Abstract
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Application of the consolidated species concept to Cercospora spp. from Iran
Abstract
The genus Cercospora includes many important plant pathogenic fungi associated with leaf spot diseases on a wide range of hosts. The mainland of Iran covers various climatic regions with a great biodiversity of vascular plants, and a correspondingly high diversity of cercosporoid fungi. However, most of the cercosporoid species found to date have been identified on the basis of morphological characteristics and there are no cultures that support these identifications. In this study the Consolidated Species Concept was applied to differentiate Cercospora species collected from Iran. A total of 161 Cercospora isolates recovered from 74 host species in northern Iran were studied by molecular phylogenetic analysis. Our results revealed a rich diversity of Cercospora species in northern Iran. Twenty species were identified based on sequence data of five genomic loci (ITS, TEF1-α, actin, calmodulin and histone H3), host, cultural and morphological data. Six novel species, viz. C. convolvulicola, C. conyzae-canadensis, C. cylindracea, C. iranica, C. pseudochenopodii and C. sorghicola, are introduced. The most common taxon was Cercospora cf. flagellaris, which remains an unresolved species complex with a wide host range. New hosts were recorded for previously known Cercospora species, including C. apii, C. armoraciae, C. beticola, C. cf. richardiicola, C. rumicis, Cercospora sp. G and C. zebrina.
INTRODUCTION
Species of Cercospora (Mycosphaerellaceae) are often associated with leaf spots, but also cause necrotic lesions on flowers, fruits, bracts, seeds and pedicels of many cultivated and native plants in a range of climates worldwide (Goodwin et al. 2001, Crous & Braun 2003, Agrios 2005). The genus includes many important pathogens of agricultural crops, including cereals, vegetables, ornamentals, forest trees and grasses. Examples are C. beticola on sugar beet (Weiland & Koch 2004), C. zonata on faba beans (Kimber 2011), C. zeae-maydis and C. zeina on maize (Crous et al. 2006) and C. carotae on carrots (Kushalappa et al. 1989). Some species are considered potential biocontrol agents of weeds, including C. caricis on Cyperus rotundus and C. rodmanii on water hyacinth (Morris & Crous 1994, Charudattan 2001, Inglis et al. 2001, Tessmann et al. 2001, Praveena & Naseema 2004).
The genus Cercospora was established by Fresenius (in Fuckel 1863), and C. penicillata was later designated as the type species of the genus (Crous & Braun 2003). Since the description of Cercospora, the taxonomy of this genus together with the description of individual species has proven highly problematic. Morphological traits in Cercospora are generally conserved and specific morphological characters (including conidial shape and size, the presence or absence of external mycelium and conidiophore morphology), have often been used to describe and identify Cercospora species, despite their limitations. The paucity of useful morphological characters and high level of intraspecific variation has meant species definition in this genus being largely dependent on host plant association, i.e., a species of Cercospora was described as new when found on a different host species (Chupp 1954, Ellis 1971). The classification of Cercospora species is clouded by a history of taxonomic recombinations and name changes. While the description of new species from different hosts has increased the number of species on the one hand (Pollack 1987), the synonymy of names has decreased the species number on the other (Crous & Braun 2003). A significant problem for the taxonomy of Cercospora is the degree of host-specificity of the various species. Host data for Cercospora spp. is not well known, and should be avoided as the primary criterion for identification purposes. Extensive host inoculation experiments have shown that identification of Cercospora spp. by host specificity alone is error prone, because many species are not restricted to a single host. For example, several taxa including C. apii, C. beticola, C. canescens and C. zebrina, occur on different unrelated plant families and have broad host ranges (Crous & Braun 2003, Lartey et al. 2005, Bakhshi et al. 2012b, Groenewald et al. 2013).
During the course of monographic studies on Cercospora, Crous & Braun (2003) proposed that only genetically and morphologically distinguishable taxa should be treated as separate species. They recognised 659 names in the genus Cercospora, with a further 281 names referred to C. apii s.lat. Based on molecular data and morphological examinations, Crous & Braun (2003) concluded that C. apii-like fungi form a morphologically uniform, complicated assemblage of taxa in which the process of speciation has not concluded. They introduced the concept of ‘compound species‘ consisting of morphologically indistinguishable species with different races (host range) for a complex of plurivorous taxa, which were morphologically indistinguishable.
Cercospora was often linked to the sexual genus Mycosphaerella according to phylogenetic analyses based on nrDNA sequence loci, especially ITS and later 28S nrDNA (Stewart et al. 1999, Crous et al. 2000). Contrary to an earlier indication that many diverse asexual genera were linked to Mycosphaerella (Arzanlou et al. 2007, 2008), it was later shown that Mycosphaerella was polyphyletic (Crous et al. 2007). Subsequently, Mycosphaerella was split into numerous genera, correlating with different asexual morphs (Crous et al. 2009a, b, Quaedvlieg et al. 2013, Verkley et al. 2013). In this regard, Mycosphaerella s.str. is now restricted to taxa that form Ramularia asexual morphs (Verkley et al. 2004, Groenewald et al. 2013). Following a proposal accepted by the International Code of Nomenclature for Algae, Fungi and Plants (ICN) (Hawksworth 2011, Norvell 2011), the asexual name Ramularia (1833) was chosen over the younger, confused sexual name Mycosphaerella (1884) (Crous et al. 2009a, b, Hyde et al. 2013, Kirk et al. 2013). The genus Cercospora is now considered a holomorphic genus in its own right (Groenewald et al. 2013), with some species exhibiting the ability to form mycosphaerella-like sexual morphs (Corlett 1991, Crous et al. 2004b).
In recent years, multi-gene DNA sequence datasets have proven useful for Cercospora species identification (Crous et al. 2004c, Groenewald et al. 2005, 2006, 2010, Montenegro-Calderón et al. 2011). The most inclusive study to date was that of Groenewald et al. (2013), who compared 360 Cercospora isolates, isolated from 161 host species from 39 countries. One important outcome of this study was that several species originally referred to C. apii s.lat. based on morphology (Crous & Braun 2003), were separated as distinct phylogenetic species. This also led to the conclusion that morphology alone frequently provides an insufficient basis for species discrimination in the genus Cercospora. Furthermore, multilocus DNA sequence typing integrated with ecology, morphology and cultural characteristics, referred to as the Consolidated Species Concept (Quaedvlieg et al. 2014), proved the most effective method for the recognition of Cercospora spp. (Groenewald et al. 2010, 2013).
The mainland of Iran covers various climatic regions with a great biodiversity of vascular plants, and corresponding diversity of cercosporoid fungi. However, most of the species to date have been identified and described on the basis of morphological characteristics sensu Chupp (1954), with no attempt to derive cultures or molecular data. In order to further an understanding of this group of fungi in Iran, we initially assembled a checklist (Bakhshi et al. 2012a). Our primary aim was to describe Cercospora spp. from the north and northwest of Iran based on freshly collected specimens, derived cultures, and DNA sequence data. To achieve this aim, we sequenced the ITS locus (including ITS1, 5.8S nrRNA gene and ITS2), together with parts of four protein coding genes, viz. translation elongation factor 1-alpha (TEF1-α), actin (ACT), calmodulin (CAL) and histone H3 (HIS), and compared these data to publically available sequence data.
MATERIALS AND METHODS
Specimens and isolates
Leaf samples colonised with Cercospora spp. were collected in the field from different provinces, including Guilan, Mazandaran, Ardabil, Zanjan, West and East Azerbaijan and taken to the laboratory. Leaves were examined directly under a Nikon SMZ 1500 stereo-microscope to observe sporulation. Conidia were scraped from a single leaf spot, and single conidial colonies were established on 2 % malt extract agar (MEA; Fluka, Hamburg, Germany) (Bakhshi et al. 2011). Dried specimens were maintained in the Fungal Herbarium of the Iranian Research Institute of Plant Protection (IRAN). Axenic cultures were deposited in the Culture Collection of Tabriz University (CCTU) and the Centraalbureau voor Schimmelcultures (CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands). A complete list of the isolates used in this study is presented in Table 1.
