgaris Netherlands CBS 688.97 Phomopsis abutilonis Abutilon sp. Netherlands . CBS 694.94 Phomopsis crustosa Ilex aquifolium Netherlands CBS 791.68 Phomopsis magnoliicola Magnolia x soulangeana Netherlands CBS 101742 Diaporthe eres Fraxinus sp. Netherlands 100 0.2 The manually adjusted, combined (ITS, TUB, CAL, TEF1 and HIS) alignment for the Bayesian analysis contained 243 isolates (including the outgroup sequences) and 2 435 characters were used in the phylogenetic analysis. The number of unique site patterns per data partition were 210, 616, 242, 281 and 183, respectively and were based on 466, 874, 355, 316 and 424 alignment positions, respectively. Based on the results of MrModeltest, the following priors were set in MrBayes for the different data partitions: all partitions had dirichlet base frequen- cies and GTR+I+G models with inverse gamma-distributed rates were implemented for ITS and HIS, and HKY+I+G with inverse gamma-distributed rates for TUB, CAL and TEF1. The Bayesian analysis lasted 14 735 000 generations and the consensus trees and posterior probabilities were calculated from the 22 104 trees left after discarding 7 368 trees (the ﬁrst 25 % of generations) for burn-in (Fig. 1). Ninety-ﬁve clades are recognised and discussed here. Persoonia – Volume 31, 2013 12 Fig. 1 (cont.) CBS 114281 Diaporthe decedens Corylus avellana Sweden Diaporthe decedens CBS 109772 Diaporthe decedens Corylus avellana Austria Diaporthe anacardii CBS 720.97 “Phomopsis anacardii” Anacardium occidentale East Africa 59 CBS 589.78 Diaporthe oncostoma Robinia pseudoacacia France CBS 100454 Diaporthe oncostoma Robinia pseudoacacia Germany 100 Diaporthe oncostoma 100 CBS 109741 Diaporthe oncostoma Robinia pseudoacacia Russia 56 CBS 809.85 Phomopsis crustosa Ilex aquifolium Germany 100 Diaporthe saccarata CBS 116311 Phomopsis saccarata Protea repens South Africa Diaporthe hickoriae CBS 145.26 Diaporthe hickoriae Carya glabra Unknown 64 Diaporthe elaeagni CBS 504.72 Phomopsis elaeagni Elaeagnus sp. Netherlands 85 100 Diaporthe stictica CBS 370.54 Phomopsis stictica Buxus sempervirens Italy 59 LGMF931 Maytenus ilicifolia Brazil 100 Diaporthe inconspicua 86 100 CBS 133813 = LGMF930 Maytenus ilicifolia Brazil LGMF922 Spondias mombin Brazil Diaporthe cinerascens CBS 719.96 Phomopsis cinerascens Ficus carica Bulgaria 87 CBS 753.70 Diaporthe sarothamni Spartium junceum Croatia Diaporthe chamaeropis 100 CBS 454.81 “Phomopsis phoenicicola” Chamaerops humilis Greece 100 CBS 171.78 Phomopsis mali f.sp. amygdali Prunus amygdalus Italy 100 CBS 400.48 Phomopsis casuarinae Unknown India CBS 116957 Phomopsis theicola Pyrus pyrifolia New Zealand 97 88 CBS 287.56 Phomopsis diospyri Diospyros kaki Italy CBS 357.69 Diaporthe seposita Wisteria sinensis Netherlands Diaporthe foeniculacea CBS 187.27 Phomopsis theicola Camellia sinensis Italy CBS 603.88 Phomopsis bougainvilleae Bougainvillea spectabilis Portugal CBS 123208 Diaporthe neotheicola Foeniculum vulgare Portugal CBS 123209 Diaporthe neotheicola Foeniculum vulgare Portugal CBS 111554 Diaporthe foeniculacea Foeniculum vulgare Portugal CBS 111553 Diaporthe foeniculacea Foeniculum vulgare Spain Diaporthe hongkongensis CBS 115448 Phomopsis pittospori Dichroa febrifuga Hong Kong Diaporthe cf. heveae 2 CBS 681.84 “Phomopsis heveae” Hevea brasiliensis India Diaporthe arengae CBS 114979 Phomopsis pittospori Arenga engleri Hong Kong 100 100 CBS 101339 Phomopsis mangiferae Mangifera indica Dominican Republic D. pseudomangiferae 89 100 CBS 388.89 Phomopsis mangiferae Mangifera indica Mexico Diaporthe eugeniae CBS 444.82 Phomopsis eugeniae Eugenia aromatica West Sumatra 72 99CBS 129519 Diaporthe musigena Musa sp. Australia Diaporthe musigena 100 83 2x 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 92 CBS 115595 Phomopsis pittospori Maesa perlarius Hong Kong Diaporthe sp. 6 CBS 115584 Phomopsis pittospori Maesa perlarius Hong Kong Diaporthe perseae CBS 151.73 Phomopsis perseae Persea gratissima Netherlands Antilles 100 CBS 535.75 Diaporthe citri Citrus sp. Suriname 97 Diaporthe arecae 100 CBS 161.64 Phomopsis phoenicicola Areca catechu India 85 Diaporthe sp. 7 CBS 458.78 “Phomopsis anacardii” Anacardium occidentale India CBS 176.77 Phomopsis mangiferae Mangifera indica Iraq Diaporthe pseudophoenicicola 100 CBS 462.69 “Phomopsis phoenicicola” Phoenix dactylifera Spain 91 Diaporthe sp. 8 LGMF925 Aspidosperma tomentosum Brazil CBS 178.55 D. phaseolorum var. caulivora Glycine soja Canada 100 Diaporthe caulivora CBS 127268 Diaporthe caulivora Glycine max Croatia Diaporthe crotalariae CBS 162.33 Diaporthe crotalariae Crotalaria spectabilis USA 100 100 85 86 87 88 89 90 91 92 99 98 CBS 117168 Diaporthe aspalathi Aspalathus linearis South Africa CBS 117169 Diaporthe aspalathi Aspalathus linearis South Africa 99 100 CBS 117500 Diaporthe aspalathi Aspalathus linearis South Africa CBS 558.93 Diaporthe woodii Lupinus sp. Western Australia CBS 146.27 Diaporthe rhoina Rhus toxicodendron Unknown CBS 121124 Diaporthella corylina Diaporthe aspalathi 93 Diaporthe woodii 94 Diaporthe rhoina 95 0.2 Locus resolution and SNP detection The mtSSU and LSU regions had very few informative sites for the tested strains and were therefore not selected as good markers at species level. The ACT and GPDH regions were also discarded as suitable candidates for the multi-gene analyses because of their long branch lengths which made unambigu- ous alignments impossible. These four loci were therefore not used for further ampliﬁcation and sequencing on the complete dataset. The remaining ﬁve loci had varied success for species identiﬁcation and some phylogenetic lineages were more prone to less variability than others. Fifty-eight of the 95 spe- R.R. Gomes et al.: Diaporthe cies could be identiﬁed by all ﬁve loci. The loci are treated individually below: CAL – The locus could distinguish 74 of the 95 species (78 % success). It had difﬁculty separating: D. endophytica and D. phaseolorum (clades 4, 5); D. angelicae, D. arctii and D. subordinaria (clades 17–19); D. alleghaniensis, D. alnea, D. celastrina, D. eres, D. juglandina, D. neilliae and D. nobilis (clades 60–62, 64–67); and D. eugeniae, D. musigena, D. perseae, D. pseudomangiferae, D. pseudophoenicicola, Diaporthe sp. 6 and Diaporthe sp. 7 (clades 82–86, 88, 89). A single strain each of D. angelicae (clade 17), D. novem (clade 22) and D. terebinthifolii (clade 9) clustered separate from the other strains of the species. HIS – The locus could distinguish 84 of the 95 species (88 % success). It had difﬁculty separating: D. australafricana and D. viticola (clades 49, 50); D. celastrina, D. eres and D. nobilis (clades 66, 67, 62); D. arecae and D. perseae (clades 86, 87); and D. pseudophoenicicola and Diaporthe sp. 8 (clades 89, 90). A single strain each of D. endophytica (clade 5) and D. terebinthifolii (clade 9) clustered separate from the other strains of the species. This is the only locus that can distinguish D. angelicae (clade 17). ITS – The locus could distinguish 75 of the 95 species (79 % success). It had difﬁculty separating: D. angelicae, D. arctii and D. subordinaria (clades 17–19); D. cynaroides and D. viticola (clades 48, 50); D. alnea, D. neilliae and D. nobilis (clades 60–62); D. arengae, D. eugeniae and D. pseudomangiferae (clades 81–83); D. arecae and D. perseae (clades 86, 87); and D. aspalathi and D. woodii (clades 93, 94). A single strain each of D. arecae (clade 87), D. inconspicua (clade 75), D. novem (clade 22) and D. terebinthifolii (clade 9), and two strains each of D. impulsa (clade 51) and D. infecunda (clade 23), clustered separate from the other strains of the species. This is the only locus that can distinguish D. celastrina (clade 17) and D. eres (clade 67). TEF1 – The locus could distinguish 72 of the 95 species (76 % success). It had difﬁculty separating: D. tecomae, D. terebinthifolii (clades 9, 10); D. angelicae, D. arctii and D. subordinaria (clades 17–19); D. australafricana and D. viticola (clades 49, 50); D. celastrina and D. juglandina (clades 65, 66); D. eres and D. nobilis (clades 67, 62); D. chamaeropis, D. cinerascens and D. foeniculaceae (clades 76 –78); and D. arengae, D. arecae, D. eugeniae, D. musigena, D. perseae, D. pseudomangiferae, D. pseudophoenicicola, Diaporthe sp. 6 and Diaporthe sp. 8 (clades 81– 87, 89, 90). TUB – The locus could distinguish 84 of the 95 species (88 % success). It had difﬁculty separating: D. endophytica and D. phaseolorum (clades 4, 5); D. alleghaniensis, D. celastrina, D. eres, D. juglandina, D. nobilis and D. vaccinii (clades 62–67); and D. aspalathi and D. woodii (clades 93, 94). A single strain of D. angelicae (clade 17) clustered separate from the other strains of the species. This is the only locus that can distinguish D. perseae (clade 86). Descriptions based on DNA characters are provided for three species in the Taxonomy section, namely D. endophytica (clade 5), D. inconspicua (clade 75) and D. infecunda (clade 23). Diaporthe endophytica (clade 5) was compared to D. phaseolorum (clade 4); D. inconspicua (clade 75) to D. anacardii (clade 69), D. chamaeropis (clade 77), D. cinerascens (clade 76), D. elaeagni (clade 73), D. foeniculacea (clade 78), D. hickoriae (clade 72), D. oncostoma (clade 70), D. saccarata (clade 71) and D. stictica (clade 74); and D. infecunda (clade 23) to D. angelicae (clade 17), D. arctii (clade 19), D. cuppatea (clade 20), D. lusitanicae (clade 21), D. neoarctii (clade 16), D. novem (clade 22) and D. subordinaria (clade 18). 13 Taxonomy The multigene analyses resulted in 95 well-supported clades correlating to 243 isolates of Diaporthe (Table 1, Fig. 1). Fifteen new species are described, nine of which were isolated from medicinal plants (Aspidosperma tomentosum, Maytenus ilicifolia, Schinus terebinthifolius, Spondias mombin) in Brazil (clades 5, 9, 11, 23, 30, 31, 34, 35 and 36). Twenty-eight clades contain ex-type strains of presently known species, or strains accepted as authentic for the species name or which could be designated as epitypes in the present study, and were therefore well-resolved (7, 8, 12, 14, 17, 20–22, 24, 26–28, 40, 42, 43, 45, 48–50, 63, 64, 69, 71, 72, 84 and 91–93). The sexual-asexual relationship was resolved for several taxa, and is reported below. New combinations in Diaporthe are introduced below for several Phomopsis names that represented well-resolved taxa. Several potential epitypes were identiﬁed during this study, which are discussed below. Diaporthe acaciigena Crous, Pascoe & Jacq. Edwards, Persoonia 26: 123. 2011 Specimen examined. AustrAliA, Victoria, Otway Ranges, Anglesea, S38°23'21.7" E144°11'12.7", on leaves of Acacia retinodes, 16 Oct. 2009, P.W. Crous, I.G. Pascoe & J. Edwards (holotype CBS H-20581, ex-type culture CPC 17622 = CBS 129521). Notes — Clade 43 contains the ex-type culture of D. acaciigena isolated from Acacia retinodes in Australia. This species is morphologically similar to D. amygdali (clade 42) (Crous et al. 2011), and closely related to D. pustulata (clade 44). Diaporthe acerina (Peck) Sacc., Syll. Fung. (Abellini) 1: 611. 1882 Basionym. Valsa acerina Peck, Ann. Rep. N.Y. State Mus. Nat. Hist. 28: 73. 1876. 1874. Specimen examined. unknown, from Acer saccharum, Sept. 1927, L.E. Wehmeyer (CBS 137.27). Notes — Clade 39 is represented by D. acerina, isolated from Acer saccharum. This species is genetically similar to D. perjuncta (clade 40). It is known to occur in Europe and North America on dead limbs and trunks of Acer pseudoplatanus, A. saccharinum, A. saccharum, A. spicatum, and Acer sp. (Aceraceae) (Spielman 1985, Farr et al. 1989). Diaporthe alleghaniensis R.H. Arnold, Canad. J. Bot. 45: 787. 1967 Specimen examined. CAnAdA, Ontario, on branches of Betula alleghaniensis, June 1972, R.H. Arnold (ex-type culture CBS 495.72 = ATCC 24097 = DAOM 45776). Notes — Clade 64 contains the ex-type strain of D. alleghaniensis, isolated from Betula alleghaniensis in Canada. Diaporthe alleghaniensis causes canker and dieback of B. alleghaniensis, B. lenta, B. papyrifera and B. pendula in Canada (Arnold 1975), but has also been reported from Japan (Farr & Rossman 2012). Diaporthe alnea Fuckel, Jahrb. Nassauischen Vereins Naturk. 23–24: 207. 1870 (1869 –1870) = Phomopsis alnea Höhn., Sber. Akad. Wiss. Wien, Math.-naturw. Kl., Abt. 1 115: 681 (33 of repr.). 1906. Specimens examined. unknown, on Alnus sp., June 1946, S. Truter (CBS 146.46); on Alnus sp., Aug. 1947, S. Truter (CBS 159.47). Notes — Clade 61 consists of two isolates from Alnus (presumably collected in the Netherlands). Diaporthe alnea causes dieback of Alnus glutinosa (alder) and A. incana (grey alder). 14 It has been reported from Europe, Russia and the USA (Munk 1957, Oak & Dorset 1983, Moricca 2002, Mel’nik et al. 2008, Farr & Rossman 2012). Diaporthe ambigua Nitschke, Pyrenomycetes Germanici 2: 311. 1870 Specimens examined. itAly, Sicily, Catania, on Platanus acerifolia, G. Granata (CBS 127746 = IMI 395956); Perugia, on Helianthus annuus, Mar. 1987, A. Zazzerini (CBS 187.87). – PortugAl, Vale Andeiro, on Foeniculum vulgare, J.M. Santos (CBS 123210 = Di-C003/10, CBS 123211 = Di-C002/9). – south AfriCA, Western Cape Province, from Pyrus communis, deposited 2002, S. Denman (ex-epitype culture CBS 114015 = CPC 2657); Western Cape Province, on crown of Aspalathus linearis, 15 May 1997, J.C. Janse van Rensburg (CBS 117167 = CPC 5414). Notes — Clade 26 represents D. ambigua, which contains two isolates previously misidentiﬁed as D. scabra (CBS 127746) and D. helianthi (CBS 187.87), and four isolates of D. ambigua, including the ex-epitype culture. Diaporthe ambigua is an important pathogen of Malus domestica, Prunus salicina and Pyrus communis in South African fruit orchards. Infection by D. ambigua is associated with sunken lesions with longitudinal cracks on affected fruit trees. The fungus rapidly kills nursery rootstocks, but also kills mature rootstocks over a longer period of time (Smit et al. 1996). This species is also found as saprobe on wild fennel (Santos & Phillips 2009). It has been reported on Aspalathus linearis (van Rensburg et al. 2006), Foeniculum vulgare, Malus domestica (Smit et al. 1996, Santos & Phillips 2009), Malus sylvestris (Crous et al. 2000), Prunus spp. (Smit et al. 1996, Mostert et al. 2001a), Pyrus communis (Nitschke 1867), Pyrus ussuriensis (Tai 1979) and Vitis vinifera (van Niekerk et al. 2005). It is widely distributed, and is known from China, Cuba (Tai 1979), Germany (Nitschke 1867), South Africa (Smit et al. 1996), UK (Dennis 1986) and the USA (Washington) (Shaw 1973). Diaporthe ampelina (Berk. & M.A. Curtis) R.R. Gomes, C. Glienke & Crous, comb. nov. — MycoBank MB802922 Basionym. Phoma ampelina Berk. & M.A. Curtis, Grevillea 2, 18: 81. 1873. ≡ Phomopsis ampelina (Berk. & M.A. Curt.) Grove, Bull. Misc. Inform. Kew 4: 184. 1919. = Phoma viticola Sacc., Michelia 2: 92. 1880. ≡ Phomopsis viticola (Sacc.) Sacc., Ann. Mycol. 13: 118. 1915. = Fusicoccum viticolum Reddick, Cornell Univ. Agric. Exp. Sta. Bull. 263: 331. 1909. ≡ Phomopsis viticola (Reddick) Goid., Atti Reale Accad. Naz. Lincei 26: 107. 1937. = Phomopsis viticola Sacc. var. ampelopsidis Grove, Bull. Misc. Inform. Kew 4: 183. 1919. = Diaporthe neoviticola Udayanga, Crous & K.D. Hyde, Fung. Diversity 56: 166. 