Colletotrichum Corda, in Sturm, Deutschl. Fl., 3 Abt. (Pilze Deutschl.) 3(12): 41 (1831)


Colletotrichum was introduced by Corda (1831), belonging to Glomerellaceae (Glomerellales, Sordariomycetes), and is the sole member of this family (Maharachchikumbura et al. 2015, 2016; Hyde et al. 2020b). Species may occupy different lifestyles, ranging from necrotrophy to hemibiotrophy as well as endophytism (Crouch et al. 2014). Colletotrichum species are important plant pathogens in both tropical and temperate regions on many economically important crops (Hyde et al. 2009a,b, 2014; Cannon et al. 2012; Jayawardena et al. 2016b,c). Based on recognized scientific and economic importance this genus was voted the eighth most important plant pathogenic group in the world (Dean et al. 2012). Colletotrichum species have been identified as endophytes (Manamgoda et al. 2013; Tao et al. 2013; Hyde et al. 2014; Jayawardena et al. 2016c) and some are saprobes on dead plant material (Photita et al. 2005; Jayawardena et al. 2016b). A few species have been identified to be pathogenic to humans (C. coccodes, C. dematium, C. gloeosporioides (Natarajan et al. 2013)) and on insects (C. fioriniae (Damm et al. 2012b)). Colletotrichum species are cosmopolitan in distribution and show a diverse hosts association (Sharma et al. 2015). A host plant genus can be infected by many Colletotrichum species (Silva et al. 2012; Jayawardena et al. 2016c), and on the contrary, a single species of Colletotrichum can infect many host plants (Damm et al. 2012a, b; Weir et al. 2012).

Correct species identification is important to understand the species diversity, plant pathology and quarantine, concerning human infections, agriculture, bio-control, plant breeding, whole-genome sequencing, developing and maintaining knowledge databases, bioprospecting and understanding the evolutionary history (Jayawardena et al. 2016a). Due to a small number of distinctive morphological characters available for identification, misidentification of these species is frequent. Misapplication and misidentification of species are also due to the misunderstanding of their host-specific nature, ambiguous species boundaries and incorrect sequences (Cannon et al. 2012; Hyde et al. 2014; Jayawardena et al. 2016a). Therefore, having a stable taxonomy for the identification of these species is a significant practical concern (Shenoy et al. 2007). To establish a natural classification system, researchers strongly recommend the use of geographical, ecological, morphological and genetic data (Cai et al. 2009; Sharma and Shenoy 2016).

Species of Colletotrichum are extensively studied as model organisms (Cannon et al. 2012; Hyde et al. 2014). This enables the researchers to understand the pathogen variation, infection mechanism, evolution and population dynamics. Pathogenicity genes of C. graminicola, C. higginsianum and C. orbiculare have been studied (Huser et al. 2009; O’Connell et al. 2012). Asakura et al. (2009) discovered the importance of the pexophagy factor ATG26 for appressorium formation. A total of 28 genome projects that include 25 different Colletotrichum species can be found; 15 of these strains are still at the annotation stage and 13 are now at the ‘Fungal Standard Draft’ stage (Carbú et al. 2019). These genomes will allow further analysis of species diversity and evolutionary mechanisms and may serve as a foundation for genetic analysis that leads to a greater understanding of interactions between plants and fungal pathogens (Meng et al. 2020). Baroncelli et al. (2016) studied four strains of C. acutatum and illustrated the plasticity of Colletotrichum genomes and showed that major changes in host range are associated with relatively recent changes in gene content. A genome of C. fructicola from apple in China was compared with its reference genome, which identified a number of strong duplication/loss events at key phylogenetic nodes (Liang et al. 2018). Gan et al. (2019) provided the updated genome for C. orbiculare and also provided three draft genomes for C. trifolli, C. sidae and C. spinosum. Colletotrichum higginsianum has a compartmentalized genome consisting of gene-sparse, transposable elements dense regions with more effector candidate genes and gene-dense, TE-sparse regions harbouring conserved genes which help the pathogen to generate genomic diversity (Tsushima et al. 2019). Comparative genome analysis indicated that there is a rapid evolution of pathogenicity genes in C. tanaceti (Lelwala et al. 2019).