Table 1
Species | Culture accession number(s)1 | Host | Host Family | Origion | Collector | GenBank accession numbers2 | ||||
---|---|---|---|---|---|---|---|---|---|---|
ITS | TEF1-α | ACT | CAL | HIS | ||||||
Cercospora althaeina | CCTU 1001 | Althaea rosea | Malvaceae | Iran, Guilan, Talesh | M. Bakhshi | KJ886392 | KJ886231 | KJ885909 | KJ885748 | KJ886070 |
CCTU 1026 | Althaea rosea | Malvaceae | Iran, Guilan, Talesh | M. Bakhshi | KJ886393 | KJ886232 | KJ885910 | KJ885749 | KJ886071 | |
CCTU 1028 | Althaea rosea | Malvaceae | Iran, Guilan, Sowme’eh Sara | M. Bakhshi | KJ886394 | KJ886233 | KJ885911 | KJ885750 | KJ886072 | |
CCTU 1071 | Malva sylvestris | Malvaceae | Iran, Guilan, Talesh | M. Bakhshi | KJ886395 | KJ886234 | KJ885912 | KJ885751 | KJ886073 | |
CCTU 1152 | Althaea rosea | Malvaceae | Iran, Guilan, Talesh | M. Bakhshi | KJ886396 | KJ886235 | KJ885913 | KJ885752 | KJ886074 | |
CCTU 1194 | Malva sylvestris | Malvaceae | Iran, East Azerbaijan, Kaleibar | M. Arzanlou | KJ886397 | KJ886236 | KJ885914 | KJ885753 | KJ886075 | |
CCTU 1222 | Malva sylvestris | Malvaceae | Iran, Guilan, Talesh | M. Bakhshi | KJ886398 | KJ886237 | KJ885915 | KJ885754 | KJ886076 | |
CCTU 1249 | Malva sylvestris | Malvaceae | Iran, East Azerbaijan, Kaleibar | M. Arzanlou | KJ886399 | KJ886238 | KJ885916 | KJ885755 | KJ886077 | |
Cercospora apii | CCTU 1041; CPC 24910 | Plantago lanceolata | Plantaginaceae | Iran, Guilan, Chaboksar | M. Bakhshi | KJ886400 | KJ886239 | KJ885917 | KJ885756 | KJ886078 |
CCTU 1047 | Plantago lanceolata | Plantaginaceae | Iran, Zanjan, Tarom | M. Bakhshi | KJ886401 | KJ886240 | KJ885918 | KJ885757 | KJ886079 | |
CCTU 1082; CBS 138728 | Plantago lanceolata | Plantaginaceae | Iran, Ardabil, Moghan | M. Bakhshi | KJ886402 | KJ886241 | KJ885919 | KJ885758 | KJ886080 | |
CCTU 1095 | Plantago lanceolata | Plantaginaceae | Iran, East Azerbaijan, Horand | M. Bakhshi | KJ886403 | KJ886242 | KJ885920 | KJ885759 | KJ886081 | |
CCTU 1179 | Plantago lanceolata | Plantaginaceae | Iran, West Azerbaijan, Khoy | M. Arzanlou | KJ886404 | KJ886243 | KJ885921 | KJ885760 | KJ886082 | |
CCTU 1063 | Ecballium elaterium* | Cucurbitaceae | Iran, Ardabil, Moghan | M. Bakhshi | KJ886405 | KJ886244 | KJ885922 | KJ885761 | KJ886083 | |
CCTU 1217 | Ecballium elaterium | Cucurbitaceae | Iran, Ardabil, Moghan | M. Bakhshi | KJ886406 | KJ886245 | KJ885923 | KJ885762 | KJ886084 | |
CCTU 1134 | Heliotropium europaeum | Boraginaceae | Iran, Guilan, Astara | M. Bakhshi | KJ886407 | KJ886246 | KJ885924 | KJ885763 | KJ886085 | |
CCTU 1200; CBS 138581 | Heliotropium europaeum | Boraginaceae | Iran, Ardabil, Moghan | M. Bakhshi | KJ886408 | KJ886247 | KJ885925 | KJ885764 | KJ886086 | |
CCTU 1061 | Cynanchum acutum* | Apocynaceae | Iran, Ardabil, Moghan | M. Bakhshi | KJ886409 | KJ886248 | KJ885926 | KJ885765 | KJ886087 | |
CCTU 1069 | Cynanchum acutum | Apocynaceae | Iran, Ardabil, Moghan | M. Bakhshi | KJ886410 | KJ886249 | KJ885927 | KJ885766 | KJ886088 | |
CCTU 1086; CBS 136037 | Cynanchum acutum | Apocynaceae | Iran, Ardabil, Moghan | M. Bakhshi | KJ886411 | KJ886250 | KJ885928 | KJ885767 | KJ886089 | |
CCTU 1215 | Cynanchum acutum | Apocynaceae | Iran, Ardabil, Moghan | M. Bakhshi | KJ886412 | KJ886251 | KJ885929 | KJ885768 | KJ886090 | |
CCTU 1219; CBS 136155 | Cynanchum acutum | Apocynaceae | Iran, Ardabil, Moghan | M. Bakhshi | KJ886413 | KJ886252 | KJ885930 | KJ885769 | KJ886091 | |
Cercospora armoraciae | CCTU 1013 | ? | ? | Iran, East Azerbaijan, Mianeh | M. Torbati | KJ886414 | KJ886253 | KJ885931 | KJ885770 | KJ886092 |
CCTU 1022; CBS 136028 | ? | ? | Iran, East Azerbaijan, Mianeh | M. Torbati | KJ886415 | KJ886254 | KJ885932 | KJ885771 | KJ886093 | |
CCTU 1040; CBS 136131 | Tanacetum balsamita* | Asteraceae | Iran, Zanjan, Tarom | M. Bakhshi | KJ886416 | KJ886255 | KJ885933 | KJ885772 | KJ886094 | |
CCTU 1107 | ? | Asteraceae | Iran, Zanjan, Tarom | M. Bakhshi | KJ886417 | KJ886256 | KJ885934 | KJ885773 | KJ886095 | |
CCTU 1117; CBS 136132 | Cardaria draba | Brassicaceae | Iran, West Azerbaijan, Khoy | M. Arzanlou | KJ886418 | KJ886257 | KJ885935 | KJ885774 | KJ886096 | |
CCTU 1234 | Cardaria draba | Brassicaceae | Iran, West Azerbaijan, Khoy | M. Arzanlou | KJ886419 | KJ886258 | KJ885936 | KJ885775 | KJ886097 | |
CCTU 1127; CBS 136133 | Capparis spinosa* | Capparidaceae | Iran, Khuzestan, Ahvaz | E. Mohammadian | KJ886420 | KJ886259 | KJ885937 | KJ885776 | KJ886098 | |
CCTU 1127.2 | Capparis spinosa | Capparidaceae | Iran, Khuzestan, Ahvaz | E. Mohammadian | KJ886421 | KJ886260 | KJ885938 | KJ885777 | KJ886099 | |
CCTU 1190; CBS 136134 | Coronilla varia | Fabaceae | Iran, West Azerbaijan, Khoy | M. Arzanlou | KJ886422 | KJ886261 | KJ885939 | KJ885778 | KJ886100 | |
Cercospora beticola | CCTU 1035 | Malva sylvestris | Malvaceae | Iran, Zanjan, Tarom | M. Bakhshi | KJ886423 | KJ886262 | KJ885940 | KJ885779 | KJ886101 |
CCTU 1057 | Chenopodium sp. | Chenopodiaceae | Iran, Ardabil, Moghan | M. Bakhshi | KJ886424 | KJ886263 | KJ885941 | KJ885780 | KJ886102 | |
CCTU 1065 | Chenopodium sp. | Chenopodiaceae | Iran, Ardabil, Moghan | M. Bakhshi | KJ886425 | KJ886264 | KJ885942 | KJ885781 | KJ886103 | |
CCTU 1074; CPC 24909 | Malva neglecta | Malvaceae | Iran, Ardabil, Moghan | M. Bakhshi | KJ886426 | KJ886265 | KJ885943 | KJ885782 | KJ886104 | |
CCTU 1087 | Chenopodium sp. | Chenopodiaceae | Iran, Ardabil, Moghan | M. Bakhshi | KJ886427 | KJ886266 | KJ885944 | KJ885783 | KJ886105 | |
CCTU 1088; CBS 138582 | Sonchus asper* | Asteraceae | Iran, Ardabil, Moghan | M. Bakhshi | KJ886428 | KJ886267 | KJ885945 | KJ885784 | KJ886106 | |
CCTU 1089; CPC 24911 | Plantago lanceolata* | Plantaginaceae | Iran, Ardabil, Moghan | M. Bakhshi | KJ886429 | KJ886268 | KJ885946 | KJ885785 | KJ886107 | |
CCTU 1108 | Plantago lanceolata | Plantaginaceae | Iran, Zanjan, Tarom | M. Bakhshi | KJ886430 | KJ886269 | KJ885947 | KJ885786 | KJ886108 | |
CCTU 1109 | Malva sylvestris | Malvaceae | Iran, Zanjan, Tarom | M. Bakhshi | KJ886431 | KJ886270 | KJ885948 | KJ885787 | KJ886109 | |
CCTU 1135 | Beta vulgaris | Chenopodiaceae | Iran, Guilan, Astara | M. Bakhshi | KJ886432 | KJ886271 | KJ885949 | KJ885788 | KJ886110 | |
CCTU 1199; CBS 136128 | Rumex crispus* | Polygonaceae | Iran, Mazandaran, Ramsar | M. Bakhshi | KJ886433 | KJ886272 | KJ885950 | KJ885789 | KJ886111 | |
CCTU 1201 | Malva neglecta | Malvaceae | Iran, Ardabil, Moghan | M. Bakhshi | KJ886434 | KJ886273 | KJ885951 | KJ885790 | KJ886112 | |
CCTU 1205; CBS 136127 | Sesamum indicum* | Pedaliaceae | Iran, Ardabil, Moghan | M. Bakhshi | KJ886435 | KJ886274 | KJ885952 | KJ885791 | KJ886113 | |
CCTU 1208 | Sonchus sp.* | Asteraceae | Iran, Ardabil, Moghan | M. Bakhshi | KJ886436 | KJ886275 | KJ885953 | KJ885792 | KJ886114 | |
Cercospora chenopodii | CCTU 1033 | Chenopodium album | Chenopodiaceae | Iran, Guilan, Talesh | M. Bakhshi | KJ886437 | KJ886276 | KJ885954 | KJ885793 | KJ886115 |
CCTU 1060 | Chenopodium album | Chenopodiaceae | Iran, Guilan, Bandar-e Anzali | M. Bakhshi | KJ886438 | KJ886277 | KJ885955 | KJ885794 | KJ886116 | |
CCTU 1157 | Chenopodium album | Chenopodiaceae | Iran, Guilan, Langroud | M. Bakhshi | KJ886439 | KJ886278 | KJ885956 | KJ885795 | KJ886117 | |
CCTU 1163 | Chenopodium album | Chenopodiaceae | Iran, Guilan, Lahijan | M. Bakhshi | KJ886440 | KJ886279 | KJ885957 | KJ885796 | KJ886118 | |
Cercospora convolvulicola | CCTU 1083; CBS 136126 (ex-type) | Convolvulus arvensis | Convolvulaceae | Iran, Ardabil, Moghan | M. Bakhshi | KJ886441 | KJ886280 | KJ885958 | KJ885797 | KJ886119 |
CCTU 1083.2 | Convolvulus arvensis | Convolvulaceae | Iran, Ardabil, Moghan | M. Bakhshi | KJ886442 | KJ886281 | KJ885959 | KJ885798 | KJ886120 | |
Cercospora conyzae-canadensis | CCTU 1008 | Conyza canadensis | Asteraceae | Iran, Guilan, Talesh | M. Bakhshi | KJ886443 | KJ886282 | KJ885960 | KJ885799 | KJ886121 |
CCTU 1105 | Conyza canadensis | Asteraceae | Iran, Zanjan, Tarom | M. Bakhshi | KJ886444 | KJ886283 | KJ885961 | KJ885800 | KJ886122 | |
CCTU 1119; CBS 135978 (ex-type) | Conyza canadensis | Asteraceae | Iran, Guilan, Talesh | M. Bakhshi | KJ886445 | KJ886284 | KJ885962 | KJ885801 | KJ886123 | |
Cercospora cylindracea | CCTU 1016 | Cichorium intybus | Asteraceae | Iran, West Azerbaijan, Khoy | M. Arzanlou | KJ886446 | KJ886285 | KJ885963 | KJ885802 | KJ886124 |
CCTU 1044; CBS 136021 | Lactuca serriola | Asteraceae | Iran, West Azerbaijan, Khoy | M. Arzanlou | KJ886447 | KJ886286 | KJ885964 | KJ885803 | KJ886125 | |
CCTU 1049 | Lactuca serriola | Asteraceae | Iran, Zanjan, Tarom | M. Bakhshi | KJ886448 | KJ886287 | KJ885965 | KJ885804 | KJ886126 | |
CCTU 1081; CBS 138580 (ex-type) | Lactuca serriola | Asteraceae | Iran, Ardabil, Moghan | M. Bakhshi | KJ886449 | KJ886288 | KJ885966 | KJ885805 | KJ886127 | |
CCTU 1114 | Cichorium intybus | Asteraceae | Iran, Zanjan, Tarom | M. Bakhshi | KJ886450 | KJ886289 | KJ885967 | KJ885806 | KJ886128 | |
CCTU 1183 | Lactuca serriola | Asteraceae | Iran, West Azerbaijan, Khoy | M. Arzanlou | KJ886451 | KJ886290 | KJ885968 | KJ885807 | KJ886129 | |