2012 (a nom. nov. based on Phoma viticola Sacc.). Persoonia – Volume 31, 2013 Conidiomata pycnidial, eustromatic, subepidermal, brown to black, scattered or aggregated, globose, flask-like to conical, outer surface smooth, convoluted to unilocular, singly ostiolate, up to 430 µm wide and 190–300 µm tall, including short necks which rarely occur. Pycnidial wall consisting out of two regions of textura angularis; the outer region brown, 2–3 cells thick, 5–7 µm wide, inner region brown, 3–4 cells thick, 7–15 µm wide, with the outside cells compressed. Conidial mass globose or in cirrhi, white, pale-yellow to yellow, but predominantly paleyellow. Alpha conidiophores cylindrical, some ﬁliform, rarely septate and branched, 5–35 × 1–3 µm (av. = 25 × 2 µm). Alpha conidiogenous cells subcylindrical, tapering towards the apex, collarettes and periclinal thickening present, 3–19 × 1–2 µm (av. = 10 × 1.5 µm). Alpha conidia commonly found, fusoidellipsoidal, apex acutely rounded, base obtuse to subtruncate, multi-guttulate with guttules grouped at the polar ends, rarely biguttulate, (7–)9.5–10.5(–13) × (1.5–)2–3(–3.5) µm (av. = 10 × 2.5 µm). Beta conidiophores ampulliform to subcylindrical, rarely branched, 10–34 × 1–2 µm (av. = 26 × 1.5 µm). Beta conidiogenous cells subcylindrical, tapering towards the apex, collarette and periclinal thickening present, 7–14 × 1–2 µm (av. = 11–1.5 µm). Beta conidia less common than alpha conidia, straight, curved or hamate, 20–25 × 0.5–1 µm (av. = 23–1 µm). Gamma conidia rarely observed, fusoid to subcylindrical, apex acutely rounded, base subtruncate, multi-guttulate, 12–18 × 1.5–2 µm (av. = 15 × 2 µm). Description adapted from Mostert et al. (2001a). Specimens examined. frAnCe, Bordeaux, Naujan-et-Postiac, on Vitis vinifera (Cabernet Sauvignon grapevine), May 1998, P. Larignon (PREM 56460 neotype, ex-neotype culture CBS 114016). – itAly, Perugia, on Vitis vinifera, May 1980, A. Zazzerini (CBS 267.80 = CPC 2671). – turkey, from Vitis vinifera, 1 Dec. 2001, M. Erkan (CBS 114867 = CPC 4708). – USA, California, on Vitis vinifera, J.D. Cucuzza (CBS 111888 = ATCC 48153 = CPC 2673). Notes — Grove (1919) distinguished P. ampelina (K 58408) from P. viticola by its external appearance on the host. However, Mostert et al. (2001a) re-examined the type specimen, and found alpha conidia to be ellipsoid-fusoid, 8–12 × 2.5–3.5 µm, within the range of P. viticola (Mostert et al. 2001a: f. 29), and thus considered them to be synonymous. Udayanga et al. (2012) proposed D. neoviticola as a nom. nov. for P. viticola, but this name is superfluous, as the older epithet ‘ampelina’ has precedence and should be adopted. Diaporthe ampelina (clade 53) is a well-resolved species. It causes cane and leaf spot and infections of pruning wounds of Vitis and Ampelopsidis spp. (Vitaceae). Several species of Diaporthe can infect the host and cause variable symptoms in different parts of the vine (canes, leaves and fruits) causing considerable confusion in the taxonomy of these species on grapevine (Phillips 1999, Scheper et al. 2000, Mostert et al. Fig. 2 Diaporthe anacardii (CBS 720.97). a. Conidiomata sporulating on PNA; b. conidiomata sporulating on PDA; c, d. conidiogenous cells; e. beta conidia; f. alpha conidia. — Scale bars = 10 µm. R.R. Gomes et al.: Diaporthe 2001a). Merrin et al. (1995) studied the variation of Diaporthe in Australia using morphology. They identiﬁed two taxa (Phomopsis taxon 1 and taxon 2), which cause cane and leaf blight of Vitis spp.; and taxon 2 was identiﬁed as showing more resemblance to P. viticola. Mostert et al. (2001a) studied the species occurring on grapevines in South Africa using morphological, cultural, molecular and pathological characterisation and clariﬁed the taxonomy of this complex. Diaporthe ampelina (= Phomopsis viticola, D. neoviticola, Phomopsis taxon 2 from Australia) was found to be the cause of cane and leaf spot disease, and was neotypiﬁed. Although the sexual morph has never been reported, Santos et al. (2010) found both MAT loci to be present in this species, and showed that it is heterothallic. However, the sexual morph could not be induced in culture by crossing opposing mating types. Diaporthe amygdali (Delacr.) Udayanga, Crous & K.D. Hyde, Fung. Diversity 56: 166. 2012 Basionym. Fusicoccum amygdali Delacr., Bull. Soc. Mycol. France 21: 280. 1905. ≡ Phomopsis amygdali (Delacr.) J.J. Tuset & M.T. Portilla, Canad. J. Bot. 67, 5: 1280. 1989. Specimens examined. PortugAl, Mirandela, from Prunus dulcis, 2010, E. Diogo (ex-epitype culture CBS 126679); Tavira, on Prunus dulcis, 2010, E. Diogo (CBS 126680). – south AfriCA, Western Cape Province, on Vitis vinifera, 1 Mar. 1997, L. Mostert (CBS 111811 = CPC 2632); Western Cape Province, in wood on Prunus salicina, 2008, U. Damm (CBS 120840 = CPC 5833). – usA, Georgia, cankers on Prunus persica, Mar. 1994, W. Uddin (CBS 115620 = FAU 1005). Notes — Diaporthe amygdali (clade 42) is the causal agent of twig canker and blight of almonds (Prunus dulcis) and peach (P. persica) wherever these hosts are grown (Diogo et al. 2010). It was ﬁrst described as Fusicoccum amygdali causing cankers on almonds in France (Delacroix 1905). Tuset & Portilla (1989) re-examined the type specimen of F. amygdali and, based on morphology and symptomatology, they considered that it would be best accommodated in the genus Phomopsis. Clade 42 contains the ex-epitype strain (CBS 126679), ﬁve Phomopsis amygdali isolates from Prunus dulcis in Portugal, from P. persica in USA, P. salicina in South Africa, and from Vitis vinifera in South Africa. 15 Diaporthe anacardii (Early & Punith.) R.R. Gomes, C. Glienke & Crous, comb. nov. — MycoBank MB802923; Fig. 2 Basionym. Phomopsis anacardii Early & Punith., Trans. Brit. Mycol. Soc. 59, 2: 345. 1972. Conidiomata pycnidial, sporulating profusely on OA, globose, up to 600 µm diam, multilocular, black, erumpent; cream conidial droplets exuding from central ostioles; walls consisting of 3–6 layers of medium brown textura angularis. Conidiophores hyaline, smooth, 1– 3-septate, branched, densely aggregated, cylindrical, straight to sinuous, 10–25 × 2–3 µm. Conidiogenous cells 9–16 × 1.5–2 µm, phialidic, cylindrical to cymbiform, terminal and lateral, with slight taper towards apex, 1–1.5 µm diam, with visible periclinal thickening; collarette slightly flared, up to 2 µm long when present. Paraphyses rarely present, hyaline, smooth, 1–3-septate, cylindrical with obtuse ends, extending above conidiophores. Alpha conidia aseptate, hyaline, smooth, guttulate, fusoid to ellipsoid, tapering towards both ends, straight, apex subobtuse, base bluntly rounded with flattened hilum, (6.5–)7–8(–9) × (2–)3(–3.5) µm. Gamma conidia not observed. Beta conidia spindle-shaped, aseptate, smooth, hyaline, apex subacutely rounded, base truncate, tapering from lower third towards apex, curved, (15 –)20–25 × 1.5(–2) µm. Culture characteristics — Colonies covering dish after 2 wk in the dark at 25 °C. On OA dirty white with moderate aerial mycelium and patches of iron-grey. On PDA having patches of dirty white and umber, reverse bay with patches of umber. On MEA having patches of dirty white and olivaceous-grey, reverse umber with patches of olivaceous-grey. Specimens examined. eAst AfriCA, on Anacardium occidentale, Apr. 1997, M. Puccioni (epitype designated here CBS H-21101, culture ex-epitype CBS 720.97). – kenyA, on Anacardium occidentale, 4 Dec. 1969, M.P. Early (holotype IMI 144866). Notes — Phomopsis anacardii (clade 69 as D. anacardii) was described from Anacardi occidentalis in Kenya, and also recorded from Nigeria, Guinea and Cuba (Early & Punithalingam 1972). Fig. 3 Diaporthe angelicae (CBS 111591). a, b. Transverse section through conidiomata, showing conidiomatal wall; c, d. conidiogenous cells; e. alpha and beta conidia; f. conidiogenous cells giving rise to beta conidia; g. beta conidia. — Scale bars: a = 140 µm, all others = 10 µm. 16 Persoonia – Volume 31, 2013 Diaporthe angelicae (Berk.) D.F. Farr & Castl., Mycoscience 44: 204. 2003. — Fig. 3 Diaporthe arctii (Lasch) Nitschke, Pyrenomycetes Germanici 2: 268. 1870 Basionym. Sphaeria angelicae Berk., Mag. Zool. Bot.: 28. 1837. ≡ Diaporthopsis angelicae (Berk.) Wehm., The genus Diaporthe Nitschke: 228. 1933. ≡ Mazzantia angelicae (Berk.) Lar. N. Vassiljeva, Pyrenomycetes of the Russia Far East. I. Gnomoniaceae: 49. 1993. = Leptosphaeria nigrella Auersw., Mycol. Eur. Pyr. 5/6, pl. 12, f. 163. 1869. ≡ Diaporthe nigrella (Auersw.) Niessl, Beitr.: 51. 1872. ≡ Diaporthopsis nigrella (Auersw.) Fabre, Ann. Sci. Nat., Bot. 6 15: 35. 1883. Basionym. Sphaeria arctii Lasch, in Rabenh., Klotzsch. Herb. Vivum Mycol.: no. 1046. 1846. ≡ Phomopsis arctii (Lasch) Traverso, Fl. Ital. Crypt., Pars 1: Fungi. Pyrenomycetae. Xylariaceae, Valsaceae, Ceratostomataceae: 226. 1906. Conidiomata pycnidial, globose to ellipsoidal, aggregated or scattered, dark brown to black, immersed, ostiolate, 100–281 μm wide, 70–200 μm tall, lacking necks, with outer surface covered in hyphae; pycnidal wall consisting of brown, thickwalled cells of textura angularis; conidial mass globose or exuding in cirrhi, white to pale luteous or pale yellow. Conidiophores hyaline, subcylindrical, rarely branched, tapering towards the apex, aseptate, (12–)13–16(–18) × 3(–4) μm. Conidiogenous cells hyaline, subcylindrical, straight to curved, tapering towards the apex, collarette not flared, periclinal thickening inconspicuous, 8–10(–11) × 3(–3.5) μm. Alpha conidia hyaline, oblong to ellipsoid, apex bluntly rounded, base obtuse to subtruncate, bi- to multi-guttulate, (7–)8–10(–11) × 3(–4) μm. Beta conidia hyaline, smooth, spindle shaped, slightly curved, (19–)22–26 (–28) × (1–)2 μm. Gamma conidia not observed (CBS 111592). Culture characteristics — See Castlebury et al. (2003). Specimens examined. AustriA, Karnten, St. Margareten, decaying stems of Heracleum sphondylium, Aug. 2001, A.Y. Rossman (CBS 111591 = AR 3724); Niederosterreich, Ottenstein, decaying stems of Heracleum sphondylium, Aug. 2001, A.Y. Rossman (ex-epitype culture CBS 111592 = AR3776). – frAnCe, Bretagne, La Ville Borée, near Quessoy, on seeds of Heracleum sphondylium, 27 July 1990, H.A. van der Aa (CBS 501.90); sea dunes near Seignose le Penon, on Eryngium maritimum, leaf spots, 10 June 1986, H.A. van der Aa (CBS 344.86). – itAly, San Casciano, Prov., Florence, twig blight of Foeniculum vulgare, July 1996, L. Mugnai (CBS 100871). – PortugAl, Malveira da Serra, Sintra, on Foeniculum vulgare, A.J.L. Phillips (CBS 123215 = Ph-C133/1). Notes — Diaporthe angelicae (clade 17) is known to cause stem decay in several hosts including Heracleum sphondylium (Apiaceae) and Foeniculum vulgare (Apiaceae) in Europe and North America (Santos & Phillips 2009). Wehmeyer (1933) not only linked the conidial form of Phomopsis asteriscus to the sexual state Diaporthopsis angelicae, but also stated that Diaporthe berkeleyi was a synonym of Diaporthopsis angelicae. However, Castlebury et al. (2003) showed that Diaporthopsis is a synonym of Diaporthe, and also designated an epitype for D. angelicae. Specimen examined. unknown, from Arctium sp., Sept. 1925, A.W. Archer (CBS 136.25). Notes — There are several clades that contain isolates previously identiﬁed as D. arctii (clades 16, 19, part 2 and 67, part 4). We suspect that clade 19 may represent the real D. arctii, as it is basal to D. subordinaria, and Wehmeyer (1933) regarded the latter (from Plantago lanceolata) as synonym of D. arctii (from Arctium). Diaporthe arecae (H.C. Srivast., Zakia & Govindar.) R.R. Gomes, C. Glienke & Crous, comb. nov. — MycoBank MB802924 Basionym. Subramanella arecae H.C. Srivast., Zakia & Govindar., Mycologia 54, 1: 7. 1962. Specimens examined. indiA, on fruit of Areca catechu, Feb. 1964, H.C. Srivastava (isotype CBS H-7808, ex-isotype culture CBS 161.64). – surinAme, on fruits of Citrus sp., Oct. 1975, I. Block (CBS 535.75). Notes — The Diaporthe isolate from citrus (CBS 535.75) could well be distinct, but more strains are required to resolve this clade (clade 87). Diaporthe arengae R.R. Gomes, C. Glienke & Crous, sp. nov. — MycoBank MB802925; Fig. 4 Etymology. Named after the host genus from which it was collected, Arenga. Pycnidia in culture on PNA sporulating poorly, subglobose, up to 250 µm diam, black, erumpent; cream conidial droplets exuding from central ostiole; walls consisting of 3–6 layers of medium brown textura angularis. Conidiophores hyaline in upper region, pale brown at base, smooth, 0–6-septate, branched, densely aggregated, cylindrical, straight to sinuous, 10–60 × 2.5–4 µm. Conidiogenous cells 8–15 × 1.5–2.5 µm, phialidic, cylindrical, terminal and lateral, with slight taper towards apex, 1–1.5 µm diam, with visible periclinal thickening; collarette not flared, up to 2 µm long when present. Paraphyses not observed. Alpha conidia aseptate, hyaline, guttulate, fusoid-ellipsoid, tapering towards both ends, apex subobtuse, base with flattened hilum, (5–)6–7(–9) × (2–)2.5(–3) µm. Gamma conidia not observed. Beta conidia rarely observed, subcylindrical, aseptate, smooth, hyaline, apex bluntly rounded, base truncate, tapering absent to very slight, curved, 20–25 × 1.5 µm. Fig. 4 Diaporthe arengae (CBS 114979). a. Conidiomata sporulating on PNA; b, c. conidiogenous cells; d. beta conidia; e, f. alpha conidia. — Scale bars = 10 µm. 17 R.R. Gomes et al.: Diaporthe Culture characteristics — Colonies covering dish after 2 wk in the dark at 25 °C. On MEA surface with fluffy aerial mycelium, pale luteous, in reverse orange with patches of sienna. On OA umber with patches of sienna and saffron, in reverse umber with patches of saffron. On PDA surface with fluffy white aerial mycelium, umber with patches of saffron, in reverse umber with patches of pale luteous to luteous. Notes — Clade 49 contains two isolates of D. australafricana, one of them being the ex-type strain (CBS 111886), which is a sibling species of D. viticola in clade 50 (van Niekerk et al. 2005). Both species were described from Vitis vinifera, but D. australafricana is thus far only known from grapevines in Australia and South Africa. Specimen examined. hong kong, Victoria Peak, from Arenga engleri, 7 Oct. 1999, K.D. Hyde (holotype CBS H-21104, culture ex-type CBS 114979 = HKUCC 5527). Diaporthe batatas Harter & E.C. Field, Phytopathology 2: 121. 1912 Notes — The Diaporthe species occurring on palms are summarised by Fröhlich et al. (1997). Diaporthe arengae (clade 81) is distinguished from known species based on a combination of its conidial morphology and host. Diaporthe aspalathi E. Jansen, Castl. & Crous, Stud. Mycol. 55: 71. 2006 Basionym. Diaporthe phaseolorum var. meridionalis F.A. Fernández, Mycologia 88: 438. 1996 (non D. meridionalis Sacc., Syll. Fung. 1: 638. 1878). Specimen examined. USA, on Ipomoea batatas, Feb. 1921, L.L. Harter (CBS 122.21). Notes — Clade 8 consists of a single strain of D. batatas isolated from Ipomoea batatas in the USA. This species and D. phaseolorum have in the past been considered as varieties, namely D. phaseolorum var. batatatis and D. phaseolorum var. batatae. However, the genetic data revealed no homology between the two species. Although it is not certain if CBS 122.21 (culture sterile) is an ex-type strain of D. batatas, it is regarded as authentic for the name. Specimens examined. south AfriCA, Western Cape Province, Clanwilliam, Langebergpunt, in branch on Aspalathus linearis, J.C. Janse van Rensburg (ex-type culture CBS 117169 = CPC 5428); in crown on Aspalathus linearis, 17 Oct. 1997, J.C. Janse van Rensburg (CBS 117168 = CPC 5420); on Aspalathus linearis, 2 Dec. 1996, S. Lamprecht (CBS 117500 = CPC 5408). Diaporthe beckhausii Nitschke, Pyrenomycetes Germanici 2: 295. 1870 Notes — Diaporthe aspalathi (clade 93) causes soybean stem canker in the South-eastern USA (Fernández & Hanlin 1996), and is not closely related to D. phaseolorum as might be expected. Although morphologically similar, this species clustered apart from the reference strain of D. phaseolorum (clade 4). Diaporthe aspalathi is also the main causal organism of canker and dieback of rooibos (Aspalathus linearis), and not D. phaseolorum as reported earlier (Smit & Knox-Davies 1989a, b, van Rensburg et al. 2006). Notes — Clade 47 is represented by D. beckhausii, which was isolated from Viburnum sp. (origin unknown, presumably North America, whereas the species was originally described from Viburnum collected in Germany). Diaporthe beckhausii is known from woody stems of Betula sp., Cydonia japonica, Elaeagnus angustifolia, Halesia sp., Menispermum canadense, Menispermum sp., V. opulus, Viburnum sp. and V. tinus in temperate North America and Europe (Farr & Rossman 2012). Diaporthe australafricana Crous & Van Niekerk, Australas. Pl. Pathol. 34: 33. 2005 Specimens examined. AustrAliA, on Vitis vinifera, 1 July 1995, R.W.A. Schepers (ex-type culture CBS 111886 = CPC 2676). – south AfriCA, on V. vinifera, 1 Nov. 1997, L. Mostert (CBS 113487 = CPC 2655). Specimen examined. unknown, from Viburnum sp., Sept. 1927, L.E. Wehmeyer (CBS 138.27). Diaporthe brasiliensis R.R. Gomes, C. Glienke & Crous, sp. nov. — MycoBank MB802926; Fig. 5 Etymology. Named after the country where it was collected, Brazil. Conidiomata pycnidial, globose to conical, immersed, scattered or aggregated, brown to black, ostiolate, 70 –160 μm wide, Fig. 5 Diaporthe brasiliensis (CBS 133183). a. Conidiomata sporulating on PDA; b, c. transverse section through conidiomata, showing conidiomatal wall; d, e. conidiogenous cells; f, g. alpha conidia. — Scale bars: b = 80 µm, all others = 10 µm. 18 60–140 μm tall, necks 60–130 μm tall, outer surface smooth; pycnidal wall consisting of brown, thick-walled cells of textura angularis; conidial mass globose, white to pale-luteous. Conidiophores hyaline, cylindrical, ﬁliform, straight to curved, 1–3-septate, (17–)20–27(–30) × 2(–4) μm. Alpha conidiogenous cells hyaline, cylindrical, ﬁliform, straight to curved, collarette flared, with slight periclinal thickening, (7–)8–12(–14) × 2(–3) μm. Alpha conidia hyaline, ellipsoid to irregular, apex bluntly rounded, base obtuse to subtruncate, bi- to multi-guttulate, 6–7(–8) × 2–3 μm. Beta and gamma conidia not observed. Culture characteristics — Colonies on PDA flat, with an entire edge, surface mycelium dense and felty, buff, grey-olivaceous or olivaceous-grey; colonies covering dish after 2 wk at 25 °C in the dark; reverse olivaceous, dull green, olivaceous-buff. On OA raised, entire edge, surface mycelium dense felty, smokegrey to grey-olivaceous; reverse purplish grey to pale purplish grey, grey olivaceous or olivaceous buff. On MEA raised, with an entire edge, buff, smoke-grey, with patches of olivaceousgrey and vinaceous-buff; reverse dark mouse-grey, buff. Specimens examined. BrAzil, Rio de Janeiro, endophytic species isolated from leaf of Aspidosperma tomentosum (popular name Peroba-do-campo), July 2007, K. Rodriguez (holotype CBS H-21100, ex-type culture CBS 133183 = LGMF 924 = CPC 20300); same collection details (LGMF 926 = CPC 20302). Notes — Endophytic isolates (clade 36) from a medicinal plant in Brazil. Diaporthe carpini (Pers.) Fuckel, Jahrb. Nassauischen Vereins Naturk. 23–24: 205. 1870 (1869 –1870) Basionym. Sphaeria carpini Pers., Syn. Meth. Fung. (Göttingen) 1: 39. 