Species of Colletotrichum can be used as biocontrol agents and as biocatalysts (C. dematium, C. gloeosporioides, C. graminicola, C. lindemuthianum, C. orbiculare, C.theobromicola, C. trifoli (Jayawardena et al. 2016b)). Jayawardena et al. (2016b) discussed the importance of secondary metabolites produced by species with relation to pathogenesis, medicines, disease control and toxins.

Classification – Ascomycota, Pezizomycotina Sordariomycetes, Hypocreomycetidae, Glomerellales, Glomerellaceae

Type species Colletotrichum lineola Corda, in Sturm, Deutschl. Fl., 3 Abt. (Pilze Deutschl.) 3(12): 41 (1831)

Distribution – Worldwide

Disease symptoms – Anthracnose disease, red rot, crown and stem rots, ripe rot, seedling blights and brown blotch.

Anthracnose disease symptoms include defined, often sunken necrotic spots on leaves, stems, flowers or fruits and may show a lot of variation depending on the host (Fig 1a−e).

Hosts – Pathogens on many host families including, Amaryllidaceae, Amaranthaceae, Anacardiaceae, Annonaceae, Apiaceae, Apocynaceae, Araceae, Araliaceae, Arecaceae, Asparagaceae, Asteraceae, Bignoniaceae, Campanulaceae, Caricaceae, Crassulaceae, Cucurbitaceae, Euphorbiaceae, Fabaceae, Iridaceae, Lamiaceae, Lauraceae, Malvaceae, Melastomataceae, Menispermaceae, Moraceae, Myrtaceae, Oleaceae, Olivaceae, Orchidaceae, Passifloraceae, Pinaceae, Piperaceae, Plumbaginaceae, Poaceae, Podocarpaceae, Polemoniaceae, Proteaceae, Ranunculaceae, Rosaceae, Rubiaceae, Rutaceae, Solanaceae, Theaceae and Vitaceae.

Pathogen biology, disease cycle and epidemiology

For Colletotrichum biology, disease cycle and epidemiology see Cannon et al. (2012) and De Silva et al. (2017).

Morphological based identification and diversity

Due to the overlapping morphological characters, species delimitation based on morphology alone is hardly possible (Jayawardena et al. 2016b; Marin-Felix et al. 2017; Fig 1 f-l).

Fig. 1 Colletotrichum sp. a. Chilli anthracnose symptoms b. Crown rot of strawberry c. Leaf blight of Cannas sp. d-e strawberry anthracnose symptoms f-g Conidiomata and spore mass h Conidiophore i Setae j Conidiogenous cells and curved conidia k Conidia of C. gloeosporioides l Appressoria

Molecular based identification and diversity

Cai et al. (2009) proposed the use of a polyphasic approach with multi-loci sequence analyses combined with geographical, ecological and morphological data for reliable species delimitation. Application of this polyphasic approach resulted in the delimitation of almost 200 species, most of them belonging to species complexes such as acutatum, boninense and gloeosporioides. There is no universal set of loci to use when identifying Colletotrichum species. Cannon et al. (2012), Damm et al. (2012a,b, 2013, 2014, 2019, Liu et al. 2016) used ITS, gapdh, chs, act, his and tub2 (with some also gs or cal) for studying species within the acutatum, boninense, dematium, destructivum, gigasporum, orbiculare, spaethianum and truncatum species complexes, while Weir et al. (2012) additionally applied gs, cal and sod2 within the gloeosporioides species complex. Hyde et al. (2014), Jayawardena et al. (2016b), Marin-Felix et al. (2017) used ITS, gapdh, chs, act and tub2 to differentiate the species. Using five loci for the whole genus gave similar results to 6-7 loci used for the whole genus. In contrast, Crouch et al. (2009b) applied ITS, sod2, apn2 and mat1/apn2, to study the graminicola and caudatum species complexes. Use of ApMat locus to delimit the species within gloeosporioides species complex was emphasized by Silva et al. (2012) and Sharma et al. (2015) as it provides a higher resolution when compared to previously used loci. However, studies by Liu et al. (2015, 2016) revealed that using this locus with other loci would provide a satisfactory species delimitation within the gloeosporioides species complex. For species delimitation, application of the Genealogical Concordance Phylogenetic Species Recognition (GCPSR) has proven to be a powerful tool (Cai et al. 2009). Coalescent-based species delimitation methods can also be used to infer the dynamic of divergence, evolutionary process and the relationships among species (McCormack et al. 2009, Liu et al. 2016).