CCTU 1189 | Lactuca serriola | Asteraceae | Iran, West Azerbaijan, Khoy | M. Arzanlou | KJ886452 | KJ886291 | KJ885969 | KJ885808 | KJ886130 | |
CCTU 1207 | Lactuca serriola | Asteraceae | Iran, Ardabil, Moghan | M. Bakhshi | KJ886453 | KJ886292 | KJ885970 | KJ885809 | KJ886131 | |
Cercosporacf. flagellaris | CCTU 1005 | Xanthium strumarium* | Asteraceae | Iran, Guilan, Talesh | M. Bakhshi | KJ886454 | KJ886293 | KJ885971 | KJ885810 | KJ886132 |
CCTU 1006; CBS 136030 | Impatiens balsamina* | Balsaminaceae | Iran, Guilan, Talesh | M. Bakhshi | KJ886455 | KJ886294 | KJ885972 | KJ885811 | KJ886133 | |
CCTU 1007; CBS 136031 | Hydrangea sp. | Hydrangeaceae | Iran, Guilan, Talesh | M. Bakhshi | KJ886456 | KJ886295 | KJ885973 | KJ885812 | KJ886134 | |
CCTU 1010; CBS 136032 | Pelargonium hortorum* | Geraniaceae | Iran, Guilan, Talesh | M. Bakhshi | KJ886457 | KJ886296 | KJ885974 | KJ885813 | KJ886135 | |
CCTU 1021; CBS 136033 | Amaranthus retroflexus | Amaranthaceae | Iran, Guilan, Fuman | M. Bakhshi | KJ886458 | KJ886297 | KJ885975 | KJ885814 | KJ886136 | |
CCTU 1027; CBS 136034 | Lepidium sativum* | Brassicaceae | Iran, Guilan, Chamkhaleh | M. Bakhshi | KJ886459 | KJ886298 | KJ885976 | KJ885815 | KJ886137 | |
CCTU 1029; CBS 136035 | Cucurbita maxima* | Cucurbitaceae | Iran, Guilan, Rudsar | M. Bakhshi | KJ886460 | KJ886299 | KJ885977 | KJ885816 | KJ886138 | |
CCTU 1031; CBS 136036 | Urtica dioica* | Urticaceae | Iran, Guilan, Sowme’eh Sara | M. Bakhshi | KJ886461 | KJ886300 | KJ885978 | KJ885817 | KJ886139 | |
CCTU 1048; CBS 136029 | Xanthium strumarium | Asteraceae | Iran, Zanjan, Tarom | M. Bakhshi | KJ886462 | KJ886301 | KJ885979 | KJ885818 | KJ886140 | |
CCTU 1055 | Hibiscus trionum* | Malvaceae | Iran, Ardabil, Moghan | M. Bakhshi | KJ886463 | KJ886302 | KJ885980 | KJ885819 | KJ886141 | |
CCTU 1059; CBS 136136 | Ecballium elaterium* | Cucurbitaceae | Iran, Ardabil, Moghan | M. Bakhshi | KJ886464 | KJ886303 | KJ885981 | KJ885820 | KJ886142 | |
CCTU 1064 | Amaranthus retroflexus | Amaranthaceae | Iran, Ardabil, Moghan | M. Bakhshi | KJ886465 | KJ886304 | KJ885982 | KJ885821 | KJ886143 | |
CCTU 1068 | Xanthium spinosum* | Asteraceae | Iran, Ardabil, Moghan | M. Bakhshi | KJ886466 | KJ886305 | KJ885983 | KJ885822 | KJ886144 | |
CCTU 1070; CBS 136137 | Gossypium herbaceum* | Malvaceae | Iran, Ardabil, Moghan | M. Bakhshi | KJ886467 | KJ886306 | KJ885984 | KJ885823 | KJ886145 | |
CCTU 1072 | Amaranthus blitoides | Amaranthaceae | Iran, Ardabil, Moghan | M. Bakhshi | KJ886468 | KJ886307 | KJ885985 | KJ885824 | KJ886146 | |
CCTU 1075 | Raphanus sativus* | Brassicaceae | Iran, Guilan, Sowme’eh Sara | M. Bakhshi | KJ886469 | KJ886308 | KJ885986 | KJ885825 | KJ886147 | |
CCTU 1084; CBS 136156 | Amaranthus sp. | Amaranthaceae | Iran, Ardabil, Moghan | M. Bakhshi | KJ886470 | KJ886309 | KJ885987 | KJ885826 | KJ886148 | |
CCTU 1085 | Xanthium strumarium | Asteraceae | Iran, Ardabil, Moghan | M. Bakhshi | KJ886471 | KJ886310 | KJ885988 | KJ885827 | KJ886149 | |
CCTU 1093 | Buxus microphylla* | Buxaceae | Iran, Mazandaran, Abbas abad | M. Bakhshi | KJ886472 | KJ886311 | KJ885989 | KJ885828 | KJ886150 | |
CCTU 1115; CBS 136139 | Cercis siliquastrum* | Caesalpinaceae | Iran, Guilan, Astara | M. Bakhshi | KJ886473 | KJ886312 | KJ885990 | KJ885829 | KJ886151 | |
CCTU 1118; CBS 136140 | Populus deltoides | Salicaceae | Iran, Guilan, Astara | M. Bakhshi | KJ886474 | KJ886313 | KJ885991 | KJ885830 | KJ886152 | |
CCTU 1120 | Raphanus sativus | Brassicaceae | Iran, Guilan, Talesh | M. Bakhshi | KJ886475 | KJ886314 | KJ885992 | KJ885831 | KJ886153 | |
CCTU 1128; CBS 136141 | Phaseolus vulgaris* | Fabaceae | Iran, Guilan, Astara | M. Bakhshi | KJ886476 | KJ886315 | KJ885993 | KJ885832 | KJ886154 | |
CCTU 1130; CBS 136142 | Olea europaea* | Oleaceae | Iran, Zanjan, Tarom | M. Torbati | KJ886477 | KJ886316 | KJ885994 | KJ885833 | KJ886155 | |
CCTU 1136 | Cucurbita pepo* | Cucurbitaceae | Iran, Guilan, Astara | M. Bakhshi | KJ886478 | KJ886317 | KJ885995 | KJ885834 | KJ886156 | |
CCTU 1138 | Phaseolus vulgaris | Fabaceae | Iran, Guilan, Astara | M. Bakhshi | KJ886479 | KJ886318 | KJ885996 | KJ885835 | KJ886157 | |
CCTU 1139 | Phaseolus vulgaris | Fabaceae | Iran, Guilan, Astara | M. Bakhshi | KJ886480 | KJ886319 | KJ885997 | KJ885836 | KJ886158 | |
CCTU 1140; CBS 136143 | Calendula officinalis* | Asteraceae | Iran, Guilan, Astara | M. Bakhshi | KJ886481 | KJ886320 | KJ885998 | KJ885837 | KJ886159 | |
CCTU 1141; CBS 136144 | Tagetes patula* | Asteraceae | Iran, Guilan, Rudsar | M. Bakhshi | KJ886482 | KJ886321 | KJ885999 | KJ885838 | KJ886160 | |
CCTU 1142 | Phaseolus vulgaris | Fabaceae | Iran, Guilan, Talesh | M. Bakhshi | KJ886483 | KJ886322 | KJ886000 | KJ885839 | KJ886161 | |
CCTU 1143; CBS 136145 | Datura stramonium* | Solanaceae | Iran, Guilan, Talesh | M. Bakhshi | KJ886484 | KJ886323 | KJ886001 | KJ885840 | KJ886162 | |
CCTU 1145 | Cucurbita sp.* | Cucurbitaceae | Iran, Guilan, Fuman | M. Bakhshi | KJ886485 | KJ886324 | KJ886002 | KJ885841 | KJ886163 | |
CCTU 1147 | Urtica dioica | Urticaceae | Iran, Guilan, Masal | M. Bakhshi | KJ886486 | KJ886325 | KJ886003 | KJ885842 | KJ886164 | |
CCTU 1149; CBS 136146 | Leucanthemum superbum* | Asteraceae | Iran, Guilan, Talesh | M. Bakhshi | KJ886487 | KJ886326 | KJ886004 | KJ885843 | KJ886165 | |
CCTU 1150 | Buxus microphylla | Buxaceae | Iran, Guilan, Fuman | M. Bakhshi | KJ886488 | KJ886327 | KJ886005 | KJ885844 | KJ886166 | |
CCTU 1154; CBS 136147 | Abutilon theophrasti* | Malvaceae | Iran, Guilan, Rasht | M. Bakhshi | KJ886489 | KJ886328 | KJ886006 | KJ885845 | KJ886167 | |
CCTU 1155.11 | Phaseolus vulgaris | Fabaceae | Iran, Guilan, Fuman | M. Bakhshi | KJ886490 | KJ886329 | KJ886007 | KJ885846 | KJ886168 | |
CCTU 1156 | Xanthium strumarium | Asteraceae | Iran, Guilan, Rasht | M. Bakhshi | KJ886491 | KJ886330 | KJ886008 | KJ885847 | KJ886169 | |
CCTU 1158 | Xanthium strumarium | Asteraceae | Iran, Guilan, Langroud | M. Bakhshi | KJ886492 | KJ886331 | KJ886009 | KJ885848 | KJ886170 | |
CCTU 1159; CBS 136148 | Arachis hypogaea* | Fabaceae | Iran, Guilan, Lahijan | M. Bakhshi | KJ886493 | KJ886332 | KJ886010 | KJ885849 | KJ886171 | |
CCTU 1160; CBS 136149 | Vicia faba* | Fabaceae | Iran, Guilan, Astara | M. Bakhshi | KJ886494 | KJ886333 | KJ886011 | KJ885850 | KJ886172 | |
CCTU 1161 | Phaseolus vulgaris | Fabaceae | Iran, Guilan, Lahijan | M. Bakhshi | KJ886495 | KJ886334 | KJ886012 | KJ885851 | KJ886173 | |
CCTU 1162 | Citrullus lanatus | Cucurbitaceae | Iran, Guilan, Lahijan | M. Bakhshi | KJ886496 | KJ886335 | KJ886013 | KJ885852 | KJ886174 | |
CCTU 1164 | Phaseolus vulgaris | Fabaceae | Iran, Guilan, Lahijan | M. Bakhshi | KJ886497 | KJ886336 | KJ886014 | KJ885853 | KJ886175 | |
CCTU 1167; CBS 136150 | Anubias sp.* | Araceae | Iran, Guilan, Kiashahr | M. Bakhshi | KJ886498 | KJ886337 | KJ886015 | KJ885854 | KJ886176 | |
CCTU 1168 | Phaseolus vulgaris | Fabaceae | Iran, Guilan, Kiashahr | M. Bakhshi | KJ886499 | KJ886338 | KJ886016 | KJ885855 | KJ886177 | |
CCTU 1171 | Raphanus sativus | Brassicaceae | Iran, Guilan, Kiashahr | M. Bakhshi | KJ886500 | KJ886339 | KJ886017 | KJ885856 | KJ886178 | |
CCTU 1172 | ? | ? | Iran, Guilan, Kiashahr | M. Bakhshi | KJ886501 | KJ886340 | KJ886018 | KJ885857 | KJ886179 | |
CCTU 1175 | Phaseolus vulgaris | Fabaceae | Iran, Guilan, Sowme’eh Sara | M. Bakhshi | KJ886502 | KJ886341 | KJ886019 | KJ885858 | KJ886180 | |
CCTU 1195 | Datura stramonium | Solanaceae | Iran, Guilan, Talesh | M. Bakhshi | KJ886503 | KJ886342 | KJ886020 | KJ885859 | KJ886181 | |
CCTU 1198; CBS 136151 | Acer velutinum* | Aceraceae | Iran, Mazandaran, Ramsar | M. Bakhshi | KJ886504 | KJ886343 | KJ886021 | KJ885860 | KJ886182 | |
CCTU 1204 | Abutilon theophrasti | Malvaceae | Iran, Ardabil, Moghan | M. Bakhshi | KJ886505 | KJ886344 | KJ886022 | KJ885861 | KJ886183 | |
CCTU 1209; CBS 136152 | Glycine max* | Fabaceae | Iran, Ardabil, Moghan | M. Bakhshi | KJ886506 | KJ886345 | KJ886023 | KJ885862 | KJ886184 | |
CCTU 1210 | Glycine max | Fabaceae | Iran, Ardabil, Moghan | M. Bakhshi | KJ886507 | KJ886346 | KJ886024 | KJ885863 | KJ886185 | |
CCTU 1211 | Glycine max | Fabaceae | Iran, Ardabil, Moghan | M. Bakhshi | KJ886508 | KJ886347 | KJ886025 | KJ885864 | KJ886186 | |
CCTU 1212; CBS 136153 | Silybum marianum* | Asteraceae | Iran, Ardabil, Moghan | M. Bakhshi | KJ886509 | KJ886348 | KJ886026 | KJ885865 | KJ886187 | |
CCTU 1216 | Ecballium elaterium | Cucurbitaceae | Iran, Ardabil, Moghan | M. Bakhshi | KJ886510 | KJ886349 | KJ886027 | KJ885866 | KJ886188 | |
CCTU 1218 | Hibiscus trionum | Malvaceae | Iran, Ardabil, Moghan | M. Bakhshi | KJ886511 | KJ886350 | KJ886028 | KJ885867 | KJ886189 | |
CCTU 1223; CBS 136154 | Eclipta prostrata* | Asteraceae | Iran, Guilan, Talesh | M. Bakhshi | KJ886512 | KJ886351 | KJ886029 | KJ885868 | KJ886190 | |
Cercospora iranica | CCTU 1137; CBS 136124 (ex-type) | Vicia faba | Fabaceae | Iran, Guilan, Astara | M. Bakhshi | KJ886513 | KJ886352 | KJ886030 | KJ885869 | KJ886191 |
CCTU 1137.2 | Vicia faba | Fabaceae | Iran, Guilan, Astara | M. Bakhshi | KJ886514 | KJ886353 | KJ886031 | KJ885870 | KJ886192 | |