1801. Specimen examined. sweden, Skåne, S. Mellby par., Stenshuvud, on Carpinus betulus, 14 Apr. 1989, K. & L. Holm (CBS 114437 = UPSC 2980). Notes — Diaporthe carpini (clade 55) is known from several European countries, where it occurs on Carpinus spp. Diaporthe caulivora (Athow & Caldwell) J.M. Santos, Vrandečić & A.J.L. Phillips, Persoonia 27: 13. 2011 Basionym. Diaporthe phaseolorum var. caulivora Athow & Caldwell, Phytopathology 44: 323. 1954. Persoonia – Volume 31, 2013 Specimens examined. CAnAdA, Ontario, in mature stem on Glycine soja, Mar. 1955, A.A. Hildebrand (CBS 178.55 = ATCC 12048 = CECT 2023). – CroAtiA, in stem on Glycine max, K. Vrandečić (ex-neotype culture CBS 127268). Notes — Clade 91 is represented by two isolates of D. caulivora on Glycine soja and G. max, respectively obtained from Canada (CBS 178.55) and Croatia (ex-neotype: CBS 127268). The soybean canker species complex was recently treated by Santos et al. (2011). Diaporthe celastrina Ellis & Barthol., J. Mycol. 8, 4: 173. 1902 Specimen examined. unknown, on Celastrus scandens, Sept. 1927, L.E. Wehmeyer (CBS 139.27). Notes — Strains from the USA are required to conﬁrm the identity of this culture (clade 66). Diaporthe chamaeropis (Cooke) R.R. Gomes, C. Glienke & Crous, comb. nov. — MycoBank MB802927; Fig. 6 Basionym. Phoma chamaeropis Cooke, Grevillea 13 (no. 68): 95. 1885. ≡ Phomopsis chamaeropsis (Cooke) Petr., as ‘Phomopsis chamaeropis’, Ann. Mycol. 17, 2/6: 83. 1920 (1919). Conidiomata pycnidial in culture on PNA, globose, up to 400 µm diam (up to 600 µm diam on OA), black, erumpent; cream conidial droplets exuding from central ostioles; walls consisting of 3–6 layers of medium brown textura angularis. Conidiophores hyaline, smooth, 1–5-septate, branched, densely aggregated, cylindrical, straight to sinuous, 10–50 × 2–2.5 µm. Conidiogenous cells 10–20 × 1.5–2 µm, phialidic, cylindrical, terminal and lateral, with slight taper towards apex, 1–1.5 µm diam, with visible periclinal thickening; collarette not observed. Paraphyses not observed. Alpha conidia aseptate, hyaline, smooth, guttulate, fusoid to ellipsoid, tapering towards both ends, straight, apex subobtuse, base subtruncate, (5 –)6 – 8(– 9) × 2(– 2.5) µm. Gamma conidia not observed. Beta conidia spindleshaped, aseptate, smooth, hyaline, apex acutely rounded, base truncate, tapering from lower third towards apex, curved, (20–)22–27(–30) × 1.5(–2) µm. Culture characteristics — Colonies covering dish after 2 wk in the dark at 25 °C. On OA with moderate aerial mycelium, surface dirty white with patches of pale olivaceous-grey, reverse with patches of dirty white and sienna. On MEA surface Fig. 6 Diaporthe chamaeropis (CBS 454.81). a. Conidiomata sporulating on PDA; b. conidiomata sporulating on PNA; c–e. conidiogenous cells; f. alpha conidia; g. beta conidia. — Scale bars = 10 µm. 19 R.R. Gomes et al.: Diaporthe dirty white with patches of olivaceous-grey, reverse sienna, with patches of luteous. On PDA surface olivaceous-grey with patches of dirty white, reverse iron-grey. Specimens examined. CroAtiA, Rab, slope behind Hotel ‘Imperial’, on dead branch of Spartium junceum, July 1970, J.A. von Arx (CBS 753.70). – greeCe, Thessaloniki, dead part of leaf of Chamaerops humilis, Aug. 1981, H.A. van der Aa (CBS 454.81). Notes — Conidial dimensions closely ﬁt those provided in the original description (on Chamaerops humulis from Czechoslovakia; Uecker 1988), suggesting that these cultures (clade 77) could be authentic for the name. Diaporthe cinerascens Sacc., Syll. Fung. (Abellini) 1: 679. 1882. — Fig. 7 = Phoma cinerescens Sacc., Michelia 1 (no. 5): 521. 1879. ≡ Phomopsis cinerascens (Sacc.) Traverso, Fl. Ital. Crypt. Pyrenomycetae 2, 1: 278. 1906. Conidiomata pycnidial, sporulating poorly on MEA, globose, up to 300 µm diam, black, erumpent; creamy-luteous conidial droplets exuding from central ostioles; walls consisting of 3–6 layers of medium brown textura angularis. Conidiophores hyaline, smooth, 1–3-septate, branched, densely aggregated, cylindrical, straight to sinuous, 17–30 × 2–3 µm. Conidiogenous cells 8–18 × 2–3 µm, phialidic, cylindrical, terminal and lateral, with slight taper towards apex, 1.5–2 µm diam, with visible periclinal thickening; collarette mostly absent, slightly flared when present, up to 2 µm long. Paraphyses not observed. Alpha conidia aseptate, hyaline, smooth, guttulate, fusoid to ellipsoid, tapering towards both ends, straight, apex subobtuse, base subtruncate, 7–8(–9) × (2.5–)3 µm. Gamma conidia aseptate, hyaline, smooth, ellipsoid-fusoid, apex acutely rounded, base subtruncate, 8–12 × 3 µm. Beta conidia not observed. Culture characteristics — Colonies covering dish after 2 wk in the dark at 25 °C. On MEA with profuse aerial mycelium, surface dirty white, reverse ochreous with patches of umber. On PDA with sparse aerial mycelium, surface olivaceous-grey, reverse iron-grey. On OA surface with moderate aerial mycelium, olivaceous-grey to pale olivaceous-grey. Specimen examined. BulgAriA, Kostinbrod, Plant Protection Institute, on branch of Ficus carica, 1995, E. Ilieva (CBS 719.96). Notes — Diaporthe cinerascens (clade 76) represents a European species occurring on Ficus, so the present culture could be authentic for the name, as the conidial dimenions match those provided in the original description. This species was orginally associated with canker and dieback of Ficus spp. in Italy (Saccardo 1879), and the causal organism identiﬁed as Phomopsis cinerascens (sexual morph: Diaporthe cinerascens) by Grove (1935). Diaporthe cinerascens affects all commercial ﬁgs in California (Ogawa & English 1991), and is found in several geographical locations of the world (Hampson 1981, Anderson & Hartman 1983, Benschop et al. 1984, Banihashemi & Javadi 2009). Ficus spp. are important exotic garden ornamentals across the USA and Canada as well as in the tropics. Diaporthe citri F.A. Wolf, J. Agric. Res. 33, 7: 625. 1926 = Phomopsis citri H.S. Fawc., Phytopathology 2, 3: 109. 1912. Specimens examined. BrAzil, on seed of Glycine max, A. Almeida EMBRAPA/PR (LGMF 946 = CPC 20322). – itAly, unknown host, June 1939, G. Goidánich (CBS 199.39). – surinAme, Paramaribo, on decaying fruit of Citrus sinensis, Apr. 1932, N.J. van Suchtelen (CBS 230.52). Notes — Clade 6 is represented by three isolates. One isolate (CBS 199.39) was previously identiﬁed as D. conorum from Italy, while another originates from soybean seed collected in Brazil (LGMF 946), and the third isolate is from Citrus sinensis in Suriname (CBS 230.52). Because D. conorum is regarded as synonym of D. eres (clade 67), we tentatively refer to this clade as D. citri, awaiting more isolates from Citrus. Diaporthe citri is a serious pathogen that is widely distributed, and associated with melanosis and stem-end rot of citrus fruits (Punithalingam & Holliday 1973, McKenzie 1992, Mondal et al. 2007, Farr & Rossman 2012). Diaporthe convolvuli (Ormeno-Nuñez, Reeleder & A.K. Watson) R.R. Gomes, C. Glienke & Crous, comb. nov. — MycoBank MB802928 Basionym. Phomopsis convolvuli Ormeno-Nuñez, Reeleder & A.K. Watson, Canad. J. Bot. 66, 11: 2232. 1988. Specimen examined. turkey, isolated from leaves with anthracnose on Convolvulus arvensis, D. Berner (CBS 124654 = DP 0727). Notes — Phomopsis convolvuli (clade 3) was originally described from diseased leaves of Convolvulus arvensis in Québec (Ormeno-Nuñez et al. 1988). The isolate of Phomopsis convolvuli studied here (CBS 124654), was found causing anthracnose on ﬁeld bindweed (Convolvulus arvensis), a troublesome perennial weed to many important agricultural crops in the world, and was considered potentially useful as biological control agent (Kuleci et al. 2009). Diaporthe crataegi (Curr.) Fuckel, Jahrb. Nassauischen Vereins Naturk. 23 –24: 204. 1870 Basionym. Valsa crataegi Curr., Trans. Linn. Soc. London 22: 278. 1858. Specimen examined. sweden, Skåne, Trolle-Ljungby par., Tosteberga, on Crataegus oxyacantha, 15 Apr. 1989, K. & L. Holm (CBS 114435 = UPSC 2938). Notes — Clade 41 is represented by D. crataegi isolated from Crataegus oxyacantha in Sweden. The species is common on C. chrysocarpa, C. laevigata and C. oxyacantha in Canada and Europe (Farr & Rossman 2012). Fig. 7 Diaporthe cinerascens (CBS 719.96). a. Conidiomata sporulating on PDA; b, c. conidiogenous cells; d. alpha conidia. — Scale bars = 10 µm. Persoonia – Volume 31, 2013 20 Diaporthe crotalariae G.F. Weber, Phytopathology 23: 602. 1933 = Phomopsis crotalariae G.F. Weber, Phytopathology 23: 602. 1933. Specimen examined. USA, on Crotalaria spectabilis, Oct. 1933, G.F. Weber (ex-type culture CBS 162.33). Notes — Clade 92 contains the ex-type strain (CBS 162.33) of D. crotalariae isolated from Crotalaria spectabilis in the USA. Diaporthe cuppatea (E. Jansen, Lampr. & Crous) Udayanga, Crous & K.D. Hyde, Fung. Diversity 56: 166. 2012 Basionym. Phomopsis cuppatea E. Jansen, Lampr. & Crous, Stud. Mycol. 55: 72. 2006. Specimen examined. south AfriCA, Western Cape Province, on Aspalathus linearis, 2006, J. Janse van Rensburg (holotype CBS H-19687, ex-type culture CBS 117499 = STE-U 5431 = CPC 5431). Notes — Diaporthe cuppatea (clade 20) is known only from the original collection made from dying branches of Aspalathus linearis in South Africa (van Rensburg et al. 2006). Diaporthe cynaroidis Marinc., M.J. Wingf. & Crous, CBS Biodiversity Ser. (Utrecht) 7: 39. 2008 Specimen examined. south AfriCA, Western Cape Province, on leaf litter of Protea cynaroides, 26 June 2000, S. Marincowitz (ex-type culture CBS 122676 = CMW 22190 = CPC 13180). Notes — Clade 48 contains the ex-type culture of D. cynaroidis (CBS 122676), which was isolated from Protea cynaroides in South Africa (Marincowitz et al. 2008). This species is closely related to D. australafricana and D. viticola (clades 49 and 50, respectively). Diaporthe decedens (Pers.) Fuckel, Jahrb. Nassauischen Vereins Naturk. 23 –24: 30. 1871 Basionym. Sphaeria tessella var. decedens Pers., Syn. Meth. Fung. (Göttingen) 1: 48. 1801. Specimens examined. AustriA, on Corylus avellana, Oct. 2001, W. Jaklitsch (CBS 109772 = AR 3459). – sweden, Öland, Kastlösa par., on Corylus avellana, 7 June 1989, K. & L. Holm (CBS 114281 = UPSC 2957). Notes — Diaporthe decedens represents a European species on Corylus. Clade 68 consists of two isolates obtained on Corylus avellana from Austria and Sweden. Diaporthe detrusa (Fr.) Fuckel, Jahrb. Nassauischen Vereins Naturk. 23–24: 205. 1870 (1869 –1870) Basionym. Sphaeria detrusa Fr., in Kunze & Schmidt, Mykologische Hefte (Leipzig) 2: 43. 1823. = Phoma detrusa Sacc., Michelia 2: 96. 1880. ≡ Phomopsis detrusa (Sacc.) Traverso, Fl. Ital. Crypt. Pars 1: Fungi. Pyrenomycetae. Xylariaceae, Valsaceae, Ceratostomataceae 1, 1: 195. 1906. Specimens examined. AustriA, on Berberis vulgaris, Oct. 2001, A.Y. Rossman (CBS 109770 = AR 3424). – sweden, Uppland, Hållnäs par., on Berberis vulgaris, 14 May 1991, K. & L. Holm (CBS 114652 = UPSC 3371). – unknown, on Berberis vulgaris, Sept. 1927, L.E. Wehmeyer (CBS 140.27). Notes — Clade 54 contains three isolates of D. detrusa obtained from Berberis vulgaris in Austria, Sweden and one of them with an unknown origin (presumably North America). This European species is known to also occur in the USA (Farr & Rossman 2012). Diaporthe elaeagni Rehm, Syll. Fung. 14: 546. 1899. — Fig. 8 ?= Phoma elaeagni Sacc., Michelia 1, 3: 354. 1878. ≡ Phomopsis elaeagni (Sacc.) Petr., Ann. Mycol. 19, 1–2: 48. 1921. Specimen examined. netherlAnds, Maassluis, on twig of Elaeagnus sp., May 1972, J. Gremmen (CBS 504.72). Notes — In culture CBS 504.72 (clade 73) primarily produces beta conidia (spindle shaped, 16–22 × 2 µm, thus wider than seen on average in most other species); alpha conidia rarely observed, fusoid-ellipsoidal, 7–10 × 2–3 µm, thus correlating with dimensions of Phomopsis elaeagni (Sacc.) Petr., which is a homonym of P. elaeagni Sacc. Furthermore, conidial dimensions of the asexual state of D. elaeagni are not known. Additional collections and type studies are thus required to resolve the complex occurring on Elaeagnus. Diaporthe endophytica R.R. Gomes, C. Glienke & Crous, sp. nov. — MycoBank MB802929 Etymology. Named after its endophytic growth habit. Cultures sterile. Diaporthe endophytica (clade 5) differs from its closest phylogenetic neighbour, D. phaseolorum (clade 4), by unique ﬁxed alleles in ﬁve loci based on alignments of the separate loci deposited in TreeBase as study S13943: ITS positions 357 (C), 359 (G), 360 (T), 368 (A), 369 (A), 371 (A), 372 (G) and 373 (G); TUB positions 135 (C) and 592 (T); CAL position 145 (G); TEF1 positions 18 (G), 26 (T), 40 (T), 42 (A), 63 (A), 124 (A), 175 (A) and 343 (A); HIS position 369 (C). Culture characteristics — Colonies with sparse aerial mycelium, covering the dish after 2 wk at 25 °C. On PDA buff, honey to isabelline; reverse smoke-grey. On OA smoke-grey to olivaceous-grey. On MEA buff with umber patches; reverse dark mouse-grey, with patches of isabelline. Specimens examined. BrAzil, endophytic in leaf on Schinus terebinthifolius, July 2007, J. Lima (LGMF 911 = CPC 20287, LGMF 919 = CPC 20295), (holotype CBS H-21107, culture ex-type LGMF 916 = CPC 20292 Fig. 8 Diaporthe elaeagni (CBS 504.72). a. Conidiomata sporulating on PNA; b. conidiomata sporulating on PDA; c, d. conidiogenous cells; e. beta conidia. — Scale bars = 10 µm. R.R. Gomes et al.: Diaporthe = CBS 133811); endophytic in petiole on Maytenus ilicifolia, July 2007, R.R. Gomes (LGMF 928 = CPC 20304, LGMF 934 = CPC 20310, LGMF 935 = CPC 20311, LGMF 937 = CPC 20313); in seed on Glycine max, A. Almeida EMBRAPA/PR (LGMF 948 = CPC 20324). Notes — Clade 5 represents a distinct lineage, containing eight sterile isolates originating from Brazil. Four of them were isolated from Maytenus ilicifolia, three from S. terebinthifolius and one from soybean seeds. Isolates could not be induced to sporulate on any of the media deﬁned in this study, nor on sterilised plant host tissue placed on WA. Diaporthe eres Nitschke, Pyrenomycetes Germanici 2: 245. 1870 = Phomopsis cotoneastri Punith., Trans. Brit. Mycol. Soc. 60, 1: 157. 1973. = Phoma oblonga Desm., Ann. Nat. Sci. Bot. 20: 218. 1853. ≡ Phomopsis oblonga (Desm.) Traverso, Fl. Ital. Crypt. Pars 1: Fungi. Pyrenomycetae. Xylariaceae, Valsaceae, Ceratostomataceae: 248. 1906. Specimens examined. AustriA, on Acer campestre, Oct. 2001, W. Jaklitsch (CBS 109767 = AR 3538 = WJ 1643). – germAny, Monheim, on leaf spot of Hordeum sp., 5 Aug. 1984, M. Hossfeld (CBS 841.84). – itAly, Milano, on twig of Juglans regia, Dec. 1980, M. Bisiach (CBS 102.81). – lAtviA, on Rhododendron sp., I. Apine (CBS 129168). – netherlAnds, Oostvoorne, on dead stems of Arctium sp., 13 Dec. 1984, M. de Nooij (CBS 110.85); Soest, Dalweg, on fallen fruit of Fraxinus sp., 21 Feb. 1999, G. Verkley (CBS 101742); Veldhoven, on dead branch of Sorbus aucuparia, Nov. 1973, W.M. Loerakker (CBS 287.74); Baarn, garden Chopinlaan, on dead branch of Wisteria sinensis, 6 June 1983, H.A. van der Aa (CBS 528.83); Soest, inside house, on Abutilon sp., 26 Mar. 1997, A. Aptroot (CBS 688.97); Baarn, potted plant, on cladodes of Opuntia sp., 23 Sept. 1996, H.A. van der Aa (CBS 365.97); on Alliaria officinalis, Feb. 1962, G.H. Boerema (CBS 445.62); Baarn, on dead leaf of Ilex aquifolium, 11 June 1967, H.A. van der Aa (CBS 370.67 = MUCL 9931); Prov. Zuid-Holland, Huize Oud-Poelgeest, Oegstgeest, dieback of Ilex aquifolium, 21 Nov. 1994, G.J.M. Verkley (CBS 694.94); Baarn, garden Eemnesserweg 90, on dead stem of Rumex hydrolapathum, 19 Mar. 1996, H.A. van der Aa (CBS 485.96); Baarn, Cantonspark, on withering leaf of Magnolia × soulangeana, 23 Oct. 1968, H.A. van der Aa (CBS 791.68); ZuidHolland, Ridderkerk, Huys ten Donck, on leaf tip of Osmanthus aquifolium, 7 May 1977, H.A. van der Aa (CBS 297.77); on Phaseolus vulgaris, Sept. 1950, Goossens (CBS 422.50); Baarn, on dead stem of Allium giganteum, May 1985, H.A. van der Aa (CBS 283.85); from Laburnum × watereri ‘Vossii’, Apr. 1935, I. de Boer (CBS 267.55); Boskoop, nursery, dying twigs of Skimmia japonica, Nov. 1981, H.A. v. Kesteren (CBS 122.82). – uk, Scotland, on living and dead twig of Fraxinus excelsior, Feb. 1938, J.A. MacDonald 21 (CBS 250.38); on Cotoneaster sp., 1971, H. Butin (ex-type culture of P. crotoneaster CBS 439.82 = BBA P- 407 = IMI 162181a); Oxford, on Picea abies seedling, Nov. 1937, T.R. Peace (CBS 186.37). – unknown, on rotten fruit of Malus sylvestris, May 1961, Geigy (CBS 375.61); May 1932, W.G. Hutchinson (CBS 267.32). Notes — Diaporthe eres (clade 67) is the type species of the genus Diaporthe, and is present in several hosts, though it is known to be morphologically highly variable (Castlebury et al. 2002). Wehmeyer (1933) described this species on more than 60 hosts, and listed several synonymies based on morphological data. A detailed morphological study is required to designate a suitable epitype strain for D. eres, and to resolve the status of all its purported synonyms. Diaporthe eugeniae (Punith.) R.R. Gomes, C. Glienke & Crous, comb. nov. — MycoBank MB802930 Basionym. Phomopsis eugeniae Punith., Trans. Brit. Mycol. Soc. 63, 2: 232. 1974. Specimens examined. west sumAtrA, on Eugenia aromatica, May 1973, J. Waller (holotype IMI 177560); Lampung, on leaf of Eugenia aromatica, July 1982, R. Kasim (CBS 444.82). Notes — Diaporthe eugeniae (clade 83) was originally described on Eugenia aromatica from West Sumatra. Although the present isolate could be authentic for the name, it unfortunately proved to be sterile. Diaporthe fibrosa (Pers.) Fuckel, Jahrb. Nassauischen Vereins Naturk. 23–24: 204. 1870 (1869 –1870) Basionym. Sphaeria fibrosa Pers., Syn. Meth. Fung. (Göttingen) 1: 40. 1801. Specimens examined. AustriA, Vienna, on Rhamnus cathartica, Oct. 2001, A.Y. Rossman (CBS 109751 = AR 3425). – sweden, Uppland, Dalby par., Hässleborg, on Rhamnus cathartica, 10 Mar. 1987, K. & L. Holm (CBS 113830 = UPSC 2117). Notes — Clade 52 consists of two isolates from Rhamnus cathartica collected in Sweden and Austria. Diaporthe fibrosa was originally described from Europe on Rhamnus, so these cultures may well prove to be authentic for the name. Fig. 9 Diaporthe foeniculacea (CBS 111554). a. Conidiomata sporulating on PDA; b, c. transverse section through conidiomata, showing conidiomatal wall; d–f. conidiogenous cells; g. beta conidia; h. alpha conidia. — Scale bars: b = 250 µm, all others = 10 µm. Persoonia – Volume 31, 2013 22 Diaporthe foeniculacea Niessl, in von Thümen, Contr. Ad. Fl. Myc. Lusit. 2: 30. 1880. — Fig. 9 = Phoma foeniculina Sacc., Syll. Fung. 3: 125. 1884. ≡ Phomopsis foeniculina (Sacc.) Câmara, Agron. Lusit. 9: 104. 1947. = Phomopsis theicola Curzi, Atti Ist. Bot. Univ. Pavia, 3 sér., 3: 65. 1927. = Diaporthe neotheicola A.J.L. Phillips & J.M. Santos, Fung. Diversity 34: 120. 2009. Conidiomata pycnidial, eustromatic, multilocular, immersed, ostiolate, dark brown, scattered or aggregated, 350–890 μm wide, 160–320 μm tall, necks absent, outer surface covered with hyphae; pycnidal wall consisting of brown, thick-walled cells of textura angularis; conidial mass globose to conical and exuding in cirrhi, yellow to reddish brown. Conidiophores hyaline, subcylindrical and cylindrical, ﬁliform, branched above the septa, tapering towards the apex, 1– 3-septate, (19 –)20 – 28(– 32) × 2(–3) μm. Conidiogenous cells hyaline, subcylindrical and ﬁliform, straight, slightly tapering towards the apex, collarette not flared, prominent periclinal thickening, (10–)11–15(–17) × 2(–3) μm. Alpha conidia hyaline, oblong to ellipsoidal, apex bluntly rouded, base obtuse to subtruncate, bi- to multi-guttulate (6 –)7– 9 × 2(– 3) μm. Beta conidia hyaline, smooth, slightly curved, (26 –)28 – 32(– 34) × 1(– 2) μm. Gamma conidia not observed (based on isolate CBS 111554). Specimens examined. indiA, Calcutta, unknown host, Feb. 1948, S.R. Bose (CBS 400.48). – itAly, on leaves and branches of Camellia sinensis, Oct. 1927, M. Curzi (ex-type culture of P. theicola CBS 187.27); Perugia, on Diospyros kaki, June 1956, M. Ribaldi (CBS 287.56); Apulia, near Bari, on Prunus amygdalus, winter 1974/ 75, A. Ciccarone (CBS 171.78). – netherlAnds, Baarn, ‘Madoera’, back frond, on Wisteria sinensis, 24 Apr. 1969, H.A. van der Aa (CBS 357.69). – new zeAlAnd, Waikato region, on Pyrus pyrifolia, 2001, W. Kandula (CBS 116957). – PortugAl, near Lisbon, São Marcos, base of senescent stem of Foeniculum vulgare, Apr. 2002, A.J.L. Phillips (CBS 111554); Évora, Foeniculum vulgare, 1 Nov. 2007, A.J.L. Phillips (extype cultures of Diaporthe neotheicola CBS 123209, CBS 123208); Pedras del Rei, near Tavira, on Bougainvillea spectabilis, 15 June 1988, H.A. van der Aa (CBS 603.88); Madeira, Serra da Agua, base of senescent stem of Foeniculum vulgare, Aug. 2001, A.J.L. Phillips (CBS 111553). Notes — Diaporthe foeniculacea (clade 78) was originally described from Foeniculum vulgare in Portugal, and represents an older name for D. theicola and D. neotheicola. There are many described species that occur on Foeniculum vulgare (wild fennel). Among them, P. theicola and its teleomorph D. neotheicola (Santos & Phillips 2009), and D. foeniculacea, the causal agent of stem necrosis of fennel. Phillips (2003) redescribed D. foeniculacea, and established the sexual-asexual connection between D. foeniculacea and Phomopsis foeniculina. The synonymy of D. neotheicola under D. foeniculacea is based on the fact that the cultures matching the original descriptions are in fact genetically identical. However, as there are no extype strains of D. foeniculacea, this synonymy strongly relies on the earlier opinion of Phillips (2003). Either way, this matter can only be resolved once an epitype has been designated for D. foeniculacea, ﬁxing the application of the name. We recommend that additional collections linked to stem necrosis of fennel in Portugal are obtained, before this decision is made. Diaporthe ganjae (McPartl.) R.R. Gomes, C. Glienke & Crous, comb. nov. — MycoBank MB802932 Basionym. Phomopsis ganjae McPartl., Mycotaxon 18, 2: 527. 1983. Specimen examined. USA, Illinois, Hannah City, dead leaf of Cannabis sativa, deposited Mar. 1991, J.M. McPartland (holotype HA 10987, ex-type culture ILLS 43621 = CBS 180.91). Notes — Diaporthe ganjae (clade 24) is known only from the original collection taken from wilted, dead leaves of Cannabis sativa in Illinois, USA (McPartland 1983). Phylogenetically D. ganjae is closely related to an isolate identiﬁed as D. mani- hotia (CBS 505.76), isolated from Manihot utilissima in Rwanda (clade 25). Diaporthe gardeniae (Buddin & Wakef.) R.R. Gomes, C. Glienke & Crous, comb. nov. — MycoBank MB802933 Basionym. Phomopsis gardeniae Buddin & Wakef., Gard. Chron., ser. 3 103: 45. 1938. = Phomopsis gardeniae H.N. Hansen & Barrett, Mycologia 30, 1: 18. 1938 (homonym). Specimen examined. itAly, on stem of Gardenia florida, June 1956, M. Ribaldi (CBS 288.56). Notes — Diaporthe gardeniae (clade 59) causes gardenia canker in Gardenia jasminoides, G. lucida and Gardenia sp. (Farr & Rossman 2012). This disease is considered as serious (Tilford 1934, Huber 1936, Miller 1961). It was originally observed in 1894 in England (Cooke 1894), and has since been reported from the USA (Preston 1945) and India (Mathur 1979). All parts of the plant are susceptible to infection, including roots, stems and leaves (McKenzie et al. 1940), although cankered stems are the most diagnostic symptoms for this disease. Diaporthe helianthi Munt.-Cvetk., Mihaljč. & M. Petrov, Nova Hedwigia 34: 433. 1981 = Phomopsis helianthi Munt.-Cvetk., Mihaljč. & M. Petrov, Nova Hedwigia 34: 433. 1981. Specimens examined. serBiA, Vojvodina, overwintering stem on Helianthus annuus, 1980, M. Muntañola-Cvetkovic (ex-type culture CBS 592.81 = CBS H-1540). – unknown, on seed of H. annuus, June 1994, Vanderhave Res., Rilland, Netherlands (CBS 344.94). Notes — Diaporthe helianthi (clade 14) is associated worldwide with stem canker and grey spot disease of sunflower (Helianthus annuus) (Muntañola-Cvetkovic´ et al. 1981). Yield reductions of up to 40 % have been recorded in Europe (Masirevic & Gulya 1992) including the former Yugoslavia as well as France where it was considered a major pathogen of sunflower (Battilani et al. 2003, Debaeke et al. 2003). Diaporthe helianthi is also widespread in the sunflower growing regions of the USA (Gulya et al. 1997). The wide geographic distribution, and high genetic variability of the pathogen lead to the evolution of new strains that could be more aggressive, causing large yield losses and a decline in disease control (Pecchia et al. 2004, Rekab et al. 2004). Diaporthe cf. heveae 1 Specimen examined. BrAzil, São Paulo, from Hevea brasiliensis, Apr. 1997, D.S. Attili (CBS 852.97) (originally identiﬁed as Phomopsis heveae). Notes — Diaporthe heveae and Phomopsis heveae were both described from Hevea in Sri Lanka, and could represent the same species. Two isolates deposited in CBS under this name, CBS 852.97 (from Hevea brasiliensis in Brazil) and CBS 681.84 (from Hevea brasiliensis in India) were shown to represent two distinct species (clades 46 and 80, respectively). However, as both were found to be sterile, their taxonomy could not be resolved. Diaporthe cf. heveae 2 Specimen examined. indiA, Kerala, Kottayam, in leaf on Hevea brasiliensis, Sept. 1984, K. Jayarathnam (CBS 681.84). Notes — Isolate CBS 681.84 (clade 80, P. heveae from Hevea brasiliensis in India) is sterile, and thus its taxonomy could not be resolved. Diaporthe heveae has been reported from Brazil, China, India, Indonesia, Malaysia, Sri Lanka and Thailand (Holliday 1980, Zhuang 2001, Udayanga et al. 2011). R.R. Gomes et al.: Diaporthe 23 Diaporthe hickoriae Wehm., Monogr. Gen. Diaporthe Nitschke & Segreg., Univ. Michigan Stud., Sci. Ser. 9: 149. 1933 Diaporthe hordei (Punith.) R.R. Gomes, C. Glienke & Crous, comb. nov. — MycoBank MB802935 Specimen examined. USA, Michigan, on Carya glabra, June 1926, L.E. Wehmeyer (ex-type culture CBS 145.26). Basionym. Phomopsis hordei Punith., Trans. Brit. Mycol. Soc. 64, 3: 428. 1975. Notes — Diaporthe hickoriae (clade 72) occurs on the bark of Carya glabra in the USA (Wehmeyer 1933). Specimen examined. norwAy, Fellesbygget, As, on root of Hordeum vulgare, Oct. 1992, L. Sundheim (CBS 481.92). Diaporthe hongkongensis R.R. Gomes, C. Glienke & Crous, sp. nov. — MycoBank MB802934; Fig. 10 Notes — Diaporthe hordei (clade 13) was described from Hordeum vulgare in the UK. Although the present culture could be authentic (from Hordeum collected in Norway), it proved to be sterile, so its morphology could not be conﬁrmed. Etymology. Named after the location where it was collected, Hong Kong. Conidiomata pycnidial, superﬁcial to embedded on PDA, solitary to aggregated, globose with central ostiole, exuding a creamy conidial cirrhus; pycnidial up to 200 µm diam; wall of 3–6 layers of brown textura angularis. Conidiophores lining the inner cavity, reduced to conidiogenous cells. Conidiogenous cells phialidic, hyaline, smooth, ampulliform to subcylindrical with prominent apical taper, 5–12 × 2–4 µm; apex with periclinal thickening and minute collarette, 1 µm long. Paraphyses intermingled among conidiophores, hyaline, smooth, frequently branched below, up to 4-septate, with clavate terminal cell, up to 80 µm long, apex 2–8 µm diam. Alpha conidia hyaline, smooth, granular to guttulate, aseptate, fusiform, tapering towards both ends, mostly straight, apex acutely rounded, base truncate, (5–)6–7(–8) × (2–)2.5(–3) µm. Gamma conidia aseptate, hyaline, smooth, ellipsoid-fusoid, apex subobtuse, base truncate, 10–13 × 2 µm. Beta conidia aseptate, hyaline, smooth, spindle-shaped, apex acutely rounded, base truncate, widest in mid region, mostly curved in upper part, 18 –22 × 1.5–2 µm. Culture characteristics — Colonies covering dish after 2 wk in the dark at 25 °C, with moderate aerial mycelium. On OA surface dirty white with patches of pale olivaceous-grey, reverse dirty white with patches of olivaceous-grey and iron-grey. On PDA surface iron-grey, with patches of dirty white, reverse iron-grey. On MEA surface dirty white with patches of olivaceous-grey, reverse iron-grey with patches of dirty white. Specimen examined. hong kong, Tai Po Kau, on fruit of Dichroa febrifuga, 20 Feb. 2002, K.D. Hyde (holotype CBS H-21103, culture ex-type CBS 115448 = HKUCC 9104). Notes — Isolate CBS 115448 (clade 79; reported as Phomopsis pittospori on Dichroa febrifuga from Hong Kong) is morphologically distinct from P. pittospori (from Pittosporum twigs in California; alpha conidia 6–8 × 1.5 µm, beta conidia 18–20 × 1 µm), with wider alpha and beta conidia. Diaporthe impulsa (Cooke & Peck) Sacc., Syll. Fung. (Abellini) 1: 618. 1882 Basionym. Valsa impulsa Cooke & Peck, Ann. Rep. N.Y. State Mus. Nat. Hist. 27: 109. 1875 (1874). Specimens examined. sweden, Uppland, Dalby par., Jerusalem, on Sorbus aucuparia, 24 Oct. 1989, K. & L. Holm (CBS 114434 = UPSC 3052). – unknown, on Sorbus americana, Sept. 1927, L.E. Wehmeyer (CBS 141.27). Notes — Clade 51 is represented by two isolates of D. impulsa occurring on Sorbus spp. Diaporthe impulsa is a known pathogen of Sorbus spp., and has a wide geographic distribution (Farr & Rossman 2012). It was originally described from Sorbus in the USA, thus CBS 141.27 may well prove to be a good reference strain for the species. Diaporthe inconspicua R.R. Gomes, C. Glienke & Crous, sp. nov. — MycoBank MB802936 Etymology. Referring to its inconspicuous nature, growing as endophyte in host tissue. Cultures sterile. Diaporthe inconspicua (clade 75) differs from its closest phylogenetic neighbours, clade 68–74 and 76–78, by unique ﬁxed alleles in four loci based on alignments of the separate loci deposited in TreeBase as study S13943: TUB positions 33 (A), 102–104 and 106–111 (indels), 127 (G), 149 (C), 151 (A), 195 (C), 204 (T), 357 (G), 446 (G), 449 (C), 465 (T), 484 (T), 559 (A), 592 (A), 629 (T), 653 (T), 708 (C), 732 (C), 754 (A), 763 (C), 784 (A) and 787 (G); CAL positions 28 (C), 102 (G), 114 (T), 148 (T), 152 (T), 153 (A), 157 (C), 170 (G), 199 (C) and 281 (C); TEF1 positions 9 (T), 16 (A), 22 (A), 29 (G), 30 (G), 81 (C), 86 (C), 87 (A), 88 (A), 89 (T), 131 (A), 275 (A), 298 (C) and 315 (T); HIS positions 139 (T), 211 (T), 244 (T) and 408 (T). Culture characteristics — Colonies covering the dish after 2 wk in the dark at 25 °C. On OA spreading, flat with sparse aerial mycelium, surface cream in centre, umber in outer region. Fig. 10 Diaporthe hongkongensis (CBS 115448). a, b. Conidiomata sporulating on PDA; c, d. conidiogenous cells; e. beta conidia; f. alpha conidia. — Scale bars = 10 µm. Persoonia – Volume 31, 2013 24 On PDA surface and reverse cream to dirty white with sparse aerial mycelium. On MEA with sparse aerial mycelium, surface becoming folded, dirty white in centre, sienna in outer region, and luteous in reverse. Specimens examined. BrAzil, on petiole of Maytenus ilicifolia, July 2007, R.R. Gomes (holotype CBS H-21102, ex-type culture LGMF 930 = CPC 20306 = CBS 133813); same collection details (LGMF 931 = CPC 20307); on Spondias mombin, 2007, K. Rodriguez (LGMF 922 = CPC 20298). Notes — Sterile endophytic isolates (clade 75) from medicinal plants in Brazil. Diaporthe infecunda R.R. Gomes, C. Glienke & Crous, sp. nov. — MycoBank MB802937 Diaporthe longispora (Wehm.) R.R. Gomes, C. Glienke & Crous, comb. nov. — MycoBank MB802938 Basionym. Diaporthe strumella var. longispora Wehm., Mycologia 28, 1: 46. 1936. Specimen examined. CAnAdA, Ontario, Toronto, on Ribes sp., May 1936, L.E. Wehmeyer (ex-type culture CBS 194.36). Notes — Clade 27 comprises the ex-type culture of D. strumella var. longispora isolated from Ribes sp., and forms a sister clade with D. sclerotioides (clade 28). Diaporthe strumella is found on woody limbs, especially of Ribes spp. in temperate North America and Europe (Farr & Rossman 2012). As D. strumella var. longispora is morphologically clearly a distinct species, we elevate this variety to species status. Etymology. Named after its sterile growth in culture. Cultures sterile. Diaporthe infecunda (clade 23) differs from its closest phylogenetic neighbours, clade 16–22, by unique ﬁxed alleles in ﬁve loci based on alignments of the separate loci deposited in TreeBase as study S13943: ITS positions 108 (T), 279 (C), 292 (G), 359 (C) and 360 (G); TUB positions 11 (indel), 106 (G), 138 (T), 140 (A), 153 (G), 155 (T), 184 (A), 197 (G), 202 (C), 302 (A), 354 (A), 369–374 (indels), 398 (G), 407 (indel), 414 (C), 422 (T), 424 (G), 425 (C), 432 (G), 452 (C), 454 (C), 458 (C), 461 (G), 479 (T), 482 (T), 486 (C), 540 (T), 572 (C), 622 (A), 694 (T), 696 (T), 697 (G), 716 (C), 728 (C), 776 (G), 778 (G) and 796 (C); CAL positions 64 (T), 83 (T), 104 (G), 146 (C), 151 (C), 155 (G), 159 (C), 172 (C), 176 (T), 179 (A), 184 (G), 197 (T), 206 (T), 212 (C) and 221 (T); TEF1 positions 6 (A), 9 (G), 13 (G), 16 (C), 21 (A), 30 (G), 32 (indel), 39 (A), 40 (A), 41 (G), 42 (T), 43 (A), 79 (G), 83 (T), 90 (T), 92 (T), 96 (A), 97 (C), 106 (C), 116 (A), 120 (C), 123 (A), 127 (A), 132 (A), 135 (G), 173 (G), 255 (T), 284 (A), 294 (C), 299 (C) and 309 (A); HIS positions 173 (T), 196 (T), 197 (G), 199 (C/T), 221 (C), 222 (C), 230 (G), 263 (C), 264 (T), 268 (C), 273 (T) and 279 (C). Culture characteristics — Colonies covering the dish after 2 wk in the dark at 25 °C. On PDA surface umber with patches of white, reverse chestnut. On MEA surface dirty white, reverse umber. On OA surface with patches of dirty white and umber. Specimens examined. BrAzil, on leaf of Schinus terebinthifolius, July 2007, J. Lima (holotype CBS H-21095, ex-type culture LGMF 906 = CPC 20282 = CBS 133812); additional isolates with same collection details (LGMF 908 = CPC 20284, LGMF 912 = CPC 20288, LGMF 917 = CPC 20293, LGMF 918 = CPC 20294, LGMF 920 = CPC 20296); in petiole of Maytenus ilicifolia, July 2007, R.R. Gomes (LGMF 933 = CPC 20309, LGMF 940 = CPC 20316). Notes — Clade 23 represents endophytic isolates from leaves of medicinal plants growing in Brazil. It consists of eight isolates, two from Maytenus ilicifolia, and six from Schinus terebinthifolius. Diaporthe juglandina (Fuckel) Nitschke, Pyrenomycetes Germanici 2: 281. 1870 Basionym. Aglaospora juglandina Fuckel, Fungi Rhenani Exsicc., suppl. 7 (no. 2101–2200): no. 2159. 1868. Specimen examined. USA, Tennessee, Great Smoky Mts National Park, dead wood of Juglans sp., L. Vasilyeva (CBS 121004). Notes — Diaporthe juglandina (clade 65) represents a European taxon described from Juglans. European collections are required to conﬁrm whether this name can be applied to the clade. Diaporthe lusitanicae A.J.L. Phillips & J.M. Santos, Fung. Diversity 34: 118. 