CCTU 1196; CBS 136123 | Hydrangea sp. | Hydrangeaceae | Iran, Mazandaran, Ramsar | M. Bakhshi | KJ886515 | KJ886354 | KJ886032 | KJ885871 | KJ886193 | |
Cercospora pseudochenopodii | CCTU 1038; CBS 136022 | (ex-type) Chenopodium sp. | Chenopodiaceae | Iran, Zanjan, Tarom | M. Bakhshi | KJ886516 | KJ886355 | KJ886033 | KJ885872 | KJ886194 |
CCTU 1045 | Chenopodium sp. | Chenopodiaceae | Iran, West Azerbaijan, Khoy | M. Arzanlou | KJ886517 | KJ886356 | KJ886034 | KJ885873 | KJ886195 | |
CCTU 1176 | Chenopodium album | Chenopodiaceae | Iran, West Azerbaijan, Khoy | M. Arzanlou | KJ886518 | KJ886357 | KJ886035 | KJ885874 | KJ886196 | |
Cercosporacf. richardiicola | CCTU 1004 | Bidens tripartita* | Asteraceae | Iran, Guilan, Talesh | M. Bakhshi | KJ886519 | KJ886358 | KJ886036 | KJ885875 | KJ886197 |
Cercospora rumicis | CCTU 1121 | Urtica dioica* | Urticaceae | Iran, Guilan, Talesh | M. Bakhshi | KJ886520 | KJ886359 | KJ886037 | KJ885876 | KJ886198 |
CCTU 1123 | Rumex crispus | Polygonaceae | Iran, Guilan, Talesh | M. Bakhshi | KJ886521 | KJ886360 | KJ886038 | KJ885877 | KJ886199 | |
CCTU 1129 | Rumex crispus | Polygonaceae | Iran, Guilan, Talesh | M. Bakhshi | KJ886522 | KJ886361 | KJ886039 | KJ885878 | KJ886200 | |
Cercospora solani | CCTU 1043; CBS 136038 | Solanum nigrum | Solanaceae | Iran, West Azerbaijan, Khoy | M. Arzanlou | KJ886523 | KJ886362 | KJ886040 | KJ885879 | KJ886201 |
CCTU 1050 | Solanum nigrum | Solanaceae | Iran, West Azerbaijan, Khoy | M. Arzanlou | KJ886524 | KJ886363 | KJ886041 | KJ885880 | KJ886202 | |
Cercospora sorghicola | CCTU 1173; CBS 136448 | (ex-type) Sorghum halepense | Poaceae | Iran, Guilan, Kiashahr | M. Bakhshi | KJ886525 | KJ886364 | KJ886042 | KJ885881 | KJ886203 |
CCTU 1173.2 | Sorghum halepense | Poaceae | Iran, Guilan, Kiashahr | M. Bakhshi | KJ886526 | KJ886365 | KJ886043 | KJ885882 | KJ886204 | |
Cercospora sp. G | CCTU 1002 | Celosia cristata | Amaranthaceae | Iran, Guilan, Talesh | M. Bakhshi | KJ886527 | KJ886366 | KJ886044 | KJ885883 | KJ886205 |
CCTU 1015; CBS 136024 | Plantago major | Plantaginaceae | Iran, Guilan, Talesh | M. Bakhshi | KJ886528 | KJ886367 | KJ886045 | KJ885884 | KJ886206 | |
CCTU 1020; CBS 136023 | Sorghum halepense | Poaceae | Iran, Guilan, Talesh | M. Bakhshi | KJ886529 | KJ886368 | KJ886046 | KJ885885 | KJ886207 | |
CCTU 1030; CBS 136026 | Bidens tripartita | Asteraceae | Iran, Guilan, Talesh | M. Bakhshi | KJ886530 | KJ886369 | KJ886047 | KJ885886 | KJ886208 | |
CCTU 1046 | Plantago major | Plantaginaceae | Iran, Zanjan, Tarom | M. Bakhshi | KJ886531 | KJ886370 | KJ886048 | KJ885887 | KJ886209 | |
CCTU 1053; CBS 136027 | Cichorium intybus | Asteraceae | Iran, Guilan, Sowme’eh Sara | M. Bakhshi | KJ886532 | KJ886371 | KJ886049 | KJ885888 | KJ886210 | |
CCTU 1054 | Amaranthus sp. | Amaranthaceae | Iran, Ardabil, Moghan | M. Bakhshi | KJ886533 | KJ886372 | KJ886050 | KJ885889 | KJ886211 | |
CCTU 1058 | ? | Asteraceae | Iran, Ardabil, Moghan | M. Bakhshi | KJ886534 | KJ886373 | KJ886051 | KJ885890 | KJ886212 | |
CCTU 1079; CBS 136025 | Amaranthus retroflexus | Amaranthaceae | Iran, Ardabil, Moghan | M. Bakhshi | KJ886535 | KJ886374 | KJ886052 | KJ885891 | KJ886213 | |
CCTU 1090 | Abutilon theophrasti | Malvaceae | Iran, Ardabil, Moghan | M. Bakhshi | KJ886536 | KJ886375 | KJ886053 | KJ885892 | KJ886214 | |
CCTU 1116 | Plantago major | Plantaginaceae | Iran, Zanjan, Tarom | M. Bakhshi | KJ886537 | KJ886376 | KJ886054 | KJ885893 | KJ886215 | |
CCTU 1122 | Amaranthus sp. | Amaranthaceae | Iran, Guilan, Talesh | M. Bakhshi | KJ886538 | KJ886377 | KJ886055 | KJ885894 | KJ886216 | |
CCTU 1144; CBS 136130 | Cucurbita maxima | Cucurbitaceae | Iran, Guilan, Masal | M. Bakhshi | KJ886539 | KJ886378 | KJ886056 | KJ885895 | KJ886217 | |
CCTU 1197 | Bidens tripartita | Asteraceae | Iran, Guilan, Talesh | M. Bakhshi | KJ886540 | KJ886379 | KJ886057 | KJ885896 | KJ886218 | |
Cercospora sp. T | CCTU 1148; CBS 136125 | Coreopsis sp. | Asteraceae | Iran, Guilan, Rasht | M. Bakhshi | KJ886541 | KJ886380 | KJ886058 | KJ885897 | KJ886219 |
CCTU 1148.2 | Coreopsis sp. | Asteraceae | Iran, Guilan, Rasht | M. Bakhshi | KJ886542 | KJ886381 | KJ886059 | KJ885898 | KJ886220 | |
Cercospora violae | CCTU 1025 | Viola sp. | Violaceae | Iran, Mazandaran, Nowshahr | M. Bakhshi | KJ886543 | KJ886382 | KJ886060 | KJ885899 | KJ886221 |
Cercospora zebrina | CCTU 1012; CBS 136129 | Medicago sp. | Fabaceae | Iran, Guilan, Talesh | M. Bakhshi | KJ886544 | KJ886383 | KJ886061 | KJ885900 | KJ886222 |
CCTU 1039 | Alhagi camelorum* | Fabaceae | Iran, Zanjan, Tarom | M. Bakhshi | KJ886545 | KJ886384 | KJ886062 | KJ885901 | KJ886223 | |
CCTU 1110 | Medicago sativa | Fabaceae | Iran, Zanjan, Tarom | M. Bakhshi | KJ886546 | KJ886385 | KJ886063 | KJ885902 | KJ886224 | |
CCTU 1180 | Medicago sativa | Fabaceae | Iran, West Azerbaijan, Khoy | M. Arzanlou | KJ886547 | KJ886386 | KJ886064 | KJ885903 | KJ886225 | |
CCTU 1181 | Trifolium repens | Fabaceae | Iran, West Azerbaijan, Khoy | M. Arzanlou | KJ886548 | KJ886387 | KJ886065 | KJ885904 | KJ886226 | |
CCTU 1185 | Vicia sp.* | Fabaceae | Iran, West Azerbaijan, Khoy | M. Arzanlou | KJ886549 | KJ886388 | KJ886066 | KJ885905 | KJ886227 | |
CCTU 1225 | Medicago sativa | Fabaceae | Iran, East Azerbaijan, Marand | M. Bakhshi | KJ886550 | KJ886389 | KJ886067 | KJ885906 | KJ886228 | |
CCTU 1239; CBS 135977 | Vitis vinifera* | Vitaceae | Iran, East Azerbaijan, Kaleibar | M. Arzanlou | KJ886551 | KJ886390 | KJ886068 | KJ885907 | KJ886229 | |
Cercospora cf. zinniae | CCTU 1003 | Zinnia elegans | Asteraceae | Iran, Guilan, Talesh | M. Bakhshi | KJ886552 | KJ886391 | KJ886069 | KJ885908 | KJ886230 |
Ramularia endophylla | CBS 113265 | Leaf litter | – | The Netherlands, Utrecht | G.J.M. Verkley | KF251329 | KF253276 | KF253634 | KF253981 | KP207603 |
1 CBS: CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands; CCTU: Culture Collection of Tabriz University, Tabriz, Iran.
2 ITS: internal transcribed spacers and intervening 5.8S nrDNA; TEF1-α: translation elongation factor 1-alpha; ACT: actin; CAL: calmodulin; HIS: histone H3
* new host records.
DNA extraction, amplification and sequencing
Isolates were grown on MEA for 10 d at 25 °C in the dark, and genomic DNA was extracted using the protocol of Möller et al. (1992). The DNA samples were subsequently diluted 50–100 times in preparation for further DNA amplification reactions. Five loci were sequenced for each isolate. The primers V9G (de Hoog & Gerrits van den Ende 1998) and ITS4 (White et al. 1990) were used to amplify part of the nuclear rRNA operon (ITS) spanning the 3’ end of 18S rRNA gene, the first internal transcribed spacer, the 5.8S rRNA gene, the second ITS region and the 5’ end of the 28S rRNA gene. Part of the actin gene (ACT) was amplified using the primer set ACT-512F and ACT-783R (Carbone & Kohn 1999), whereas the primer set CylH3F and CylH3R (Crous et al. 2004c) was used to amplify part of the histone H3 gene (HIS). Primers employed for the amplification of translation elongation factor 1-alpha (TEF1-α) included EF1-728F and EF1-986R (Carbone & Kohn 1999) or EF-2 (O‘Donnell et al. 1998), while the primer set CAL-228F and CAL-737R (Carbone & Kohn 1999) or CAL-2Rd (Groenewald et al. 2013) was used to amplify part of the calmodulin gene (CAL). The PCRs were performed in a total volume of 12.5 μL. The ITS, HIS, TEF1-α and ACT mixtures contained 5–10 ng genomic DNA, 1X PCR buffer (Bioline, London, UK), 2 mM MgCl2 (Bioline), 40 μM of each dNTP, 0.7 μL DMSO, 0.2 μM of each primer and 0.5 Unit GoTaq® Flexi DNA polymerase (Promega, Madison, USA). The CAL PCR mixture differed from the original mix by containing 2.5 mM MgCl2 and 10–20 ng genomic DNA. The PCR conditions for ITS, HIS, TEF1-α and ACT consisted of an initial denaturation step of 5 min at 95 °C followed by 40 cycles of 30 s at 95 °C, 30 s at 52 °C and 45 s at 72 °C, then 5 min at 72 °C and PCR conditions for CAL consisted of an initial denaturation step of 5 min at 95 °C followed by 40 cycles of 30 s at 95 °C, 40 s at 58 °C/55 °C and 50 s at 72 °C using respectively CAL-737R or CAL-2Rd as reverse primer and final elongation step of 5 min at 72 °C. Following PCR amplification, amplicons were visualized on a 1.2 % agarose gel stained with GelRed™ (Biotium, Hayward, CA, USA) and viewed under ultra-violet light and sizes of amplicons were determined against a HyperLadder™ I molecular marker (Bioline). The ABI Prism BigDye® Terminator Cycle sequencing reaction kit v. 3.1 (Applied Biosystems™, Foster City, CA, USA) was used for sequencing of PCR products in both directions using the same primers pairs used for amplification, following the manufacturer‘s instructions. Sequencing products were purified through a 96-well multiscreen HV plate (Millipore) containing Sephadex G-50 (Sigma Aldrich, St. Louis, MO) as outlined by the manufacturer and analysed with an ABI Prism 3730XL Automated DNA analyzer (Life Technologies Europe BV, Applied Biosystems™, Bleiswijk, The Netherlands) according to manufacturer‘s recommendation.