2009 Specimen examined. PortugAl, Lisbon, Oeiras, Estação Agronómica Nacional, stem of Foeniculum vulgare, 14 Aug. 2007, J.M. Santos (ex-type cultures CBS 123212 = Di-C001/5, CBS 123213 = Di-C001/3). Notes — This species (clade 21) was described in 2009 on senescent stems of Foeniculum vulgare (wild fennel) in Portugal by Santos & Phillips (2009). Diaporthe manihotia Punith., Kavaka 3: 29. 1976 (1975) = Phomopsis manihotis Swarup, L.S. Chauhan & Tripathi, Mycopathol. Mycol. Appl. 28, 4: 345. 1966. Specimen examined. rwAndA, on leaves of Manihot utilissima, 9 July 1976, J. Semal (CBS 505.76). Notes — Phomopsis manihotis (clade 25 as D. manihotia) causes leaf spot of cassava (Manihot esculenta), though the disease is also referred to as Phomopsis blight of tapioca. Severe infection leads to defoliation and stem lesions. Affected areas become shrivelled with numerous pycnidia embedded in the tissue. On severely infected stems the bark starts to gradually peel off, leading to partial or total girdling. The disease is known from Africa (Ethiopia, Nigeria), Asia (India), Central America and West Indies (S.E. Dominica), and South America (Colombia) (Sarbhoy et al. 1971, Mathur 1979, Farr & Rossman 2012). Diaporthe mayteni R.R. Gomes, C. Glienke & Crous, sp. nov. — MycoBank MB802939; Fig. 11 Etymology. Named after the host genus from which it was collected, Maytenus. Conidiomata pycnidial, globose, immersed, scattered and aggregated, brown to black, ostiolate, 70–230 μm wide, 40–150 μm tall, with short necks, 40–140 μm; outer surface smooth or covered in hyphae; pycnidal wall consisting of brown, thick-walled cells of textura angularis; conidial mass globose or exuding in cirrhi; predominantly yellow, pale luteous to cream. Conidiophores hyaline, subcylindrical to cylindrical, rarely branched above the septa, tapering towards the apex, 1–3-septate, (10–)13–27(–36) × (2–)3(–4) μm. Conidiogenous cells hyaline, subcylindrical, rarely tapering towards the apex, collarette present and not flared, with prominent periclinal thickening, (5–)6–10(–13) × 2(–3) μm. Alpha conidia hyaline, oblong to ellipsoid, apex bluntly rounded, base obtuse; biguttulate, (5–)6(–7) × (2–)3 μm. Beta and gamma conidia absent. Culture characteristics — Colonies on PDA flat, with entire edge, cottony, olivaceous buff, with primrose aerial mycelium in concentric rings, with olivaceous patches; colonies reaching 66 mm diam after 2 wk at 25 °C; reverse olivaceous buff and greenish olivaceous. On OA flat, with entire edge, cottony 25 R.R. Gomes et al.: Diaporthe Fig. 11 Diaporthe mayteni (CBS 133185). a. Conidiomata sporulating on PNA; b, c. transverse section through conidiomata, showing conidiomatal wall; d, e. conidiogenous cells; f. beta conidia; g. alpha conidia. — Scale bars: b = 85 µm, all others = 10 µm. appressed, buff, white, the center of the colony pale olivaceousgrey, patches isabelline and luteous; colonies reaching 56 mm diam; reverse buff and pale olivaceous grey. On MEA flat, with entire edge, aerial mycelium cottony, white to pale olivaceous grey or olivaceous buff; colonies reaching 37 mm diam; reverse hazel, ochreous, with patches greenish black and olivaceous black. Specimen examined. BrAzil, Paraná, Colombo, endophytic species isolated from petiole of Maytenus ilicifolia (popular name Espinheira Santa), July 2007, R.R. Gomes (holotype CBS H-21096, ex-type culture CBS 133185 = LGMF 938 = CPC 20314). Notes — Diaporthe mayteni (clade 30) grows endophytically in Maytenus ilicifolia in Brazil. cucumbers (McKeen 1957, Punithalingam & Holliday 1975, Ohsawa & Kobayashi 1989). Diaporthe musigena Crous & R.G. Shivas, Persoonia 26: 119. 2011 Specimen examined. AustrAliA, Queensland, Brisbane Botanical Garden, on leaves of Musa sp., 14 July 2009, P.W. Crous & R.G. Shivas (ex-type culture CBS 129519 = CPC 17026). Notes — Clade 84 represents D. musigena, isolated from Musa sp. in Australia (Crous et al. 2011). Diaporthe neilliae Peck, Ann. Rep. N.Y. State Mus. Nat. Hist. 39: 52. 1887 (1886) Diaporthe megalospora Ellis & Everh., Proc. Acad. Nat. Sci. Philadelphia 42: 235. 1890 Specimen examined. unknown, on Spiraea sp., Sep. 1927, L.E. Wehmeyer (CBS 144.27). Specimen examined. unknown, from Sambucus canadensis, Sept. 1927, L.E. Wehmeyer (CBS 143.27). Notes — Diaporthe neilliae (clade 60) was originally described from Spiraea sp. from North America. The origin of the present isolate, however, remains unclear (presumably North America). Notes — Diaporthe megalospora (clade 15) is known on Sambucus canadensis from North America (Wehmeyer 1933, Hanlin 1963, Farr & Rossman 2012). Fresh collections are required to designate an epitype, and ﬁx the genetic application of the name. Diaporthe melonis Beraha & M.J. O’Brien, Phytopathol. Z. 94, 3: 205. 1979 = Phomopsis cucurbitae McKeen, Canad. J. Bot. 35: 46. 1957. Specimens examined. indonesiA, Java, Muneng, Exp. Station, on Glycine soja, Sept. 1987, H. Vermeulen (CBS 435.87). – USA, Texas, Rio Grande Valley, on Cucumis melo, 1978, L. Beraha & M.J. O’Brien (ex-isotype culture CBS 507.78, specimen derived from culture CBS H-891). Notes — Clade 7 represents D. melonis (Beraha & O’Brien 1979), and contains the ex-isotype culture, and one isolate previously identiﬁed as D. phaseolorum var. sojae (though the two isolates are not identical). Diaporthe melonis is frequently reported on soybean (Santos et al. 2011). Phomopsis cucurbitae (treated here as synonym) is reported to have a cosmopolitan distribution, and to cause black rot disease of greenhouse Diaporthe neoarctii R.R. Gomes, C. Glienke & Crous, sp. nov. — MycoBank MB802940, Fig. 12 Etymology. Named after its superﬁcial resemblance to Diaporthe arctii. Conidiomata pycnidial, ampulliform to ﬁnger-like, aggregated, dark brown to black, immersed, ostiolate, 300–450 μm wide, 200 – 670 μm tall, with prominent necks 240 – 560 μm long, outer surface covered with hyphae; pycnidal wall consisting of brown, thick-walled cells of textura angularis; conidial mass globose, pale yellow. Conidiophores hyaline, ampulliform to subcylindrical, ﬁliform, branched above the septa, tapering towards the apex, rarely septate, (12–)13–17(–18) × (2–)3 μm. Conidiogenous cells hyaline, subcylindrical, ﬁliform, straight, tapering towards the apex, collarette flared, periclinal thickening prominent, (10–)11–13(–14) × (1.5–)2(–3) μm. Alpha conidia hyaline, fusoid, apex acute, base obtusely rounded to subtruncate, bi- to multi-guttulate, (9–)11–13(–14) × 3(–4) μm. Beta and gamma conidia not observed. 26 Persoonia – Volume 31, 2013 Fig. 12 Diaporthe neoarctii (CBS 109490). a. Conidiomata sporulating on PDA; b, c. transverse section through conidiomata, showing conidiomatal wall; d–f. conidiogenous cells; g. alpha conidia. — Scale bars: b = 225 µm, all others = 10 µm. Culture characteristics — Colonies with sparse aerial mycelium, covering the dish after 2 wk in the dark at 25 °C. On MEA umber with patches of greyish sepia, umber in reverse. On PDA fuscous-black on surface and in reverse. Specimen examined. USA, New Jersey, isolated from Ambrosia trifida, May 2001, G. Bills (holotype CBS H-21094, ex-type culture CBS 109490 = GB 6421 = AR 3450). Notes — Isolates originally identiﬁed as D. arctii cluster in clades 19 and 67 (Fig. 1). Diaporthe neoarctii (clade 16) was isolated from Ambrosia trifida in New Jersey, USA, and differs morphologically from the ex-type culture of D. arctii (alpha conidia 7 × 3–3.5 µm) (clade 19). Based on these differences D. neoarctii is described as a novel species. Diaporthe nobilis complex Specimens examined. germAny, Münster, on stem of Laurus nobilis, Feb. 1939, Kotthoff (CBS 200.39). – JAPAn, isolate from Pinus pentaphylla bonzai plant imported from Japan into the Netherlands, May 1979, G.H. Boerema (CBS H-16732, culture CBS 587.79). – koreA, on imported chestnuts (Castanea sativa), collected in grocery store in Sydney, Australia, 5 July 1999, K.A. Seifert (CBS 113470 = DAOM 226800). – lAtviA, Rhododendron sp., I. Apine (CBS 129167). – new zeAlAnd, on bark of Malus pumila, G.J. Samuels (CBS 124030 = GJS 77-49); Waikato region, on Pyrus pyrifolia, 2001, isol. W. Kandula, det. L. Castlebury (CBS 116953 = NZ-26, CBS 116954 = NZ-27). – yugoslAviA, on Hedera helix, July 1989, M. Muntañola-Cvetkovic (CBS 338.89). Notes — Clade 62 is poorly resolved in this dataset, but has some internal structure, suggesting that it contains several potentially distinct species. More isolates would be required to resolve their taxonomy. Isolates in this clade were originally identiﬁed as Phomopsis fukushii (on Pyrus pyrifolia, New Zealand), P. conorum (on Pinus pentaphylla, the Netherlands), P. castanea (on Castanea sativa, UK), Diaporthe perniciosa (Malus pumila, New Zealand), D. pulla (on Hedera helix, Yugoslavia) and D. nobilis (on Laurus nobilis, Germany). Diaporthe nomurai Hara, in Hara, Diseases of cultivated plants: 140. 1925. — Fig. 13 Conidiomata in culture on OA sporulating poorly, globose, up to 300 µm diam, black, erumpent; cream conidial droplets exuding from central ostioles; walls consisting of 3–6 layers of medium brown textura angularis. Conidiophores hyaline, smooth, 0–1septate, rarely branched, densely aggregated, cylindrical, straight to sinuous, 10 – 20 × 2 – 3 µm. Conidiogenous cells 6 –10 × 1.5–3 µm, phialidic, cylindrical, terminal, with slight taper towards apex, 1–1.5 µm diam, with visible periclinal thickening; collarette not flared, minute. Paraphyses not observed. Alpha conidia aseptate, hyaline, smooth, guttulate, fusoid-ellipsoid to clavate, straight to variously curved, tapering towards both ends, straight, apex subobtuse, base truncate, (7–)9–11(–13) × (2.5–)3 µm. Gamma conidia not observed. Beta conidia spindle- Fig. 13 Diaporthe nomurai (CBS 157.29). a. Conidiomata sporulating on PDA; b–e. conidiogenous cells; f. alpha conidia; g. beta conidia. — Scale bars = 10 µm. R.R. Gomes et al.: Diaporthe shaped, aseptate, smooth, hyaline, apex acutely rounded, base truncate, tapering from lower third towards apex, gently curved, (20–)25–27(–30) × 1.5(–2) µm. Culture characteristics — Colonies reaching up to 8 cm diam after 2 wk in the dark at 25 °C. On MEA surface isabelline, reverse sepia. On OA surface pale mouse grey with concentric rings of mouse grey; reverse mouse grey. On PDA surface and reverse fuscous-black, with sparse aerial mycelium. Specimen examined. JAPAn, on Morus sp., Dec. 1929, K. Togashi (CBS 157.29). Notes — Clade 58 represents D. nomurai from Morus sp. in Japan. Diaporthe nomurai is known from hosts such as Morus alba, M. bombycis, M. latifolia and Morus sp. (Farr & Rossman 2012). Diaporthe novem J.M. Santos, Vrandečić & A.J.L. Phillips, Persoonia 27: 14. 2011 = Phomopsis sp. 9 van Rensburg et al., Stud. Mycol. 55: 65. 2006. Specimens examined. BrAzil, endophytic in petiole on Maytenus ilicifolia, July 2007, R.R. Gomes (LGMF 943 = CPC 20319). – CroAtiA, Slavonija, in seed on Glycine max, Sept. 2008, T. Duvnjak (holotype CBS H-20462, ex-type cultures CBS 127270 = 4-27/3-1, CBS 127271 = 5/27/3-3, CBS 127269 = 5-27/3-1). – romAniA, Calugareni, Distr. Mizil, living leaves on Polygonatum odoratum, 31 July 1970, O. Constantinescu (CBS 354.71). Notes — Clade 22 represents D. novem (Santos et al. 2011), and contains an endophytic isolate (LGMF 43) from Maytenus ilicifolia, one isolate previously identiﬁed as Diaporthe pardalota on Polygonatum odoratum from Romania, and three isolates of D. novem which includes the ex-type isolate. Isolate LGMF 943 represents higher genetic variation than the other isolates, and appears to represent a different species. Since this isolate did not sporulate, further morphological characterisation was not possible and we refrain from excluding it from the species pending collection of more strains to clarify its status. Diaporthe novem was reported as pathogen of Aspalathus linearis (van Rensburg et al. 2006) as Phomopsis sp. 9. It was recently described as pathogen of Glycine max (Santos et al. 2011). This species was also reported on Hydrangea macrophylla (Santos et al. 2010), Helianthus annuus and Vitis vinifera 27 (Santos et al. 2011). It is known to occur in Brazil, Romania, Croatia, Italy (Rekab et al. 2004), Portugal (Santos et al. 2010) and South Africa (van Niekerk et al. 2005, van Rensburg et al. 2006). Diaporthe oncostoma (Duby) Fuckel, Jahrb. Nassauischen Vereins Naturk. 23–24: 205. 1870. (1869–1870). — Fig. 14 Basionym. Sphaeria oncostoma Duby, in Rabenh., Klotzsch. Herb. Vivum Mycol.: no. 253. 1854. Conidiomata pycnidial, globose to ellipsoidal, aggregated as well as scattered, dark brown to black, immersed, ostiolate, 430–1170 μm wide, 370–790 μm tall, lacking necks, with outer surface covered in brown hyphae; pycnidal wall consisting of brown, thick-walled cells of textura angularis; conidial mass globose or exuding in cirrhi, white to pale luteous or pale yellow. Conidiophores hyaline, subcylindrical, branched above the septa, tapering towards the apex, 1–2-septate, (10–)11–19(–22) × 3(–4) μm. Conidiogenous cells hyaline, subcylindrical, straight or curved, tapering towards the apex, collarette not flared, periclinal thickening prominent, (6 –)7– 9(–10) × (2 –)3 μm. Alpha conidia hyaline, fusoid to ellipsoidal, straight to slightly curved, acute at apex, subobtuse at base, bi- or multi-guttulate, (7.5 –)9 –11(–12) × (2 –)3(– 4) μm. Gamma conidia hyaline, smooth, ellipsoid-fusoid, apex acutely rounded, and tapering towards truncate base, (11–)12–16 × 3(–3.5) µm. Beta conidia and sexual morph not observed in culture. Culture characteristics — Colonies covering dish after 2 wk in the dark at 25 °C. On MEA surface dirty white with profuse aerial mycelium, reverse umber. On OA surface dirty white with patches of umber, same in reverse. On PDA surface and reverse sienna, with sparse aerial mycelium. Specimens examined. frAnCe, Hte Savoie, Aigueblanche-Bellecombe, outlet of river Morel in Isère, on dead branches of Robinia pseudoacacia, 17 July 1978, H.A. van der Aa (CBS 589.78). – germAny, Wolfenbüttel, on leaf spot of Robinia pseudoacacia, 15 Nov. 1996, H. Butin (CBS 100454); Berlin, on leaf of Ilex aquifolium, Nov. 1985, M. Hesse (CBS 809.85). – russiA, on Robinia pseudoacacia, June 2000, L. Vasilyeva (CBS 109741 = AR 3445). Notes — Diaporthe oncostoma (clade 70) has been considered to be a saprobic, or low virulence pathogen, which plays some role in natural pruning and self-thinning of black locust Fig. 14 Diaporthe oncostoma (CBS 100454). a. Conidiomata sporulating on OA; b, c. transverse section through conidiomata, showing conidiomatal wall; d–f. conidiogenous cells; g. alpha conidia. — Scale bars: b = 225 µm, all others = 10 µm. 28 forests (Robinia pseudoacacia) (Vajna 2002). However, this fungus has been reported as a causal agent of canker and severe dieback disease of black locust in Russia (ScerbinParfenenko 1953) and in Greece (Michalopoulos-Skarmoutsos & Skarmoutsos 1999). Although isolate CBS 809.85 was obtained from Ilex aquifolium in Germany, we treat it as belonging to D. oncostoma, as it matches the other strains phylogenetically as well as morphologically. Diaporthe oxe R.R. Gomes, C. Glienke & Crous, sp. nov. — MycoBank MB802941; Fig. 15 Etymology. The word ‘oxe’ is an expression used in northeastern Brazil that means amazement or surprise, in relation to the number of novel species isolated as endophytes from medicinal plants in Brazil. Conidiomata pycnidial ampulliform to ﬁnger-like, eustromatic, convoluted to unilocular, semi-immersed, scattered, dark brown to black, ostiolate, 60–170 μm wide, 60–220 μm tall; necks variable in length, 20 –150 μm, outer surface covered with hyphae; pycnidal wall consisting of brown, thick-walled cells of textura angularis; conidial mass globose or exuding in cirrhi, pale-luteous to cream or pale-yellow. Conidiophores hyaline, ampulliform to subcylindrical, branched above the septa, tapering towards the apex, 1–2-septate, (14–)17– 25(–27) × (2–)3 μm. Conidiogenous cells hyaline, subcylindrical, ﬁliform, straight to curved, tapering towards the apex, collarette flared, periclinal thickening prominent, (5 –)6–10(–12) × 2(– 3) μm. Alpha conidia hyaline, oblong to ellipsoid, apex bluntly rounded, base obtuse to subtruncate, bi- to multi-guttulate, (5–)6–7(–8) × (2–)3 μm. Beta conidia hyaline, smooth, curved or hamate, (17–)22–30(–33) × 2–3 μm. Gamma conidia not observed. Culture characteristics — Colonies on PDA flat, with an entire edge, surface mycelium dense and felty, ochreous to fulvous, dark brick, honey, buff, exudates rarely present as colourless drops; colonies reaching 49 mm diam after 2 wk at 25 °C; reverse umber, ochreous to fulvous. On OA flat, with an entire edge, surface mycelium dense and felty, rosy buff, pale olivaceous-grey, iron-grey, with patches olivaceous buff, exudates in colourless and pale luteous drops; colonies reaching 40 mm diam; reverse dark brick, olivaceous. On MEA raised, with an entire edge, surface mycelium dense and felty, buff, Persoonia – Volume 31, 2013 rosy-buff, with chestnut coloured exudates in the centre of the colony, and pale luteous at the periphery; colonies reaching 49 mm diam; reverse chestnut and bay. Specimens examined. BrAzil, on petiole of Maytenus ilicifolia, July 2007, R.R. Gomes (holotype CBS H-21098, ex-type culture CBS 133186 = LGMF 942 = CPC 20318); same collection details (CBS 133187 = LGMF 936 = CPC 20312); on leaf of Schinus terebinthifolius, July 2007, J. Lima (LGMF 915 = CPC 20291); on petiole of M. ilicifolia, S.A.V. Pileggi (LGMF 939 = CPC 20315); on petiole of M. ilicifolia, July 2007, R.R. Gomes (LGMF 945 = CPC 20321). Notes — Endophytic isolates (clade 34) from medicinal plants in Brazil. Diaporthe padi var. padi G.H. Otth, Mitth. Naturf. Ges. Bern: 99. 1871 (1870) Specimens examined. sweden, Uppland, Dalby par., Tuna, on Prunus padus, 17 Apr. 1988, K. & L. Holm (CBS 114200 = UPSC 2569); Dalarna, Folkärna par., Sonnbo, on Alnus glutinosa, Dec. 1992, K. & L. Holm (CBS 114649 = UPSC 3496). Notes — Diaporthe padi var. padi (clade 56) represents a European taxon occurring on Prunus. We chose the name D. padi over D. decorticans, as the basionym of the latter, Sphaeria decorticans, is an illegitimate homonym. Diaporthe paranensis R.R. Gomes, C. Glienke & Crous, sp. nov. — MycoBank MB802942, Fig. 16 Etymology. Named after Paraná, the state in Brazil from where it was collected. Conidiomata pycnidial, ampulliform, semi-immersed, scattered, brown to black, ostiolate, 130–220 μm wide, 60–130 μm tall; prominent necks 50–210 μm long, outer surface smooth or covered in hyphae; pycnidal wall consisting of brown, thickwalled cells of textura angularis; conidial mass globose, predominantly pale-luteous to yellow and some cases greenolivaceous. Conidiophores hyaline, subcylindrical to cylindrical, ﬁliform, branched above the septa on a globose cell, not tapering towards the apex, 2–3-septate, (14–)15–22(–26) × (2 –)3(– 4) μm. Conidiogenous cells hyaline, subcylindrical, ﬁliform, rarely tapering towards the apex, collarette present and flared, slight periclinal thickening, (5–)8–14(–15) × 2(–3) μm. Fig. 15 Diaporthe oxe (CBS 133186). a. Conidiomata sporulating on PDA; b, c. transverse section through conidiomata, showing conidiomatal wall; d, e. conidiogenous cells; f. beta conidia; g. alpha conidia. — Scale bars: b = 100 µm, all others = 10 µm. 29 R.R. Gomes et al.: Diaporthe Fig. 16 Diaporthe paranensis (CBS 133184). a. Conidiomata sporulating on PDA; b, c. transverse section through conidiomata, showing conidiomatal wall; d, e. conidiogenous cells; f. alpha and beta conidia. — Scale bars: b = 100 µm, all others = 10 µm. Alpha conidia hyaline, fusoid-ellipsoidal, apex bluntly rounded, base obtuse to subtruncate, bi- to multi-guttulate, (6–)7–8(–9) × (2–)3 μm. Beta conidia hyaline, smooth, curved or hamate and slightly curved, (16 –)17– 21(– 23) × (1–)2 μm. Gamma conidia not observed. Culture characteristics — Colonies on PDA flat, with an entire edge, mycelium growing in concentric rings, cottony texture, white to smoke-grey; colonies reaching up to 64 mm diam after 2 wk at 25 °C; reverse buff and isabelline. On OA flat, with an entire edge, aerial mycelium in concentric rings, ranging in colour from smoke-grey to grey-olivaceous and white in the centre; colonies reaching 44 mm diam; reverse irongrey, grey-olivaceous to olivaceous-buff. On MEA flat, with an entire edge, aerial mycelium growing in concentric rings, with cottony texture, pale olivaceous-grey to grey-olivaceous and buff; colonies reaching 56 mm diam; reverse umber, fulvous with patches of greenish black. Specimen examined. BrAzil, Paraná, Colombo, endophytic species isolated from petiole of Maytenus ilicifolia (popular name Espinheira Santa), July 2007, R.R. Gomes (holotype CBS H-21099, ex-type culture CBS 133184 = LGMF 929 = CPC 20305). Notes — Endophytic isolate (clade 35) from medicinal plant in Brazil. Diaporthe perjuncta Niessl, Hedwigia 15: 153. 1876 Specimen examined. AustriA, from Ulmus glabra, Oct. 2001, A.Y. Rossman (ex-epitype culture CBS 109745 = ARSEF 3461 = AR 3461). Notes — Diaporthe perjuncta (clade 40) is associated with fallen branches of Ulmus campestris and U. glabra (Ulmaceae). This species is found in Austria, Germany and Portugal. Diaporthe perjuncta is distinguished from D. viticola and D. australafricana based on morphology and DNA sequence data (van Niekerk et al. 2005). Pathogenicity studies and endophytic isolation of ‘D. perjuncta’ from grapevines in Australia and South Africa in fact represent isolates of D. australafricana (Mostert et al. 2001a, Rawnsley et al. 2004, van Niekerk et al. 2005). Diaporthe perseae (Zerova) R.R. Gomes, C. Glienke & Crous, comb. nov. — MycoBank MB802944; Fig. 17 Basionym. Phomopsis perseae Zerova, J. Bot. Acad. Sci. RSS Ukraine 1, 1–2: 307. 1940. Conidiomata pycnidial in culture on MEA, globose, up to 400 µm diam, black, erumpent; cream conidial droplets exuding from central ostioles; walls consisting of 3–6 layers of medium brown textura angularis. Conidiophores hyaline, smooth, 1–3-septate, branched, densely aggregated, cylindrical, straight to sinuous, 15–35 × 3–4 µm. Conidiogenous cells 8–17 × 1.5–2.5 µm, Fig. 17 Diaporthe perseae (CBS 151.73). a. Conidiomata sporulating on PDA; b–d. conidiogenous cells; e. alpha and beta conidia. — Scale bars = 10 µm. 30 phialidic, cylindrical, terminal and lateral, with slight taper towards apex, 1–1.5 µm diam, with visible periclinal thickening; collarette prominent, up to 5 µm long. Paraphyses hyaline, smooth, subcylindrical with obtuse ends, 2–4-septate, up to 60 µm long, 3 µm diam. Alpha conidia aseptate, hyaline, smooth, guttulate, fusoid to ellipsoid, tapering towards both ends, straight, apex subobtuse, base subtruncate, (6 –)7– 8(– 9) × 2(– 2.5) µm. Gamma conidia aseptate, hyaline, smooth, ellipsoid-fusoid, apex acutely rounded, base subtruncate, 9–14 × 1.5–2 µm. Beta conidia spindle-shaped, aseptate, smooth, hyaline, apex acutely rounded, base truncate, tapering from lower third towards apex, curved, (15 –)22–25(–28) × 1.5(–2) µm. Culture characteristics — Colonies covering dish after 2 wk in the dark at 25 °C, with moderate aerial mycelium. On OA surface ochreous, with patches of dirty white and iron-grey. On PDA surface dirty white with patches of sienna, reverse sienna with patches of umber. On MEA surface sienna, with patches of umber, reverse umber with patches of sienna. Specimen examined. netherlAnds Antilles, Martinique, on young fruit of Persea gratissima, 10 July 1972, E. Laville (CBS 151.73). Notes — Diaporthe perseae (clade 86) was originally described from branches of dying Persea gratissima trees in Russia. Based on the morphology (alpha conidia 7–10.2 × 2.3–2.5 µm; Uecker 1988), this strain could be authentic for the name. Diaporthe phaseolorum (Cooke & Ellis) Sacc., Syll. Fung. 1: 692. 1882 Basionym. Sphaeria phaseolorum Cooke & Ellis, Grevillea 6, 39: 93. 1878. Specimens examined. BrAzil, endophytic in petiole on Maytenus ilicifolia, July 2007, R.R. Gomes (LGMF 927 = CPC 20303, LGMF 941 = CPC 20317). – new zeAlAnd, from Olearia cf. rani, 22 Jan. 2003, G.J.M. Verkley (CBS 113425); Actinidia chinensis, rotting fruit, kiwifruit orchard, S.R. Pennycook (CBS 127465 = GJS 83-379). – unknown, Apr. 1980, L. Beraha (CBS 257.80). – USA, Mississippi, from Caperonia palustris, Oct. 2003, A. Mengistu (CBS 116019); Mississippi, from Aster exilis, Oct. 2003, A. Mengistu (CBS 116020). Notes — Clade 4 represents isolates of D. phaseolorum. It includes two endophytic isolates from Maytenus ilicifolia collected in Brazil, one isolate previously misidentiﬁed as D. melonis (CBS 257.80), two isolates respectively from Caperonia palustres and Aster exilis in the USA (Mengistu et al. 2007), one isolate from Olearia cf. rami, and one from Actinidia chinensis. The ITS and TEF1 sequences of this clade are similar to sequences (GenBank U11323, U11373 and EU222020, respectively) of a well-characterised isolate of D. phaseolorum (ATCC 64802 = FAU458). By accepting this clade as authentic for Persoonia – Volume 31, 2013 D. phaseolorum, we follow the precedent set by van Rensburg et al. (2006), Mengistu et al. (2007) and Santos et al. (2011). Diaporthe pseudomangiferae R.R. Gomes, C. Glienke & Crous, sp. nov. — MycoBank MB802945; Fig. 18 Etymology. Named after its morphological similarity to Phomopsis mangiferae. Conidiomata pycnidial, erumpent to superﬁcial on PDA, globose, up to 300 µm diam with elongated necks with central ostioles that exude yellow-orange to cream conidial droplets; walls of 6–8 layers of brown textura angularis. Conidiophores hyaline, smooth, 1–3-septate, branched, densely aggregated, cylindrical, straight to sinuous, 20–30 × 2–2.5 µm. Conidiogenous cells phialidic, cylindrical, terminal and lateral with slight apical taper, 10–15 × 2–3 µm; collarette flared, up to 3 µm long. Paraphyses hyaline, smooth, cylindrical, septate, extending above conidiophores, straight to flexuous, unbranched or branched below, up to 80 µm long, 2–3 µm wide at base. Alpha conidia aseptate, hyaline, smooth, guttulate to granular, fusiform, tapering towards both ends, apex acutely rounded, base truncate, (6–)7–9(–10) × (2–)2.5(–3) µm. Beta and gamma conidia not seen (description based on CBS 101339). Culture characteristics — Colonies covering dish after 2 wk in the dark at 25 °C, with moderate aerial mycelium. On OA surface and reverse dirty white with patches of iron-grey. On PDA surface dirty white to ochreous, reverse umber. On MEA surface greyish sepia with patches of iron-grey, reverse greyish sepia with patches of iron-grey. Specimens examined. dominiCAn rePuBliC, from Mangifera indica, P. de Leeuw, ATO-DLO, Wageningen (holotype CBS H-21105, culture ex-type CBS 101339). – mexiCo, on fruit peel of Mangifera indica (CBS 388.89). Notes — Although these isolates (clade 82) were originally described as representative of P. magiferae (dead leaves of Mangifera indica, Pakistan), they differ in having larger conidiomata, longer conidiophores and larger alpha conidia. Diaporthe pseudophoenicicola R.R. Gomes, C. Glienke & Crous, sp. nov. —MycoBank MB803839; Fig. 19 Etymology. Named after its morphological similarity to Diaporthe phoenicicola. Conidiomata pycnidial on MEA, up to 400 µm diam, erumpent, globose with neck; ostiole exuding yellow-orange conidial droplets; walls consisting of 3–6 layers of medium brown textura angularis. Conidiophores hyaline, smooth, densely aggregated, 1–3-septate, branched, cylindrical, straight to curved, 12–45 × 1.5–3 µm. Conidiogenous cells phialidic, cylindrical, terminal Fig. 18 Diaporthe pseudomangiferae (CBS 101339). a. Conidiomata sporulating on PNA; b. conidiomata sporulating on PDA; c, d. conidiogenous cells; e. beta conidia; f. alpha conidia. — Scale bars = 10 µm. R.R. Gomes et al.: Diaporthe 31 Fig. 19 Diaporthe pseudophoenicicola (CBS 462.69). a, b. Conidiomata sporulating on PDA; c, d. conidiogenous cells; e. alpha conidia. — Scale bars = 10 µm. and lateral with slight apical taper, 12 –20 × 1.5–2 µm, with visible periclinal thickening; collarette flared, 2 – 5 µm long. Paraphyses hyaline, smooth, cylindrical, 1–3-septate, extending above conidiophores, straight to flexuous, unbranched or branched, up to 100 µm long, and 3 µm wide at base. Alpha conidia aseptate, hyaline, granular, smooth, fusiform, tapering towards both ends, straight, acutely rounded apex, and truncate base, (6–)7–8(–9) × (2–)2.5(–3) µm. Beta and gamma conidia not seen (description based on CBS 462.69). Culture characteristics — Colonies covering dish after 2 wk in the dark at 25 °C, with sparse aerial mycelium. On MEA surface dirty white with patches of sienna, reverse umber with patches of sienna. On OA surface dirty white with patches of sienna. On PDA surface ochreous with patches of olivaceousgrey, reverse iron-grey with patches of ochreous. Specimens examined. irAq, Prov. Basrah, Shalt El Arab, showing dieback on Mangifera indica, 1976, M.S.A. Al-Momen (CBS 176.77). – sPAin, Mallorca, Can Pastilla, dead tops of green leaves on Phoenix dactylifera, 27 May 1969, H.A. van der Aa (holotype CBS H-21106, culture ex-type CBS 462.69). Notes — Diaporthe pseudophoenicicola (clade 89) is distinct from D. phoenicicola (conidia 8–12 × 2–2.5 µm; Uecker 1988) by having shorter, and wider alpha conidia. A similar strain was isolated from Mangifera indica in Iraq (CBS 176.77), suggesting that this species has a wider host range. Diaporthe pustulata Sacc., Syll. Fung. (Abellini) 1: 610. 1882 Specimens examined. AustriA, on Acer pseudoplatanus, Oct. 2001, A.Y. Rossman (CBS 109742 = AR 3430 and CBS 109760 = AR 3535); Raab, Au Wald, on Prunus padus, Oct. 2001, A.Y. Rossman (CBS 109784 = AR 3419). Notes — Clade 44 contains one isolate from Prunus padus and two isolates from Acer pseudoplatanus, all isolated from Austria. Clade 56 contains another isolate on Prunus padus from Sweden. Clearly there are two different species from Prunus, one isolated in Austria and another in Sweden. Because D. pustulata was originally described on Acer pseudoplatanus, we tentatively apply this name to isolates in clade 44. To clarify the status of isolates in clades 44 and 56, however, additional isolates and a comparison with type materials would be required. Diaporthe raonikayaporum R.R. Gomes, C. Glienke & Crous, sp. nov. — MycoBank MB802947; Fig. 20 Etymology. Raoni + Kayapo = after the name of a leader (Raoni) of the indigenous Kayapo ethnic tribe in Brazil. The Kayapos are inhabitants of the Amazon region in Brazil. They use the medicinal plant Spondias mombin, from which this species was isolated, as adornment or ornament, and for its medicinal properties. Conidiomata pycnidial, globose to conical or ampullifom, eustromatic and convoluted or unilocular, scattered, dark brown to black, immersed, ostiolate, 110–200 μm wide, 50–130 μm tall, Fig. 20 Diaporthe raonikayaporum (CBS 133182). a. Conidiomata sporulating on PNA; b, c. transverse section through conidiomata, showing conidiomatal wall; d. conidiogenous cells; e. beta with a few alpha conidia; f. alpha conidia. — Scale bars: b = 100 µm, all others = 10 µm. 32 with prominent necks 40–140 μm long, outer surface smooth or covered in hyphae; pycnidal wall consisting of brown, thickwalled cells of textura angularis; conidial mass globose or exuding in cirrhi, white to pale-luteous. Conidiophores hyaline, ampulliform to subcylindrical, ﬁliform, branched above the septa, tapering towards the apex, 1–3-septate, (16–)17– 22(–26) × (2–)3 μm. Conidiogenous cells hyaline, subcylindrical, ﬁliform, straight to curved, tapering towards the apex, collarette not flared, periclinal thickening prominent, (5–)7–9(–10) × (2–)3 μm. Alpha and gamma conidia are formed in the same conidiogenous cells. Alpha conidia hyaline, oblong to ellipsoid, apex bluntly rounded, base obtuse to subtruncate, bi- to multiguttulate, (6–)7(–8) × (2–)3 μm. Beta conidia not observed. Gamma conidia hyaline, fusoid to subcylindrical, slightly curved, apex bluntly rounded, base obtuse to subtruncate, bi- to multiguttulate, or eguttulate, (7–)9–11(–13) × (1–)2 μm. Culture characteristics — Colonies on PDA flat, with an entire edge, aerial mycelium forming concentric rings with cottony texture, olivaceous-buff, isabelline to honey on surface; colonies reaching 63 mm diam after 2 wk at 25 °C; reverse pale purplish grey to smoke-grey. On OA flat, with an entire edge, aerial mycelium forming concentric rings, white, olivaceous on surface, colonies reaching 31 mm diam; reverse buff and greenish olivaceous. On MEA flat, with a lobate edge, aerial mycelium forming wooly concentric rings, olivaceous-grey, greenish olivaceous and patches of amber on surface, colonies reaching 51 mm diam; reverse brown-vinaceous. Specimen examined. BrAzil, Pará, Redenção, endophytic species isolated from leaf of Spondias mombin (popular name Cajazeira and Taperebá), July 2007, K. Rodriguez (holotype CBS H-21097, ex-type culture CBS 133182 = LGMF 923 = CPC 20299). Notes — Endophytic isolate (clade 31) from medicinal plant in Brazil. Diaporthe rhoina Feltgen, Vorstud. Pilzfl. Luxemb., Nachtr. III: 145. 1903 Specimen examined. unknown, on Rhus toxicodendron, Sept. 1927, L.E. Wehmeyer (CBS 146.27). Notes — This species (clade 95) was originally described on Rhus typhina from Luxembourg. European isolates of this Persoonia – Volume 31, 2013 pathogen will need to be collected to conﬁrm the identity of CBS 146.27, which is presumably of North American origin. Diaporthe saccarata (J.C. Kang, L. Mostert & Crous) Crous, comb. nov. — MB802948 Basionym. Phomopsis saccarata J.C. Kang, L. Mostert & Crous, Sydowia 53, 2: 230. 