Phylogenetic analyses
The raw trace files were edited using MEGA v. 5 (Tamura et al. 2011) and a consensus sequence was generated manually for each set of trace files from a given reaction. The generated sequences were compared with other fungal DNA sequences from NCBIs GenBank sequence database using BLAST; sequences with high similarity were added to the alignments. Sequences of Ramularia endophylla (isolate CBS 113265) were used as the outgroup based on availability and phylogenetic relationship with Cercospora. A basic alignment of the obtained sequences in this study together with the sequence data from GenBank and the outgroup sequences was first done using MAFFT v. 7 (http://mafft.cbrc.jp/alignment/server/index.html) (Katoh et al. 2002); and when considered necessary, manual adjustments were made by eye in MEGA v. 5 (Tamura et al. 2011).
Phylogenetic analyses were based on Bayesian inference (BI). For this purpose, the best nucleotide substitution model for each partition was determined using MrModeltest v. 2.2 (Nylander 2004). Based on the results of MrModeltest, a phylogenetic reconstruction under optimal criteria per partition was performed for the aligned combined dataset and phylogenetic trees were generated using MrBayes v. 3.2.1. (Ronquist & Huelsenbeck 2003). A Markov Chain Monte Carlo (MCMC) algorithm of four chains was started in parallel from a random tree topology with the heating parameter set at 0.15 and lasted until the average standard deviation of split frequencies came below 0.01. Trees were saved every 1 000 generations, the first 25 % of saved trees were discarded as the ‘burn-in’ phase and posterior probabilities (PP) determined from the remaining trees.
The resulting phylogenetic tree was printed with Geneious v. 5.6.7 (Drummond et al. 2012). Newly generated sequences in this study were deposited in NCBIs GenBank nucleotide database (http://www.ncbi.nlm.nih.gov; Table 1) and alignments and phylogenetic trees in TreeBASE (www.treebase.org). The GenBank accession numbers for the strains obtained from NCBI can be found in Groenewald et al. (2013).
Taxonomy
All taxonomic descriptions are based on structures from herbarium material. Diseased leaf tissues were observed under a stereo-microscope and relevant morphological structures (stromata, conidiophores and conidia) were picked up from lesions with a sterile inoculation needle and mounted on glass slides in clear lactic acid. Thirty measurements were made at × 1 000 magnification using a Nikon Eclipse 80i light microscope for each microscopic structure, and 95 % confidence intervals were derived for the measurements with extreme values given in parentheses. High-resolution photographic images of microscopic fungal structures were captured with a Nikon digital sight DS-f1 high definition colour camera mounted on the Nikon Eclipse 80i light microscope. Adobe Photoshop CS3 was used for the final editing of acquired images and photographic preparations. Colony colours on MEA were determined after 1 mo at 25 °C in the dark in duplicate. The mycological colour charts of Rayner (1970) were used to define colours of the fungal colonies. Nomenclatural novelties and descriptions were deposited in MycoBank (www.MycoBank.org; Crous et al. 2004a). The naming system for tentatively applied names used by Groenewald et al. (2013) is continued in this manuscript to simplify comparison between the studies.
RESULTS
DNA sequencing and phylogenetic analysis
A total of 161 Cercospora isolates corresponding to 74 host species and 28 host families were collected for DNA sequence analysis from the north and north-western parts of Iran. Approximately 700, 300, 200, 450 and 400 bp were obtained for ITS, TEF1-α, ACT, CAL and HIS loci, respectively.
The resulting concatenated alignment contains 294 ingroup taxa (including 133 taxa from NCBI, and 161 taxa from this study) with a total of 1 634 characters (including alignment gaps). Ramularia endophylla (isolate CBS 113265) was used as the outgroup taxon. Four sets of four Ns were used in the alignment to separate adjacent loci and were excluded from the phylogenetic analyses. The gene boundaries were 1–474 bp for ITS, 479–802 bp for TEF1-α, 807–1 006 bp for ACT, 1 011–1 268 bp for CAL and 1 273–1 634 bp for HIS. Based on the results of MrModeltest, a GTR+G model with a gamma-distributed rate variation for ITS, ACT and CAL, and HKY+G with gamma-distributed rates for TEF1-α were suggested while HIS required HKY+I+G with inverse gamma distributed. All partitions had dirichlet base frequencies. From this alignment 1 618 characters were used for the Bayesian analysis; these contained 625 unique site patterns (54, 211, 112, 124 and 124 for ITS, TEF1-α, ACT, CAL and HIS, respectively). The Bayesian analysis lasted 28 720 000 generations and delineated a total of 57 442 trees. After discarding the first 25 % of sampled trees (the first 7 180 000 generations) for burn-in, the consensus trees and posterior probabilities were calculated from the remaining 43 082 trees.
All genes were also assessed individually using Bayesian analysis under the above-mentioned substitution models, for each data partition (data not shown). The ITS region had limited resolution for almost all species in Cercospora, and was only able to distinguish C. chenopodii, C. solani and C. sorghicola from the other species examined. Based on the TEF1-α region, we were able to distinguish seven of the 20 species including C. chenopodii, C. conyzae-canadensis, C. rumicis, C. solani, C. sorghicola, C. violae and C. cf. zinniae, whereas nine of the 20 species including C. althaeina, C. chenopodii, C. conyzaecanadensis, C. cylindracea, C. pseudochenopodii, C. solani, C. sorghicola, C. violae and C. cf. zinniae were distinguished in the ACT phylogeny. Based on the CAL region, we were able to differentiate eight of the 20 lineages, i.e. C. armoraciae, C. beticola, C. conyzae-canadensis, C. solani, C. sorghicola, Cercospora sp. T, C. violae and C. cf. zinniae. Based on the HIS region, we distinguished 10 of the 20 lineages, including C. chenopodii, C. conyzae-canadensis, C. cylindracea, C. pseudochenopodii, C. rumicis, C. solani, C. sorghicola, Cercospora sp. G sensu Groenewald et al. (2013), C. violae and C. zebrina.
Based on results of the multigene concatenated BI phylogenies, the posterior probability (PP) support for the grouping of most species ranged from 1 to 0.97 as found by Groenewald et al. (2013). However support for deeper nodes were often lower, indicating that the branching may be uncertain for the root of these species. As previously stated by Groenewald et al. (2013), no single locus was found which could reliably distinguish all species and, occurrences of the same sequence(s) shared between multiple species in one locus, were observed.
Taxonomy
The Consolidated Species Concept was employed in this study to distinguish species, revealing a rich diversity among the Cercospora species studied. Twenty lineages of Cercospora from Iran were resolved based on the clustering and support in the Bayesian tree obtained from the combined ITS, TEF1-α, ACT, CAL and HIS alignment (Fig. 1). Data are alphabetically summarised in Table 1. Eight species including C. althaeina, C. apii (species complex), C. armoraciae (species complex), C. beticola, C. chenopodii, C. rumicis, C. violae and C. zebrina were assigned to existing species names. Three more species including C. cf. flagellaris (species complex), C. cf. richardiicola and C. cf. zinniae were morphologically similar to existing species, but as explained by Groenewald et al. (2013), these names could not be applied in cases where the ex-type strain was unavailable. In these cases, species were indicated with ‘cf.’ in the species name.
In addition, several new hosts were recognised for the previously known Cercospora species including C. apii, C. armoraciae, C. beticola, C. cf. richardiicola, C. rumicis, Cercospora sp. G and C. zebrina. Novel host records are shown with an asterisk in Table 1. Cercospora cf. flagellaris and Cercospora sp. G sensu Groenewald et al. (2013), two species with wide host ranges (infecting 18 and six host families respectively in this study), were common species in the sampled areas, and sometimes these two species infected the same host at the same time.
Furthermore, eight additional lineages were recognised in this study. Identification of these lineages required careful morphological comparison and consideration of host-fungus relationships, as well as knowledge of the relevant scientific literature (Crous & Braun 2003) and databases (Systematic Mycology and Microbiology Laboratory (SMML), http://nt.ars-grin.gov/fungaldatabases/fungushost/fungushost.cfm).
Cercospora chenopodii Fresen., Beitr. Mykol.: 92. 1863 — Fig. 2
Additional synonyms in Groenewald et al. (2013)
Description in planta — Leaf spots amphigenous, distinct, circular to subcircular, 2–6 mm diam, pale brown with black dots (stroma with conidiophores), definite margin, surrounded by a dark pink border. Mycelium internal. Caespituli amphigenous, brown. Conidiophores aggregated in dense fascicles (5–35), arising from the upper cells of a moderately developed brown stroma, up to 70 μm wide; conidiophores medium brown, becoming pale brown towards the apex, 2–8-septate, straight to variously curved, unbranched, (40–)62–72(–90) × 4–6 μm, width of conidiogenous cells immediately behind the fertile region is often narrower. Conidiogenous cells intercalary and terminal, unbranched, pale brown, smooth, proliferating sympodially, 20–50 × 4–6 μm, mostly mono-local, sometimes multi-local; loci thickened, darkened, protuberant, refractive, apical or lateral, 2–3.5 μm diam. Conidia solitary, smooth, subcylindrical, straight to slightly curved, hyaline, distinctly (0–) 2 – 4 (– 5)-septate, apex obtuse, base obconically truncate, sometimes constricted at the septa, (20–)27– 32(–40) × 5– 6(–7) μm; hila thickened, darkened, refractive, 2 – 4 μm diam.
Specimens examined. IRAN, Guilan Province, Talesh, on leaves of Chenopodium album (Chenopodiaceae), Sept. 2011, M. Bakhshi, CCTU 1033; Guilan Province, Bandar-e Anzali, on leaves of C. album (Chenopodiaceae), June 2012, M. Bakhshi, CCTU 1060; Guilan Province, Langroud, on leaves of C. album (Chenopodiaceae), Aug. 2012, M. Bakhshi, CCTU 1157; Guilan Province, Lahijan, on leaves of C. album (Chenopodiaceae), Aug. 2012, M. Bakhshi, CCTU 1163.
Cercospora convolvulicola M. Bakhshi, Arzanlou, Babaiahari, Crous & U. Braun, sp. nov. — MycoBank MB809116; Fig. 3
Etymology. Named after the host genus on which it was collected, Convolvulus.
Description in planta — Leaf spots circular to subcircular, 2–8 mm, grey-brown to brown, not surrounded by margin of different colour. Mycelium internal. Caespituli amphigenous, brown. Conidiophores straight or sinuously geniculate, in dense fascicles, arising from the upper cells of a well-developed, intraepidermal and substomatal, brown stroma, up to 40 μm diam; conidiophores pale brown to brown, simple, rarely branched, moderately thick-walled, irregular in width, attenuated at the upper portion, often constricted at septa and proliferating point, 35–50(–70) × (3–)4–6 μm, 2–5-septate. Conidiogenous cells intercalary and terminal, proliferating sympodially, 10–20 × 3–5.5 μm, multi-local; loci distinctly thickened, apical, lateral or formed on the shoulders caused by geniculation, sometimes circumspersed, protuberant, 1.5–2.5 μm. Conidia solitary, hyaline, subcylindrical to obclavate, straight or slightly curved, truncate to somewhat obconically truncate at the base, subacute or subobtusely rounded at the apex, 35–50(–65) × (2.5–)3.5–4.5 μm, 3–8-septate, guttulate; hila thickened, darkened, refractive, 1.5–2.5 μm diam.
Cultural characteristics — Colonies on MEA reaching 55 mm diam after 20 d at 25 °C in the dark; flat with smooth, even margins and moderate aerial mycelium; surface olivaceous-grey, reverse dark iron-grey.
Specimens examined. IRAN, Ardabil Province, Moghan, on Convolvulus arvensis (Convolvulaceae), Oct. 2011, M. Bakhshi (holotype IRAN 16454 F, culture ex-type CCTU 1083 = CBS 136126); Moghan, on C. arvensis (Convolvulaceae), Oct. 2011, M. Bakhshi, CCTU 1083.2.
Notes — Based on individual gene trees, the two isolates representing this species are never supported in their own clade; in the TEF1-α and ACT phylogenies, they are intermixed with C. cf. flagellaris and C. cf. brunkii; in the CAL phylogeny with C. apii and C. cf. brunkii, and in the HIS phylogeny with C. rodmanii, C. cf. zinniae and Cercospora spp. N, P and Q sensu Groenewald et al. (2013). Shared alleles are the likely cause for the separate position of C. convolvulicola in the combined phylogeny (Fig. 1, part 3). Cercospora convolvulicola is sister to C. cf. brunkii and appears to be specific to Convolvulus arvensis. The only species known from Convolvulus arvensis, is C. ipomoea. Cercospora cf. ipomoea (tentative name for C. ipomoea) has a different phylogenetic position. Cercospora convolvulicola differs morphologically from C. ipomoea, by having dense conidiophores and shorter, guttulate, subcylindrical to obclavate conidia (Fig. 3).
Cercospora conyzae-canadensis M. Bakhshi, Arzanlou, Babai-ahari, Crous & U. Braun, sp. nov. — MycoBank MB809117; Fig. 4
Etymology. Named after the host plant from which it was collected, Conyza canadensis.
Description in planta — Leaf spots amphigenous, circular, 1–4 mm diam, grey to pale brown with dark brown margins. Mycelium internal. Caespituli amphigenous, brown. Conidiophores aggregated in loose fascicles (3–15), arising from a weakly developed, intraepidermal and substomatal, dark brown stroma, up to 30 μm diam; conidiophores brown to dark brown, 2–6-septate, straight to geniculate-sinuous due to sympodial proliferation, simple, thick-walled, uniform in width, often constricted at the proliferating point, (57–)97–112(–140) × 4.5–5.5 μm. Conidiogenous cells intercalary and terminal, pale brown to brown, proliferating sympodially, 20–40 × 4–5.5 μm, multi-local; loci distinctly thickened, darkened and somewhat refractive, apical or formed on shoulders caused by sympodial proliferation, 2–3.5 μm diam. Conidia solitary, filiform to obclavate-cylindrical, straight to slightly curved, hyaline, (32–)60–94(–170) × 3.5–5.5 μm, (3–)7–12(–17)-septate, with subobtusely rounded apices and truncate to obconically truncate bases; hila thickened, darkened, refractive, 1.5–2.5 μm diam.
Cultural characteristics — Colonies on MEA reaching 24 mm diam after 20 d at 25 °C in the dark; erumpent with smooth, irregular margins and sparse aerial mycelium; dark olivaceous-green on the surface, dark blue-green underneath.
Specimens examined. IRAN, Guilan Province, Talesh, on Conyza canadensis (Asteraceae), Nov. 2012, M. Bakhshi (holotype IRAN 16455 F, culture ex-type CCTU 1119 = CBS 135978); Talesh, on C. canadensis (Asteraceae), Aug. 2011, M. Bakhshi, CCTU 1008; Zanjan Province, Tarom, on C. canadensis (Asteraceae), Aug. 2012, M. Bakhshi, CCTU 1105.
Notes — Cercospora conyzae-canadensis must be regarded as a new species, based on its distinct phylogenetic position. In the individual gene trees (ACT, TEF1-α, CAL and HIS), it is distinguished from all other species. In the combined tree (Fig. 1, part 1), it is a sister taxon to the clade including C. cf. modiolae and Cercospora sp. E sensu Groenewald et al. (2013). Three species of Cercospora, including C. bidentis, C. erigeronicola and C. nilghirensis, have been reported from Conyza. Cercospora conyzae-canadensis is morphologically distinguished from those species by its moderately developed stroma, loose fascicles and dark brown conidiophores. Cercospora erigeronicola is distinct in having shorter and narrower, 0–3-septate conidia, 15–45 × 2–3.5 μm. Cercospora conyzae-canadensis is morphologically close to C. nilghirensis in conidial shape and size. However C. nilghirensis, described from India on Conyza ambigua, lacks stromata and has numerous longer conidiophores that are densely fasciculate. Cercospora conyzaecanadensis appears to be specific to Conyza canadensis.
Cercospora cylindracea M. Bakhshi, Arzanlou, Babai-ahari, Crous & U. Braun, sp. nov. — MycoBank MB809118; Fig. 5
Etymology. Name derived from the cylindrical conidia.
Description in planta — Leaf spots distinct, circular to subcircular, sometimes angular, pale brown, with broad brown margin, sometimes appearing as an eye spot, 1–7 mm diam. Mycelium internal. Caespituli amphigenous, brown. Conidiophores in divergent fascicles (4–25), arising from the upper cells of a moderately to well-developed, intraepidermal and substomatal, brown stroma, up to 30 μm diam; conidiophores pale brown to brown, thick-walled, 1–6-septate, straight, sinuous to distinctly geniculate, flexuous, (35–)55–65(–90) × 4–5.5 μm, irregular in wide, conically narrowed at the apex. Conidiogenous cells terminal or intercalary, unbranched, pale brown, smooth, proliferating sympodially, 15–30 × 3.5–5 μm, multi-local; loci thickened, darkened, refractive, protuberant, apical, lateral or circumspersed, 1.5–2.5 μm diam. Conidia solitary, subcylindrical to cylindrical, straight to mildly curved, hyaline, distinctly 1–10-septate, obtuse at the apex, subtruncate at the base, (30–)45–60(–90) × 3.5–5.5 μm; hila thickened, darkened, refractive, 1.5–2.5 μm diam.
Cultural characteristics — Colonies on MEA reaching 62 mm diam after 20 d at 25 °C in the dark; erumpent, folded, with smooth, even margins and sparse to moderate aerial mycelium; surface olivaceous-grey, reverse dark olivaceous-grey.
Specimens examined. IRAN, Ardabil Province, Moghan, on Lactuca serriola (Asteraceae), Sept. 2011, M. Bakhshi (holotype IRAN 16468 F, culture ex-type CCTU 1081 = CBS 138580); Moghan, on L. serriola (Asteraceae), Oct. 2012, M. Bakhshi, CCTU 1207; West Azerbaijan Province, Khoy, on Cichorium intybus (Asteraceae), June 2011, M. Arzanlou, CCTU 1016; Khoy, on L. serriola (Asteraceae), Sept. 2011, M. Arzanlou, CCTU 1044 = CBS 136021; Khoy, on L. serriola (Asteraceae), Sept. 2011, M. Arzanlou, CCTU 1049; Khoy, on L. serriola (Asteraceae), Sept. 2012, M. Arzanlou, CCTU 1183; Khoy, on L. serriola (Asteraceae), Sept. 2012, M. Arzanlou, CCTU 1189; Zanjan Province, Tarom, on C. intybus (Asteraceae), Oct. 2011, M. Bakhshi, CCTU 1114.
Notes — Cercospora cylindracea clusters as a sister taxon to the C. althaeina clade in the combined tree (Fig. 1, part 3). The host range of C. cylindracea is limited to Lactuca serriola and Cichorium intybus (both in the Asteraceae). Cercospora cylindracea is distinguished from C. althaeina in the HIS and ACT phylogenies but not in the TEF1-α phylogeny. In the CAL phylogeny, isolates are intermixed with those of C. zebrina, Cercospora sp. L sensu Groenewald et al. (2013) and C. althaeina. Three species of Cercospora including C. apii, C. lactucasativae and C. cichorii, are known from Lactuca serriola and Cichorium intybus. Cercospora cylindracea is separated in the combined gene tree from C. apii and C. lactucae-sativae as circumscribed in Groenewald et al. (2013) who studied Japanese material on Lactuca satica. Cercospora cylindracea differs from C. cichorii and C. lactucae-sativae by its cylindrical to subcylindrical conidia. Furthermore, the conidiogenous loci in C. lactucae-sativae are broader, 2.5–3.5 μm, than in C. cylindracea.
Cercospora iranica M. Bakhshi, Arzanlou, Babai-ahari, Crous & U. Braun, sp. nov. — MycoBank MB809119; Fig. 6
Etymology. Named after Iran, the country of the type location.
Description in planta — Leaf spots amphigenous, circular, 1–7 mm, first appearing as red-brown spots, later centre becoming grey with red-brown borders on upper and lower surface. Mycelium internal. Caespituli amphigenous, brown. Conidiophores aggregated in moderately dense fascicles (8–20), arising from a well-developed, erumpent, dark brown stroma, up to 40 μm diam; conidiophores brown, becoming pale brown towards the apex, 2–6-septate, straight to geniculate-sinuous due to sympodial proliferation, simple, uniform in width, sometimes constricted at the proliferating point, (30–)62–71(–90) × 4–5.5(–6) μm. Conidiogenous cells intercalary and terminal, pale brown to brown, proliferating sympodially, 15–35 × 4–5 μm, multi-local; loci distinctly thickened, darkened and somewhat refractive, apical, lateral or formed on shoulders caused by geniculation, 2–3.5 μm diam. Conidia solitary, obclavate when smaller, longer ones filiform to acicular, straight to slightly curved, hyaline, (27–)52–67(–95) × 2–4 μm, (3–)7–10(–14)-septate, with subobtusely rounded apices and truncate or long obconically truncate bases; hila thickened, darkened, refractive, 1.5–2 μm diam.
Cultural characteristics — Colonies on MEA reaching 60 mm diam after 20 d at 25 °C in the dark; erumpent with smooth, even margins and moderate aerial mycelium; surface pale grey-olivaceous in centre, vinaceous-grey in outer region, reverse iron-grey in centre, dark pink-grey in outer region.
Specimens examined. IRAN, Guilan Province, Astara, on leaves of Vicia faba (Fabaceae), June 2012, M. Bakhshi (holotype IRAN 16466 F, culture ex-type CCTU 1137 = CBS 136124); Astara, on leaves of V. faba (Fabaceae), June 2012, M. Bakhshi, CCTU 1137.2; Mazandaran Province, Ramsar, on leaves of Hydrangea sp. (Hydrangeaceae), Sept. 2012, M. Bakhshi, CCTU 1196 = CBS 136123.