2001. Specimen examined. south AfriCA, Western Cape Province, Jonkershoek Mountains, Stellenbosch, on cankers of Protea repens, Mar. 1999, S. Denman (ex-type culture CBS 116311 = CPC 3743). Note — Diaporthe saccarata (clade 71) is known to cause a canker disease on shoots of Protea repens in South Africa (Mostert et al. 2001b). Diaporthe schini R.R. Gomes, C. Glienke & Crous, sp. nov. — MycoBank MB802949; Fig. 21 Etymology. Named after the host genus from which it was isolated, Schinus. Conidiomata pycnidial, eustromatic, multilocular, immersed to erumpent, ostiolate, dark brown to black, scattered or aggregated, 80–270 μm wide, 70–240 μm tall, prominent necks 70–220 μm long, outer surface covered with hyphae; pycnidal wall consisting of brown, thick-walled cells of textura angularis; conidial mass globose, pale-luteous to cream. Conidiophores hyaline, subcylindrical, ﬁliform, rarely branched, tapering towards the apex, 0–1-septate, (11–)12 –17(– 20) × (2–)3(–4) μm. Conidiogenous cells hyaline, subcylindrical and ﬁliform, straight, tapering towards the apex, collarette not observed, with prominent periclinal thickening 5–6(–7) × (1–)2 μm. Beta conidia hyaline, smooth, curved or hamate (14–)22–28(–30) × (1–)2 μm. Alpha and gamma conidia not observed. Culture characteristics — Colonies on PDA flat, with a lobate margin, surface mycelium sparse, felty and appressed, buff, honey to isabelline; colonies reaching 30 mm diam after 2 wk at 25 °C; reverse greyish sepia, smoke-grey. On OA with a lobate margin, surface mycelium flat, sparse, felty and appressed, smoke-grey, olivaceous-grey, or olivaceous buff; colonies reaching 21 mm diam; reverse pale mouse-grey to Fig. 21 Diaporthe schini (CBS 133181). a. Conidiomata sporulating on PDA; b, c. transverse section through conidiomata, showing conidiomatal wall; d, e. conidiogenous cells; f. beta conidia. — Scale bars: b = 135 µm, all others = 10 µm. R.R. Gomes et al.: Diaporthe olivaceous-grey or buff. On MEA with a lobate margin, surface mycelium flat, dense, felty and appressed, buff with umber patches; colonies reaching 30 mm diam; reverse dark mousegrey, umber, with patches of isabelline or luteous. Specimen examined. BrAzil, Paraná, Curitiba, endophytic species isolated from leaf of Schinus terebinthifolius (popular name Aroeira), July 2007, J. Lima (holotype CBS H-21093, culture ex-type CBS 133181 = LGMF 921 = CPC 20297); same collection details (LGMF 910). Notes — Other than D. schini (clade 11), additional endophytic isolates were also obtained from Schinus terebinthifolius in Brazil, but these are morphologically different and cluster in clades 5 and 9 (D. endophytica and D. terebinthifolii). Diaporthe sclerotioides (Kesteren) Udayanga, Crous & K.D. Hyde, Fung. Diversity 56: 166. 2012 Basionym. Phomopsis sclerotioides Kesteren, Neth. Jl. Pl. Path. 73: 115. 1967. Specimens examined. netherlAnds, Maarssen, on root of Cucumis sativus, June 1967, H.A. van der Kesteren (ex-type culture CBS 296.67 = ATCC 18585 = IMI 151828 = PD 68/690); Roermond, on root of C. sativus, Dec. 1976 (CBS 710.76 = PD 76/674). Notes — Diaporthe sclerotioides (clade 28) was originally described from roots of Cucumis sativus in the Netherlands. This species has subsequently been reported to cause black root rot of Citrullus lanatus, Cucurmis sativus, C. ficifolia, C. maxima and C. moschata in various countries in the world (Udayanga et al. 2011). Diaporthe scobina Nitschke, Pyrenomycetes Germanici 2: 293. 1870 = Phomopsis scobina Höhn., Sber. Akad. Wiss. Wien, Math.-naturw. Kl., Abt. 1 115: 681 (33 of repr.). 1906. Specimen examined. sCotlAnd, living and dead twig of Fraxinus excelsior, Feb. 1938, J.A. MacDonald (CBS 251.38). Notes — Clade 38 is represented by D. scobina isolated from Fraxinus excelsior in Scotland. The fungus is known on this host from Scotland and Poland (Mulenko et al. 2008, Farr & Rossman 2012). Diaporthe sojae Lehman, Ann. Missouri Bot. Gard. 10: 128. 1923 ≡ Diaporthe phaseolorum var. sojae (Lehman) Wehm., The genus Diaporthe Nitschke and its segregates 47: 1933. = Phomopsis longicolla Hobbs, Mycologia 77: 542. 1985. ≡ Diaporthe longicolla (Hobbs) J.M. Santos, Vrandečić & A.J.L. Phillips, Persoonia 27: 13. 2011. Specimens examined. CroAtiA, on Glycine max stem, Sept. 2005, K. Vrandečić (specimen CBS H-20460, culture CBS 127267). – itAly, Bologna, from Glycine soja, 1986, P. Giunchi (specimen CBS H-16776, culture CBS 100.87). – unknown, on Glycine soja (‘Blackhawk’) mature stem, A.A. Hildebrand (CBS 180.55 = ATCC 12050 = CECT 2024). – USA, Mississippi, from Euphorbia nutans, A. Mengistu (CBS 116017 = DP 0508) and from Glycine max, Oct. 2003, A. Mengistu (CBS 116023); on Glycine soja seedling, J. Marcinkowska (CBS 659.78 = NRRL 13656). Notes — Isolates of D. phaseolorum var. sojae clustered in two distincts clades (clade 1, D. sojae; clade 7, D. melonis). Diaporthe sojae causes pod and stem blight of soybean, while P. longicolla is known to cause seed decay (Santos et al. 2011). Several authors have found it difﬁcult to distinguish them based on disease symptoms alone, and usually report them together (Almeida & Seixas 2010). Hobbs et al. (1985) described P. longicolla as a different species to D. sojae (Diaporthe phaseolorum var. sojae) based on morphological characters. Both symptom types, however, have also been linked to the same species 33 (Kulik 1984, Morgan-Jones 1989, Kulik & Sinclair 1999). Considering their genetic similarity based on the ﬁve genes studied here, disease etiology and common host, it appears that these isolates belong to the same species, which is distinct from D. phaseolorum (clade 4). Diaporthe sojae (clade 1) is an older name than D. longicolla, and is therefore applied to this clade. Diaporthe sp. 1 Specimens examined. BrAzil, EMBRAPA/PR, on Glycine max seed, A. Almeida (LGMF 947 = CPC 20323). – germAny, Bielefeld, human abscess, K. Plechulla (CBS 119639 = B 11861). Notes — Isolates from clade 2 appear to represent a novel species, Diaporthe sp. 1 (sterile). It is represented by CBS 119639, isolated from an abscess of a male patient in Germany, and isolate LGMF 947, obtained from soybean seeds in Brazil. Isolates from this clade share a low genetic homology to isolates of the clade 4 (D. phaseolorum; Fig. 1, part 1). Diaporthe species commonly described from soybean were also reported as opportunistic human pathogens. In 1999, a species of Phomopsis was reported as etiological agent of a subcutaneous infection on the ﬁnger of an immunosuppressed farmer and this genus was added to the list of fungi capable to cause human disease (Sutton et al. 1999). In 2011, D. sojae (as Phomopsis longicolla), a known pathogen of soybean, was identiﬁed as causing skin infection in an immunocompromised patient after kidney transplantation. The authors believed that this patient acquired the fungus at least 5 yr before, when he had contact with seeds or soybean plants in Equatorial Guinea (Garcia-Reyne et al. 2011). Another phytopathogenic species also described in soybean, Diaporthe phaseolorum, was reported causing osteomyelitis in patients with positive serology for human lymphotropic virus type 1 (HTLV-1), disturbing the immune response. The patient was a farmer and inoculation occurred possibly through injury with Amaranthus spinosus thorns (Iriart et al. 2011). Diaporthe sp. 2 Specimen examined. BrAzil, on petiole of Maytenus ilicifolia, July 2007, R.R. Gomes (LGMF 932 = CPC 20308). Notes — Sterile, endophytic isolate from medicinal plant in Brazil, which appears to represent a novel species (clade 29). Diaporthe sp. 3 Specimen examined. sCotlAnd, on Pseudotsuga menziesii, Mar. 1929, G.G. Hahn (CBS 287.29). Notes — Clade 32 was tentatively named Diaporthe sp. 3, and is represented by a single isolate previously identiﬁed as Phomopsis conorum, and obtained from Pseudotsuga menziesii in Scotland. This clade was not resolved, because there are at least eight different conifer species without any ex-type cultures (Udayanga et al. 2011). Diaporthe sp. 4 Specimen examined. BrAzil, endophytic in petiole on Maytenus ilicifolia, July 2007, R.R. Gomes (LGMF 944 = CPC 20320). Notes — Sterile endophytic isolate (clade 33) from a medicinal plant in Brazil, appearing to represent an undescribed species. Persoonia – Volume 31, 2013 34 Diaporthe sp. 5 Specimen examined. itAly, from Acer opalus, W. Jaklitsch (CBS 125575). Notes — This isolate (clade 37) represents a novel species occurring on Acer, which will be treated separately as part of another study (W. Jaklitsch, pers comm.). Diaporthe sp. 6 Specimens examined. hong kong, University Drive, on fruit of Maesa perlarius, 18 Dec. 2000, K.D. Hyde (CBS 115595 = HKUCC 10129, CBS 115584 = HKUCC 7784). Notes — The two strains (clade 85) studied here were originally identiﬁed as P. pittospori (described from Pittosporum twigs, USA, California), which seems highly unlikely, as they were isolated from fruit of Maesa perlarius in Hong Kong. Unfortunately both strains proved to be sterile, so their identity could not be conﬁrmed. Diaporthe sp. 7 Specimen examined. indiA, Bangalore, on Anacardium occidentale, Aug. 1978, H.C. Govindu (CBS 458.78). Notes — The identity of the present isolate (identiﬁed as Phomopsis anacardii) could not be conﬁrmed, as the culture proved to be sterile. However, phylogenetically (clade 88) it represents a distinct taxon from D. anacardii (clade 69), and when recollected, should be described as new. Diaporthe sp. 8 Specimen examined. BrAzil, from Aspidosperma tomentosum, K. Rodriguez (LGMF 925 = CPC 20301). Culture characteristics — Colonies covering dish after 2 wk in the dark at 25 °C, with moderate aerial mycelium. On PDA surface ochreous, reverse pale luteous. On OA surface and reverse luteous. On MEA surface pale luteous, reverse orange to apricot. Notes — Although this isolate (clade 90) appears to represent an undescribed species based on phylogenetic data, it proved to be sterile. As we presently only have a single strain of this taxon, its treatment will have to await further collections. Diaporthe stictica (Berk. & Broome) R.R. Gomes, C. Glienke & Crous, comb. nov. — MycoBank MB802950 Basionym. Phoma stictica Berk. & Broome, Ann. Mag. Nat. Hist., ser. II 5: 370. 1850. ≡ Phomopsis stictica (Berk. & Broome) Traverso, Fl. Ital. Crypt. 2, 1: 276. 1906. Specimen examined. itAly, Perugia, on dead twig of Buxus sempervirens, Dec. 1954, M. Ribaldi (CBS 370.54). Notes — Diaporthe stictica (clade 74) represents a European species occurring on Buxus sempervirens (Italy, Germany). Although the present isolate could be authentic for the name, this could not be conﬁrmed based on morphology, as the isolate proved to be sterile. Diaporthe subordinaria (Desm.) R.R. Gomes, C. Glienke & Crous, comb. nov. — MycoBank MB802951 Basionym. Phoma subordinaria Desm., Ann. Sci. Nat., Bot. ser. 3, 9: 284. 1849. ≡ Phomopsis subordinaria (Desm.) Traverso, Fl. Ital. Crypt. Pars 1: Fungi. Pyrenomycetae. Xylariaceae, Valsaceae, Ceratostomataceae: 232. 1906. Specimens examined. new zeAlAnd, blackened seed of Plantago lanceolata, Apr. 1999, B. Alexander (CBS 101711). – south AfriCA, Eastern Cape Province, Grahamstown, on stalks of Plantago lanceolata, 2 Dec. 1989, R. Shivas (CBS 464.90). Notes — Diaporthe subordinaria (clade 18) has a global distribution on Plantago lanceolata, on which it causes a stalk disease (de Nooij & van der Aa 1987). It is possible that the disease relates to several different species occurring on Plantago, but this matter can only be resolved following futher collections and correlation with type material. Diaporthe tecomae Sacc. & P. Syd., Syll. Fung. 14: 550. 1899 (nom. nov. for D. interrupta Niessl). — Fig. 22 ?= Phoma tecomae Sacc., Nuovo Giorn. Bot. Ital. 8: 201. 1876. ≡ Phomopsis tecomae (Sacc.) Traverso & Spessa, Bol. Soc. Brot. Coimbra, sér. 1, 25: 124. 1910. Conidiomata pycnidial, sporulating poorly on OA, globose, up to 1 mm diam, black, erumpent, multilocular; cream conidial droplets exuding from central ostioles; walls consisting of 3–6 layers of medium brown textura angularis. Conidiophores hyaline in upper region, pale brown at base, smooth, 1–3-septate, branched, densely aggregated, cylindrical, straight to sinuous, 20–30 × 2–3 μm. Conidiogenous cells 8–15 × 1.5–3 μm, phialidic, cylindrical, terminal and lateral, with slight taper towards apex, 1 μm diam, with visible periclinal thickening; collarette not flared, minute. Paraphyses not observed. Beta conidia spindleshaped, aseptate, smooth, hyaline, apex acutely rounded, base truncate, tapering from lower third towards apex, apex strongly curved, (17–)22–24(–26) × 1.5(–2) μm. Alpha and gamma conidia not observed. Culture characteristics — Colonies covering dish after 2 wk in the dark at 25 °C. On OA fluffy, dirty white with patches of grey olivaceous. On PDA dirty white with patches of olivaceous grey and isabelline, reverse with patches of dirty white, brown vinaceous and dark brick. On MEA dirty white with patches of isabelline and olivaceous grey, reverse brown vinaceous with patches of dark brick. Fig. 22 Diaporthe tecomae (CBS 100547). a. Conidiomata forming on PNA; b, c. conidiogenous cells; d. beta conidia. — Scale bars = 10 µm. R.R. Gomes et al.: Diaporthe Specimen examined. BrAzil, Sao Paulo, Serra da Mantiqueira, mycocecidium caused by Prosopodium tecomicola on living young branch of Tabebuia sp., 27 Sept. 1997, coll. A. Aptroot, isol. H.A. van der Aa (specimen CBS H-16834, culture CBS 100547). Notes — Diaporthe tecomae was a new name proposed for D. interrupta Niessl (on Tecoma radicans, Portugal), as the epithet was already occupied. The link between the Diaporthe and Phomopsis state remains to be proven. The asexual morph was originally described as Phoma tecomae (from Italy on Tecoma radicans, conidiophores 20 × 1 µm, conidia 8 × 3 µm; Saccardo 1878), and is probably distinct from the fungus represented by CBS 100547, which occurs on Tabebuia sp. in Brazil. However, as no ex-type strains are available of D. tecomae (clade 10), and no alpha conidia were observed in culture, this could not be conﬁrmed, and is pending fresh collections. Diaporthe terebinthifolii R.R. Gomes, C. Glienke & Crous, sp. nov. — MycoBank MB802952; Fig. 23 Etymology. Named after the host species from which it was isolated, Schinus terebinthifolius. Conidiomata pycnidial, globose to conical, immersed, ostiolate, brown to black, scattered or aggregated, 95 –110 μm wide, 140–160 µm tall, rarely forms necks, but when present, they are short and covered with hyphae; pycnidal wall consisting of brown, thick-walled cells of textura angularis; conidial mass globose, white or pale-luteous to cream. Conidiophores hyaline, subcylindrical, ﬁliform, branched above septa, tapering towards the apex, 1– 2-septate, (13 –)15 – 21(– 22) × 2(– 3) μm. Beta conidiogenous cells hyaline, ampulliform to subcylindrical and ﬁliform, tapering towards the apex, collarette present and not flared, slight periclinal thickening, (3–)6–10(–14) × 2(–3) μm. Beta conidia hyaline, smooth, curved or hamate, (18–)20–24 (–26) × 1(–2) μm. Alfa and gamma conidia not observed. Culture characteristics — Colonies on PDA flat, with an entire edge, aerial mycelium cottony, greyish white, colonies reaching 64 mm diam after 2 wk in the dark at 25 °C; reverse buff. On OA flat, entire edge, aerial mycelium cottony, with concentric rings, pale olivaceous-grey, smoke-grey and greyish white, colonies 35 reaching 48 mm diam; reverse olivaceous-grey and olivaceous buff. On MEA flat, with an entire edge; aerial mycelium cottony, smoke-grey, colonies reaching 60 mm diam; reverse umber with patches of fuscous-black. Specimens examined. BrAzil, Paraná, Curitiba, endophytic species isolated from leaf of Schinus terebinthifolius (popular name Aroeira), July 2007, J. Lima (holotype CBS H-21097, ex-type culture CBS 133180 = LGMF 914 = CPC 20290); same collection details (LGMF 909 = CPC 20285, LGMF 907 = CPC 20283, LGMF 913 = CPC 20289). Notes — The multigene analysis of isolates in clade 9 exhibited insigniﬁcant homology to sequences found in GenBank. An isolate previously identiﬁed as Phomopsis tecomae (CBS 100547) also resides in this clade, but is morphologically distinct. No morphologically similar isolates are known from S. terebinthifolius, and thus we designate these isolates as representative of a new taxon. Diaporthe toxica P.M. Will., Highet, W. Gams & Sivasith., Mycol. Res. 98: 1367. 1994 Specimens examined. western AustrAliA, Morawa, on stem of Lupinus angustifolius, 6 May 1991, J.B. Nunn (ex-type culture CBS 534.93 = ATCC 96741); Serpentine, on Lupinus sp., 8 June 1993, P.M. Williamson (CBS 535.93); Medina, on Lupinus sp., 8 June 1993, P.M. Williamson (CBS 546.93). Notes — Clade 45 contains three isolates of D. toxica, including the ex-type culture (CBS 534.93), isolated from Lupinus angustifolius in Western Australia. Two varieties of Phomopsis (P. leptostromiformis var. leptostromiformis and P. leptostromiformis var. occidentalis) were identiﬁed as causing disease in Lupinus sp. Diaporthe woodii was later recognised as the sexual state of P. leptostromiformis var. occientalis (Punithalingam 1974), while Williamson et al. (1994) designated the name D. toxica for the sexual state of the toxicogenic variety, P. leptostromiformis var. leptostromiformis. Lupins (Lupinus spp.) are grown in many parts of the world as a grain legume crop. The seeds are used for animal feed and increasingly as flour for human consumption. The plants increase soil nitrogen and are grown in rotation with other crops. Fig. 23 Diaporthe terebinthifolii (CBS 133180). a. Conidiomata sporulating on PNA; b, c. transverse section through conidiomata, showing conidiomatal wall; d, e. conidiogenous cells; f. beta conidia. — Scale bars: b = 100 µm, c = 25 µm, all others = 10 µm. 36 Persoonia – Volume 31, 2013 In Australia the stubble left after harvesting aids soil conservation and is a valuable summer feed for livestock. Diaporthe toxica is considered to be an important limiting factor to more extensive sowing of lupins. This organism has been reported to cause stem blight in young lupins (Lupinus luteus) (Ostazeski & Wells 1960) and to produce phomopsins (Culvenor et al. 1977). These mycotoxins cause the animal liver disease known as lupinosis (Gardiner 1975, Allen & Wood 1979). Diaporthe vaccinii Shear, U.S. Dept. Agric. Tech. Bull. 258: 7. 1931 = Phomopsis vaccinii Shear, U.S. Dept. Agric. Tech. Bull. 258: 7. 1931. Specimens examined. USA, Massachusetts, on Oxycoccus macrocarpos, Mar. 1932, C.L. Shear (ex-type culture CBS 160.32 = IFO 32646); Michigan, on Vaccinium corymbosum, G.C. Adams (CBS 118571); New Jersey, on V. macrocarpon, 1988, L. Carris (CBS 122112 = FAU 474); Michigan, on V. corymbosum, 1992, D.C. Ramsdell (CBS 122114 = FAU 634, CBS 122115 = FAU 590); North Carolina, from V. corymbosum, pre-1999, D.F. Farr (CBS 122116 = DF 5022). Notes — Clade 63 consists of six isolates of D. vaccinii, including the ex-type strain (CBS 160.32) isolated on Vaccinium corymbosum from the USA. Diaporthe vaccinii causes fruit rot and twig blight and leaf spots of Vaccinium spp. (blueberries) in the USA (Alﬁeri et al. 1984, Farr et al. 2002, Farr & Rossman 2012). The principal hosts are American and European cranberries (Vaccinium macrocarpon, V. oxycoccos, V. oxycoccos var. intermedium), highbush blueberry (V. corymbosum) and rabbiteye blueberry (V. ashei). Diaporthe vaccinii is restricted to cultivated Vaccinium species. The wild European species, V. oxycoccos, which usually occurs in mountain bogs, could be a potential reservoir for the pest. In the EPPO region it has been reported from Romania (found in experimental plots of introduced American cultivars, but did not establish (Teodorescu et al. 1985)), UK (found in plants originally imported from the Netherlands and USA, but did not establish (Wilcox & Falconer 1961, Baker 1972)). Symptoms in susceptible blueberry cultivars include blighting of 1-yr-old woody stems with flower buds. Infected succulent, current-year shoots wilt in 4 d and become covered with minute lesions. The fungus continues to travel downward through the stem, killing major branches, and often entire plants (Wilcox 1939, Daykin & Milholland 1990). Infected fruits turn reddishbrown, soft, mushy, often splitting and causing leakage of juice (Milholland & Daykin 1983). Diaporthe vexans (Sacc. & P. Syd.) Gratz, Phytopathology 32: 542. 1942 Basionym. Phoma vexans Sacc. & P. Syd., Syll. Fung. (Abellini) 14, 2: 889. 1899. ≡ Phomopsis vexans (Sacc. & P. Syd.) Harter, J. Agric. Res. 2, 5: 338. 1914. Specimen examined. USA, from Solanum melongena, Dec. 1914, L.L. Harter (CBS 127.14). Notes — Diaporthe vexans (clade 12) causes fruit rot, leaf spot, stem and tip blight disease of eggplants (Solanum melongena and S. wendlandii) and other solanaceous species, Acacia sp. (Fabaceae), Prunus sp. (Rosaceae) and Sorghum bicolor (Poaceae), Capsicum annuum and Lycopersicon esculentum (Solanaceae). The disease is widespread in North America, the West Indies, and Eastern and Central Asia, also in Africa (Senegal, Tanzania, Zambia) and Mauritius (Punithalingam & Holliday 1972). Additional records include Brunei, Haiti, Iran, Iraq and Romania (Harter 1914, Farr & Rossman 2012). Diaporthe viticola Nitschke, Pyrenomycetes Germanici 2: 264. 1870 Specimens examined. AustriA, Vienna, Risenbergbach-Weg, on Laburnum anagyroides, May 2001, A.R. Rossman (CBS 109492). – CAnAdA, British Columbia, Sidney, on Epilobium angustifolium, Oct. 2001, M. Barr (CBS 109768 = AR 3478). – frAnCe, Dordogne, near Sarlat la Canéda, 1-yrold stems on Asphodelus albus, 20 May 1995, G. Verkley (CBS 759.95). – netherlAnds, Utrecht, Baarn, in branches and twigs of Aucuba japonica, Jan. 1995, G. Verkley (CBS 106.95); on Rosa rugosa, 18 Mar. 1985, G.H. Boerema (CBS 266.85 = PD 85/25); Lelystad, in dead stem on Lupinus sp., May 1982, H.A. van der Aa (CBS 449.82); Wieringermeer, Robbenoordbos, in dead stem on Lupinus arboreus, 12 Mar. 1991, H.A. van der Aa & F. Meurs (CBS 312.91); Flevoland, trees in front of Info Centre Lepelaarsplassen, in leaf spot on Fraxinus excelsior, 31 Aug. 1997, H.A. van der Aa (CBS 100170); Baarn, in dead stem on Dipsacus fullonum, 14 June 1985, H.A. van der Aa (CBS 502.85); on twig on Salix sp., Apr. 1962, G.H. Boerema (CBS 446.62). – PortugAl, on Vitis vinifera (Galego durado), 1 Jan. 1998, A.J.L. Phillips (CBS 114011 = CPC 2677); Burgaes, Santo Tirso, on Vitis vinífera, 16 Feb. 1998, A.J.L. Phillips (ex-type culture CBS 113201 = CPC 5683). – sweden, Skåne, Maglehem par., on Sambucus cf. racemosa, 14 Apr. 1989, K. Holm & L. Holm (CBS 114436 = UPSC 2960). – UK, Shefﬁeld, on A. japonica, July 1996, G. Verkley (CBS 794.96). Notes — Diaporthe viticola (clade 50) is known from several hosts, but especially from grapevines, on which it causes a cane spot disease in Europe (Portugal, Germany). Merrin et al. (1995) referred to several Australian isolates from grapevines as Phomopsis taxon 1. The same species was reported by Phillips (1999) as D. perjuncta and by Scheper et al. (2000) as D. viticola. In a subsequent study, Mostert et al. (2001a) chose to follow Phillips (1999) and applied the name D. perjuncta to taxon 1. However, they also noted that minor morphological differences existed in perithecia and ascospores between the European and Southern Hemisphere material, which led to the description of a novel taxon, D. australafricana, for isolates from Australia and South Africa (van Niekerk et al. 2005), and the epitypiﬁcation of D. viticola based on European material. Based on the results obtained here, D. viticola (clade 50) is closely related to D. australafricana (clade 49), and is clearly distinguishable from D. perjuncta (clade 40). Diaporthe woodii Punith., Mycol. Pap. 136: 51. 1974 = Phomopsis leptostromiformis var. occidentalis, R.G. Shivas, J.G. Allen & P.M. Will., Mycol. Res. 95: 322. 1991. Specimen examined. western AustrAliA, Medina, stems of Lupinus sp., 8 July 1993, P.M. Williamson (CBS H-5319, culture CBS 558.93). Notes — Clade 94 represents Diaporthe woodii (CBS 558.93), which was characterised by Williamson et al. (1994), based on the ex-type strain (IMI 166508). Diaporthe crotalariae (clade 92), D. aspalathi (clade 93) and D. woodii are closely related species. Diaporthe woodii causes stem rot, stem cankers, leaf infections and seed decay of Lupinus angustifolius and L. cosenfinii, and blight and seed discoloration of L. albus, L. angustifolius, L. cosentinii, L. luteus, L. pilosus and Trifolium subterraneum (subterranean clover). The fungus is known to occur in Brazil, South Africa, USA (Florida), and Western Australia (Williamson et al. 1994). Diaporthe woolworthii (Peck) Sacc., Syll. Fung. (Abellini) 1: 615. 1882 Basionym. Valsa woolworthii Peck, Ann. Rep. N.Y. State Mus. Nat. Hist. 28: 73. 1876 (1875). Specimen examined. unknown, on Ulmus americana, Sept. 1927, L.E. Wehmeyer (CBS 148.27). Notes — Clade 57 contains a single isolate of D. woolworthii from Ulmus americana. This taxon represents an American species occurring on Ulmus, so this culture (presumably from North America), could prove to be authentic for the name. 37 R.R. Gomes et al.: Diaporthe DISCUSSION A major aim of the present study was to resolve the taxonomy of Diaporthe species occurring on diverse hosts, either as pathogens, saprobes, or as harmless endophytes. To delimitate these taxa, nine genes were screened, from which the best ﬁve were selected to conduct a multi-gene phylogenetic analysis (ITS, TEF1, ACT, HIS and CAL). Diaporthe represents a highly complex genus containing numerous cryptic species, several of which are newly described in the present study, while others remain unclear, awaiting fresh collections and type studies. Many Diaporthe species that are morphologically similar proved to be genetically distinct, and several isolates that were formerly identiﬁed based on their host, were shown to represent different taxa. Although the genera Diaporthe and Phomopsis have received much taxonomic attention, few phylogenetic studies have thus far been conducted, and hence the taxonomy of this group is still problematic. Due to the lack of reference strains, and the fact that few gene loci other than ITS have in the past been used for DNA analysis, most of the conclusions reached thus far have been incorrect, meaning that published literature will have to be interpreted with care. In this study we studied 15 endophytic Diaporthe species from Brazil. Three were not identiﬁed to species level, two were identiﬁed as D. novem and D. phaseolorum, while a further 10 were described as new. High genetic diversity was found amongst the analysed isolates from medicinal plants. Species of Diaporthe are commonly isolated as endophytes from several hosts in temperate and tropical regions (Bussaban et al. 2001, Murali et al. 2006, Rossman et al. 2007, Botella & Diez 2011, González & Tello 2011). Skaltsas et al. (2011) isolated 108 Diaporthe isolates from asymptomatic leaves and bark of three different hosts (Hevea brasiliensis, H. guianensis and Micandra spp.) from Cameroon, Mexico and Peru. Using a multigene approach, the authors found more than 40 phylogenetic species, of which several appeared to represent novel taxa (Skaltsas et al. 2011). Despite members of Diaporthe commonly being described as phytopathogenic, an increasing number of reports link this genus to endophytic studies, focusing on its potential as a producer of enzymes and novel secondary metabolites, with antibiotic, fungicide and anticancer activity (Dai et al. 2005, Elsaesser et al. 2005, Lin et al. 2005, Silva et al. 2005, Wu et al. 2008, Kumaran & Hur 2009, Weber 2009, Vesterlund et al. 2011). The ecology of species of Diaporthe remains poorly understood, as some endophytes isolated from the medicinal plant Maytenus ilicifolia were identiﬁed as D. phaseolorum (clade 4) and D. novem (clade 22), respectively know as pathogen of soybean (Santos et al. 2011) and Aspalathus linearis (van Rensburg et al. 2006). Diaporthe novem is also reported from hosts such as Hydrangea macrophylla (Santos et al. 2010), Helianthus annuus and Vitis vinifera (Santos et al. 2011). These reports agree with the pogo stick hypothesis, postulating that host-speciﬁc fungal plant pathogens frequently exhibit the ability to colonise non-host tissue, enabling them to disperse further, in an attempt to ﬁnd the host on which they are pathogenic (Crous & Groenewald 2005). The taxonomy of Diaporthe (incl. Phomopsis) has traditionally been based on host association, with species being described on the assumption that they are host-speciﬁc. In the present study the taxonomy of all Diaporthe isolates deposited in the CBS culture collection over time were reviewed, based on this assumption. The employment of this criterion, has led to an exponential growth in the number of taxa described in Diaporthe thus far (Uecker 1988). However, in spite of the apparent synonymies outlined in this study, there was evidence for a huge proliferation of cryptic taxa that were formerly overlooked based on a morphological approach in the absence of molecular data. Species delimitation in Diaporthe based on morphological characters is challenging, as most taxa in culture do not produce all spore states of the asexual (alpha, beta and gamma conidia) or the sexual morph. The description of novel taxa in Diaporthe in the absence of molecular data (at least ITS and HIS or TUB; see discussion in next section) should thus be strongly discouraged in the future. In conclusion thus, it seems that in spite of the fact that these taxa readily colonise or co-colonise non-hosts (see also Rehner & Uecker 1994, Mostert et al. 2001a, Farr et al. 2002, Diogo et al. 2010), there is still a multitude of undescribed taxa awaiting further study in this complex. It is thus hoped that the phylogenetic backbone generated here provides a stable platform to enable future studies by others interested in the biology of Diaporthe. Phylogenetic species recognition by genealogical concordance Taylor et al. (2000) developed the Genealogical Concordance Phylogenetic Species Recognition (GCPSR) concept to deﬁne the limits of sexual species, using the phylogenetic concordance of multiple unlinked genes. This concept has proved greatly useful in fungi, because it is more ﬁnely discriminating than other species concepts, as several species are unable to be crossed, or cannot be recognised due to the lack of distinguishing morphological characters or sterility (Reynolds 1993, Taylor et al. 2000, Cai et al. 2011). The adoption of genealogical concordance for species recognition in Diaporthe enabled us to distinguish species that were otherwise not possible to identify due to either sterility, or the loss of speciﬁc character states. For instance, D. viticola and D. australafricana are two closely related species (clades 50 and 49, respectively) associated with grapevines. They are morphologically similar, but occur on different continents (van Niekerk et al. 2005). These species have probably accumulated genetic differences due to their geographical isolation. Several cryptic species were recently described in other genera using the GCPSR criterion, some of which are consistent with allopatric divergence, because these species occupy non-overlapping areas separated by geographic barriers, e.g. in Cladosporium (Bensch et al. 2012), Colletotrichum (Damm et al. 2012a, b), Harknessia (Crous et al. 2012), Ilyonectria (Cabral et al. 2012a, b) and Phyllosticta (Glienke et al. 2011), to name but a few. Using the GCPSR concept it is possible to deﬁne the genetic variation observed in some species, but still insufﬁcient to establish them as distinct species, since genetic flow still occurs between them. For example, isolates of clades 79–90 clustered differently based on analyses of the different genes, probably because of recent gene flow among them. We have compared the location and monophyly of the strains in each clade in the phylogenetic tree of the combined alignment (Fig. 1) to those phylogenetic trees obtained from the individual loci to determine the species boundaries and species resolution. The ﬁve loci selected for the Bayesian phylogeny have a similar resolution for species discrimination, ranging from TEF1 resolving 72 out of the 95 species, to HIS and TUB resolving 84 of the 95 species. The ITS region, which is often considered to be less than optimal for closely related species, was not much better or worse (resolving 75 of the 95 species) than the other included loci. However, given the recent acceptance of the ITS region as ofﬁcial fungal barcode (Schoch et al. 2012) and its intermediate resolving power in the present study, this locus should not 38 be discarded from future studies. Also, TEF1, which has in the past been used as additional locus for phylogenetic studies of Diaporthe, performed the worst in this study (resolving 72 of the 95 species), although this was not much worse than ITS and CAL (resolving 75 and 74 of the 95 species, respectively). The HIS and TUB regions appear to have the best resolution for species discrimination in the present study and therefore are good candidates as secondary markers to the commonly used ITS region. Similar results were also reported for ITS, CAL, TEF1 and TUB by Udayanga et al. (2012), who suggested that TUB be considered as secondary phylogenetic marker for Diaporthe. The importance of epitypification in Diaporthe The best option to supplement poor type material is via epitypiﬁcation (Cannon et al. 2012). To employ the GCPSR concept in fungi, DNA is mostly extracted from poorly preserved, ancient herbarium specimens with difﬁculty, and in many cases it only results in short sequences of the ITS region (Quaedvlieg et al. 2011, Cheewangkoon et al. 2012). Therefore, epitypiﬁcation of living material, and its preservation and deposit in publically available collections and databases, are important steps to provide a stable platform to enable others to test future hypotheses. Although it is not a prerequisite, it is strongly recommended that the chosen epitype should originate from the same geographical region and host, and have morphological, cultural and pathological characteristics similar to those described in the original publication (see Damm et al. 2012a, b, Cannon et al. 2012, Weir et al. 2012). Despite the fact that close to 2 000 species of Diaporthe (incl. Phomopsis) have been described in literature, hardly any extype strains are available today, the majority of which were included in the present study. Due to the lack of ex-type strains, the taxonomy of several species continue to be unresolved, some of which are important plant pathogens. A serious effort will thus be called for to recollect and redescribe all these old names. An alternative approach would be to simply start over, ensuring that all newly described names are based not only on morphology, but also supplemented by DNA barcodes. However, as long as fungal nomenclature is governed by the ICN, this seems unobtainable. Eventually though, all mycologists will realise that a stable fungal nomenclature must incorporate DNA data, and that this is only achievable if mycology follows a code of nomenclature that incorporates this requirement. 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