Notes — In the TEF1-α, HIS and ACT phylogeny, isolates of C. iranica and Cercospora sp. T cluster together in a distinct well-supported clade. In the CAL phylogeny, C. iranica forms a distinct clade, whereas Cercospora sp. T cannot be distinguished from Cercospora spp. M, O, P and Q (sensu Groenewald et al. 2013), nor from C. alchemillicola and C. cf. sigesbeckiae. The different CAL sequences explain the basal position of Cercospora sp. T to the C. iranica clade in the combined phylogeny (Fig. 1, part 1). Cercospora zonata, the causal agent of Cercospora leaf spot of faba beans (Kimber 2011) is morphologically quite distinct from C. iranica in having much broader (3–6 μm) obclavate-cylindrical conidia with short obconical base and larger hila, 2–2.5 μm wide (various collections examined, including topotype material of C. zonata: on Vicia faba, Portugal, May 1884, F. Moller, Rabenh., Fung. Eur. Exs. 3294, B, HAL). Caespituli that arise from a well-developed, erumpent stroma on the leaf surface is a unique morphological character of this species on Vicia faba.
Cercospora pseudochenopodii M. Bakhshi, Arzanlou, Babaiahari & Crous, sp. nov. — MycoBank MB809120; Fig. 7
Etymology. Named after its superficial resemblance to Cercospora chenopodii.
Description in planta — Leaf spots amphigenous, circular to irregular, 5–12 mm diam, pale brown, with concentric rings on adaxial and abaxial surface (stroma with conidiophores), indefinite margin, not surrounded by a border of different colour. Mycelium internal. Caespituli amphigenous, brown. Conidiophores aggregated in dense fascicles (8–40), emerging through stomatal openings or erumpent through the cuticle, arising from the upper cells of a moderately developed brown stroma, up to 60 μm wide; conidiophores pale brown to brown, 2–5-septate, thick-walled, mainly straight, sometimes geniculate in upper part, unbranched, almost uniform in width, (32–)39–45(–60) × (3.5–)4.5–5(–6.5) μm. Conidiogenous cells terminal, unbranched, pale brown, smooth, tapering to flat-tipped apical loci, proliferating sympodially, 10–30 × 3.5–6.5 μm, mostly mono-local, sometimes multi-local; loci apical or formed on shoulders caused by geniculation, thickened, darkened, protuberant, somewhat refractive, 2–4 μm diam. Conidia solitary, guttulate, cylindrical to subcylindrical, straight to slightly curved, hyaline, (0–)2–4(–5)-septate, apex obtuse, base obconically truncate, (25–)37–44.5(–70) × (4–)5–5.5(–7) μm; hila thickened, darkened, refractive, 2–4 μm diam.
Cultural characteristics — Colonies on MEA reaching 24 mm diam after 20 d at 25 °C; smooth to folded, erumpent with even margins and moderate aerial mycelium; surface smoke-grey in centre, olivaceous-grey in outer region; reverse olivaceous-grey.
Specimens examined. IRAN, Zanjan Province, Tarom on leaves of Chenopodium sp. (Chenopodiaceae), 26 Sept. 2011, M. Bakhshi (holotype IRAN 16467 F, culture ex-type CCTU 1038 = CBS 136022); West Azerbaijan Province, Khoy, on Chenopodium sp. (Chenopodiaceae), 20 Sept. 2011, M. Arzanlou, CCTU 1045; Khoy, on leaves of C. album (Chenopodiaceae), 1 Sept. 2012, M. Arzanlou, CCTU 1176.
Notes — Groenewald et al. (2013) regarded this species as a cryptic taxon, C. cf. chenopodii, since they did not have sufficient isolates of C. chenopodii for comparison. In the present study, we have included additional collections of both species. Based on robust phylogenetic differences, C. pseudochenopodii must be regarded as a distinct species. There are slight differences in morphology and symptoms between C. chenopodii and C. pseudochenopodii, i.e., leaf spots with concentric rings without definite margins; conidia slightly longer and narrower (Fig. 7), which refer only to the collections examined. Cercospora chenopodii is widespread and represented by numerous collections. The two species are, however, indistinguishable, and can only be differentiated by DNA sequence analyses. Cercospora pseudochenopodii has distinct ACT and HIS phylogenies, but based on CAL sequence data, it cannot be differentiated from C. chenopodii. In the ITS and TEF1-α phylogeny, C. pseudochenopodii is intermixed with some other species, but it is distinct from C. chenopodii. In the combined tree (Fig. 1, part 2), it sits in a well-supported clade sister to C. chenopodii.
Cercospora solani Thüm., Hedwigia 19: 135. 1880 and Contr. Fl. Mycol. Lusat. II: 15. 1880 — Fig. 8
Description in planta — Leaf spots amphigenous, subcircular to irregular, 8–27 mm diam, with grey to black dots (stroma with conidiophores) and dark grey margins. Mycelium internal. Caespituli amphigenous, brown. Conidiophores aggregated in moderately dense fascicles (6–20), arising from a well-developed, intraepidermal and substomatal, brown stromata, 10–55 μm diam; conidiophores pale brown to brown, 2–6-septate, straight to geniculate-sinuous due to sympodial proliferation, simple, rarely branched, almost uniform in width, often constricted at the proliferating point, (45–)64–75(–100) × 4–5 μm. Conidiogenous cells intercalary and terminal, pale brown to brown, tapering to flat-tipped apical loci, proliferating sympodially, 20–35 × 4–5 μm, multi-local; loci distinctly thickened, darkened and somewhat refractive, apical or formed on shoulders caused by geniculation, 2–3.5 μm diam. Conidia solitary, subcylindrical or somewhat narrowed towards the tip, straight to slightly curved, hyaline, thin-walled, (26–)48–59(–92) × (3.5–)4.5–5.5 μm, distinctly (2–)3–7(–8)-septate, with subobtusely rounded apices and truncate bases; hila distinctly thickened, darkened, refractive, 1.5–2.5 μm diam.
Cultural characteristics — Colonies on MEA slow growing, reaching 15 mm diam after 20 d at 25 °C in the dark; erumpent with smooth, even margins and sparse aerial mycelium; grey-olivaceous on the surface, reverse iron-grey.
Specimens examined. IRAN, West Azerbaijan Province, Khoy, on leaves of Solanum nigrum (Solanaceae), Sept. 2011, M. Arzanlou, CCTU 1043 = CBS 136038; Khoy, on leaves of S. nigrum (Solanaceae), Sept. 2011, M. Arzanlou, CCTU 1050.
Notes — Cercospora solani is supported in all of the individual gene trees. In the combined tree, it is a sister taxon to the clade including C. conyzae-canadensis, C. cf. modiolae and Cercospora sp. E sensu Groenewald et al. (2013) (Fig. 1, part 1). Ten species of Cercospora have been reported from Solanum, including C. apii, C. canescens, C. lanugiflori, C. physalidis, C. puyana, C. sciadophila, C. solanacea, C. solani, C. solanigena and C. solani-nigri. Cercospora solani is phylogenetically distinct from C. apii, C. canescens and C. physalidis. Among the other candidate species, the status of C. lanugiflorii, C. sciadophila and C. solanigena are uncertain, as their type collections are lacking (Crous & Braun 2003); symptoms of C. puyana are different, and C. solanacea has been reduced to synonymy with Pseudocercospora trichophila var. punctata (Braun & Urtiaga 2013). Cercospora solani-nigri is also a Pseudocercospora and heterotypic synonym of P. atromarginalis (type material examined by U. Braun: on Solanum nigrum, India, Poona, 18 Dec. 1957, P.P. Chiddarwar, BPI 441404). The description of C. solani in Chupp (1954) is misleading. It is unclear on which collections Chupp‘s (1954) description was based. The name C. solani has often been confusingly applied. However, type material of C. solani has been examined by U. Braun (on Solanum nigrum, Portugal, Coimbra, Jan. 1879, F. Moller, Thüm., Mycoth. Univ. 2070, HAL) and was shown to be a true Cercospora s.str. characterised by cylindrical to subacicular (somewhat apically attenuated) conidia. The type of C. solani agrees well with the present material from Iran.
Cercospora sorghicola M. Bakhshi, Arzanlou, Babai-ahari, Crous & U. Braun, sp. nov. — MycoBank MB809121; Fig. 9
Etymology. Derived from the host genus, Sorghum.
Description in planta — Leaf spots amphigenous, initially dark purple spots that enlarge over time into linear-oblong lesions with dark purple centre and dark red-purple margins, 5–35 mm long. Mycelium internal. Caespituli amphigenous, brown.
Conidiophores aggregated in loose or dense fascicles (5–40), arising from the upper cells of a well-developed, intraepidermal and substomatal, brown stroma, up to 50 μm diam; conidiophores pale brown to brown, paler towards the apex, simple, unbranched, 1–8-septate, straight or flexuous caused by sympodial proliferation, almost uniform in width, sometimes conical at the apex, (45–)70–80(–100) × 4–5.5 μm. Conidiogenous cells terminal or intercalary, unbranched, pale brown, smooth, proliferating sympodially, 20–40 × 3.5–5.5 μm, multi-local; loci thickened, darkened, refractive, protuberant, apical, lateral, 2–4 μm diam. Conidia solitary, smooth, acicular, cylindro-obclavate to obclavate, straight or curved, successively tapering towards the apex, hyaline, (3–)8–13(–17)-septate, apex subacute to subobtuse, base truncate to obconically truncate, (21–)80–100 (–150) × 3–4(–5) μm; hila distinctly thickened, darkened, refractive, 1.5–2.5 μm diam.
Cultural characteristics — Colonies on MEA reaching 45 mm diam after 20 d at 25 °C in the dark; flat with smooth, even margins and moderate aerial mycelium; surface olivaceous-green, reverse dark olivaceous-green.
Specimens examined. IRAN, Guilan Province, Kiashahr, on Sorghum halepense (Poaceae), Aug. 2012, M. Bakhshi (holotype IRAN 16457 F, culture ex-type CCTU 1173 = CBS 136448); Kiashahr, on S. halepense (Poaceae), Aug. 2012, M. Bakhshi, CCTU 1173.2.
Notes — In the individual gene trees (TEF1-α, ACT, CAL and HIS phylogeny), C. sorghicola always resides in a well-supported clade including C. sorghicola and Cercospora sp. A sensu Groenewald et al. (2013). In the combined tree (Fig. 1, part 1), it forms a distinct clade from Cercospora sp. A and these two species are sister taxa. The variation between these two species is based on one nucleotide change in ITS (one insertion in Cercospora sp. A), three nucleotides in TEF1-α (three transitions), two nucleotides in CAL (two transversions), two nucleotides in ACT (one transition and one transversion) and four nucleotide changes in HIS (one transversion and three transitions).
Because sequences for the TEF1-α, ACT, CAL and HIS loci were not available in NCBI for C. sorghi, which has been reported from Sorghum spp., a separate tree that included C. sorghicola, Cercospora sp. A, C. sorghi (GenBank AF291707) and other closely related species was generated using only ITS sequences. In this tree C. sorghicola and C. sorghi reside in different lineages (Fig. 10). Two nucleotide changes at ITS (one transition and one insertion) explain the different position of the isolates used in the current study and C. sorghi. Cercospora sorghicola is also morphologically different from C. sorghi by its longer, wider and multi-septate conidia.
Cercospora sp. T — Fig. 11
Description in planta — Leaf spots amphigenous, subcircular to irregular, 5–12 mm diam, grey-brown with indefinite margins. Mycelium internal. Caespituli amphigenous, brown. Conidiophores aggregated in loose fascicles (2–8), arising from a weakly developed, intraepidermal and substomatal, dark brown stroma, up to 25 μm diam; conidiophores brown to dark brown, 5–14-septate, straight to geniculate-sinuous due to sympodial proliferation, simple, unbranched, thick-walled, uniform in width, (95–)152–175(–215) × 3.5–5 μm. Conidiogenous cells intercalary and terminal, proliferating sympodially, multi-local; loci thickened, darkened, protuberant, apical or formed on shoulders caused by geniculation, 1.5–3 μm diam. Conidia solitary, hyaline, filiform to acicular, straight to slightly curved, with truncate base and acute to subobtuse apices, (72–)93–115(–180) × (2–)3–4 μm, (7–)10–14(–20)-septate.
Cultural characteristics — Colonies on MEA reaching 65 mm diam after 20 d at 25 °C in the dark; smooth, flat, with even margins and moderate aerial mycelium; surface smoke-grey; reverse iron-grey.
Specimens examined. IRAN, Guilan Province, Rasht, on leaves of Coreopsis sp. (Asteraceae), June 2012, M. Bakhshi, CCTU 1148 = CBS 136125; Rasht, on leaves of Coreopsis sp. (Asteraceae), June 2012, M. Bakhshi, CCTU 1148.2.
Notes — For phylogeny, see the notes under C. iranica. Two species of Cercospora, including C. bidentis and C. coreopsidis, have been reported from Coreopsis spp. Cercospora sp. T is morphologically distinct from C. bidentis by lacking or having small stroma, loose fascicles and dark brown conidiophores. According to its independent phylogenetic position (Fig. 1, part 1), Cercospora sp. T probably represents a host-specific species. Furthermore, Cercospora sp. T and C. cf. coreopsidis (tentative name for an examined and sequenced Korean sample of C. coreopsidis sensu Shin & Kim 2001, see Groenewald et al. 2013), which are both host-specific to Coreopsis spp., are phylogenetically distinct. We presently do not have phylogenetic data from North American material on Coreopsis, which would fix the application of the name C. coreopsidis. The relationship between Cercospora sp. T on Coreopsis from Iran and C. cf. coreopsidis on Coreopsis from Korea needs resolution.
DISCUSSION
This study provides a broad framework for the genus Cercospora in Iran. These fungi are very common and widespread in different climates and regions of this country. Until now, 33 species of Cercospora s.str. have been recorded from Iran (Bakhshi et al. 2012a, Hesami et al. 2012, Pirnia et al. 2012). The identification of these taxa has mostly relied on host association and morphological characteristics sensu Chupp (1954). Unfortunately, there are few living cultures available for molecular study. In the present paper, multilocus sequence typing (MLST) was employed for the first time to discriminate among Iranian Cercospora species, which are described according to their DNA phylogeny, ecology, morphological and cultural characteristics, by employing the Consolidated Species Concept as outlined by Quaedvlieg et al. (2014).
Phylogenetic performance of the five loci (ITS, TEF1-α, ACT, CAL and HIS) employed for phylogenetic inference in this study was previously reported by Groenewald et al. (2010, 2013). Our study indicated that the ITS region has limited resolution when used for species comparison in Cercospora, especially with regard to C. apii s.lat. (Goodwin et al. 2001, Pretorius et al. 2003, Groenewald et al. 2010, 2013). The other loci screened in this study had different levels of success in resolving species boundaries. The TEF1-α region was able to distinguish only 35 % of 20 lineages, whereas the actin region had 45 % clade recovery. Although the CAL region only distinguished 40 % of the species, it remains essential to distinguish several species: C. apii from C. beticola, C. cf. flagellaris from C. convolvulicola, and C. iranica from Cercospora sp. T. The HIS region was slightly more effective and discriminated half of the detected species. These data show the importance of all five loci in combined analysis for Cercospora taxonomy and are congruent with previous studies of Groenewald et al. (2010, 2013). Despite this, the sequences of these five loci are still too conserved in Cercospora, and there is still need to find the best barcoding locus (loci) for Cercospora.
In the present study 20 species of Cercospora were identified from northern Iran based on a combination of sequence data, host-fungus relation and morphological characters. Results obtained in this study show that 60 isolates of Cercospora obtained from 18 host families in different groups of plants viz. agricultural crops, ornamentals, forest trees and weeds grouped within the C. cf. flagellaris species complex. This complex was previously treated by Groenewald et al. (2013) from nine host families (in total encompassing 23 host families). Cercospora cf. flagellaris is morphologically similar to C. flagellaris (= C. apii s.lat.), but names could not be applied with confidence, and isolates from the original host and country (Phytolaca decandra, USA) need to be included to confirm the true identity of this species. We suspect that this species could split into several species once more DNA loci are screened and pathogenicity tests are conducted.
In recent years several groups have attempted to study Cercospora spp. from Iran based solely on morphological characters and host range (Hesami et al. 2012). According to our data, most of these records are unreliable or incorrect, and probably reside in the C. cf. flagelaris clade (Hesami et al. 2012, Pirnia et al. 2012). On the other hand, many earlier records were identified as C. apii, which according to results of our study, has a much narrower host range than generally recognised.
Although the isolates investigated during this study represent the largest collection of Cercospora species so far subjected to DNA sequence analysis from Iran, there are still some issues that need to be resolved. The identity of two groups of species remains questionable. Names based on American or European type specimens should not be assumed for the identification of identical diseases on the same hosts in Asia, Africa or South America and vice versa (Crous et al. 2013, Groenewald et al. 2013). This was the case for the first group of the species with questionable identity in our study, which were indicated with ‘cf.’ in the species name, e.g. C. cf. richardiicola, C. cf. flagellaris and C. cf. zinniae. In the case of the second species group, the clade contains isolates from multiple hosts, e.g. in Cercospora sp. G, isolates from six host families (Amaranthaceae, Asteraceae, Cucurbitaceae, Malvaceae, Plantaginaceae, Poaceae) were found. To resolve these taxonomic problems, additional species described by Chupp (1954) and Crous & Braun (2003), which are not currently known from their DNA must be epitypified, thus allowing DNA sequence-based analyses to stabilize the names used in different phylogenetic lineages. Furthermore, in future studies of Cercospora, additional loci must be included in the analyses to obtain better resolution of the species.
The data presented here confirm that some Cercospora species are host-specific, e.g. C. chenopodii and C. pseudochenopodii on Chenopodium spp., C. violae on Viola spp., C. cf. zinniae on Zinnia elegans, C. conyzae-canadensis on Conyza canadensis, C. convolvulicola on Convolvulus arvensis, C. solani on Solanum nigrum and C. sorghicola on Sorghum halepense; some species are restricted to one host family e.g. C. althaeina on Malvaceae, C. cylindracea on Asteraceae; whereas others have wide host ranges, e.g. C. apii, C. armoraciae, C. beticola, C. cf. flagellaris and Cercospora sp. G. However, it is not acceptable to recognise the host range of a species without confirmatory pathogenicity tests. For example, it still remains to be seen whether isolates from different hosts with similar morphology to C. cf. flagellaris, have the ability to cross-infect hosts (Table 2).
Table 2
Host Family | Host species | Species |
Acerceae | Acer velutinum | C. cf. flagellaris |
Amaranthaceae | Amaranthus blitoides | C. cf. flagellaris |
Amaranthus retroflexus | Cercospora sp. G | |
C. cf. flagellaris | ||
Amaranthus spp. | Cercospora sp. G | |
C. cf. flagellaris | ||
Celosia cristata | Cercospora sp. G | |
Apocynaceae | Cynanchum acutum | C. apii |
Araceae | Anubias sp. | C. cf. flagellaris |
Asteraceae | Bidens tripartita | C. cf. richardiicola |
Cercospora sp. G | ||
Calendula officinalis | C. cf. flagellaris | |
Cichorium intybus | Cercospora sp. G | |
C. cylindracea | ||
Conyza canadensis | C. conyzae-canadensis | |
Coreopsis sp. | Cercospora sp. T | |
Eclipta prostrata | C. cf. flagellaris | |
Lactuca serriola | C. cylindracea | |
Leucanthemum superbum | C. cf. flagellaris | |
Silybum marianum | C. cf. flagellaris | |
Sonchus asper | C. beticola | |
Sonchus sp. | C. beticola | |
Tagetes patula | C. cf. flagellaris | |
Tanacetum balsamita | C. armoraciae | |
Xanthium spinosum | C. cf. flagellaris | |
Xanthium strumarium | C. cf. flagellaris | |
Zinnia elegans | C. cf. zinniae | |
Balsaminaceae | Impatiens balsamina | C. cf. flagellaris |
Boraginaceae | Heliotropium europaeum | C. apii |
Brassicaceae | Cardaria draba | C. armoraciae |
Lepidium sativum | C. cf. flagellaris | |
Raphanus sativus | C. cf. flagellaris | |
Buxaceae | Buxus microphylla | C. cf. flagellaris |
Caesalpinaceae | Cercis siliquastrum | C. cf. flagellaris |
Capparidaceae | Capparis spinosa | C. armoraciae |
Chenopodiaceae | Beta vulgaris | C. beticola |
Chenopodium album | C. chenopodii | |
C. pseudochenopodii | ||
Chenopodium spp. | C. beticola | |
C. pseudochenopodii | ||
Convolvulaceae | Convolvulus arvensis | C. convolvulicola |
Cucurbitaceae | Cucurbita maxima | C. cf. flagellaris |
Cercospora sp. G | ||
Cucurbita pepo | C. cf. flagellaris | |
Cucurbita sp. | C. cf. flagellaris | |
Citrullus lanatus | C. cf. flagellaris | |
Ecballium elaterium | C. apii | |
C. cf. flagellaris | ||
Fabaceae | Arachis hypogaea | C. cf. flagellaris |
Alhagi camelorum | C. zebrina | |
Coronilla varia | C. armoraciae | |
Glycine max | C. cf. flagellaris | |
Medicago sativa | C. zebrina | |
Medicago sp. | C. zebrina | |
Phaseolus vulgaris | C. cf. flagellaris | |
trifolium repens | C. zebrina | |
Vicia faba | C. cf. flagellaris | |
C. iranica | ||
Vicia sp. | C. zebrina | |
Geraniaceae | Pelargonium hortorum | C. cf. flagellaris |
Hydrangeaceae | Hydrangea sp. | C. cf. flagellaris |
C. iranica | ||
Malvaceae | Abutilon theophrasti | C. cf. flagellaris |
Cercospora sp. G | ||
Althaea rosea | C. althaeina | |
Gossypium herbaceum | C. cf. flagellaris | |
Hibiscus trionum | C. cf. flagellaris | |
Malva sylvestris | C. althaeina | |
C. beticola | ||
Malva neglecta | C. beticola | |
Oleaceae | Olea europaea | C. cf. flagellaris |
Pedaliaceae | Sesamum indicum | C. beticola |
Plantaginaceae | Plantago lanceolata | C. apii |
C. beticola | ||
Plantago major | Cercospora sp. G | |
Poaceae | Sorghum halepense | Cercospora sp. G |
C. sorghicola | ||
Polygonaceae | Rumex crispus | C. beticola |
C. rumicis | ||
Salicaceae | Populus deltoides | C. cf. flagellaris |
Solanaceae | Datura stramonium | C. cf. flagellaris |
Solanum nigrum | C. solani | |
Urticaceae | Urtica dioica | C. cf. flagellaris |
C. rumicis | ||
Violaceae | Viola sp. | C. violae |
Vitaceae | Vitis vinifera | C. zebrina |
The present study was initiated to resolve the taxonomy of the genus Cercospora in Iran by employing the Consolidated Species Concept. Our results indicate a rich diversity of this genus in the north and north-west of Iran. Future studies will be directed towards resolving the taxonomy of the genus Cercospora in other parts of Iran, and also the taxonomy of other cercospora-like pathogens of agricultural crops of major economic importance.
Acknowledgments
The Research Deputy of the University of Tabriz, the Studienstiftung für mykologische Systematik und Ökologie and the CBSKNAW Fungal Biodiversity Centre are thanked for financial support. The first author also wishes to thank the Agricultural and Natural Resources Research Center of Zanjan Province (especially Dr. Hosein Jafari) as well as the Agricultural Research and Natural Resources Center of Ardabil Province, Moghan (especially Yousef Jahani, Masoud Taghizadeh, Vahid Mahdavi and Hosein Karbalaee) for their kind assistance in sampling.
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