Jayawardena et al. (2016b) provided the accepted species for the genus with backbone trees for each species complex and with notes for each accepted species. De Silva et al. (2017) reviewed the lifestyles and how this can be applied to plant biosecurity. Ariyawansa et al. (2015), Yan et al. (2015), Li et al. (2016), De Silva et al. (2017), Hyde et al. (2017, 2020a, b), Marin-Felix et al. (2017), Tibpromma et al. (2017, 2018), Samarakoon et al. (2018), Bhunjun et al. (2019) have introduced new species based on morphology, phylogeny and GCPSR evidence. Damm et al. (2019) introduced three new species complexes namely, dracaenophilum, magnum and orchidearum based on morphology and phylogeny. Cabral et al. (2020) based on pathological, morphological, cytogenomic, biochemical and molecular data, assigned the previously known C. kahawae subsp. ciggario as a new species, C. ciggario. At present, based on multi-loci phylogeny there are 14 species complexes. With 59 new species having been added since the last treatment (Marin-Felix et al. 2017), here we present an analysis using five loci (Table 1) for all Colletotrichum species (Fig. 2). From the studies conducted on this genus, it is clear that the resolution of species differs depending on both locus and species. Therefore, to select a better genetic marker and the best secondary barcoding gene/genes is still an ongoing process.

Recommended genetic marker (genus level) – ITS

Recommended genetic markers (species level)act, apmat, apn2, cal, chs-1, gapdh, gs, his, mat1/apn2, sod2, and tub2.

Accepted number of species – There are 903 epithets listed in Index Fungorum (2020), however, 247 species with molecular data are treated as accepted (Table 1).

References – Cai et al. 2009 (polyphasic approach); Hyde et al. 2009a,b (morphology and accepted species); Cannon et al. 2012 (A review and an updated account of the genus); Crouch 2009a,b,c, 2014, Damm et al. 2009, 2012a,b, 2013, 2014, 2019, Weir et al. 2012 (morphology and phylogeny); Hyde et al. 2014, Jayawardena et al. 2016b, Marin-Felix et al. 2017 (accepted number of species).

Table 1 DNA barcodes available for Colletotrichum, isolates used in the phylogenetic analyses. Ex-type/ex-epitype/ex-neotype/ex-lectotype strains in bold and marked with an asterisk (*).Voucher strains are also in bold. Species confirmed with pathogenicity studies are marked with #.

Species name Isolate No ITS gapdh chs-1 act tub2 Complex
Colletotrichum abscissum# COAD 1877* KP843126 KP843129 KP843132 KP843141 KP843135 acutatum
C. acerbum CBS 128530* JQ948459 JQ948790 JQ949120 JQ949780 JQ950110 acutatum
C. acidae MFLUCC 17-2659* MG996505 MH003691 MH003694 MH003697 MH003700 truncatum
C. acutatum# CBS 112996* JQ005776 JQ948677 JQ005797 JQ005839 JQ005860 acutatum
C. aenigma# ICMP 18608* JX010244 JX010044 JX009774 JX009443 JX010389 gloeosporioides
C. aericola# CGMCC 3.19667* MK914635 MK935455 MK935541 MK935374 MK935498 gloeosporioides
C. aeschynomenes# ICMP 17673 JX010176 JX009930 JX009799 JX009483 JX010392 gloeosporioides
C. agaves CBS 118190* DQ286221         singleton
C. alcornii IMI176619* JX076858         caudatum
C. alatae# CBS 304.67* JX010190 JX009990 JX009837 JX009471 JX010383 gloeosporioides
C. alienum# ICMP 12071* JX010251 JX010028 JX009882 JX009572 JX010411 gloeosporioides
C. americae-borealis# CBS 136232* KM105224 KM105579 KM105294 KM105434 KM105504 destructivum
C. annellatum CBS 129826* JQ005222 JQ005309 JQ005396 JQ005570 JQ005656 boninense
C. anthrisci CBS 125334* GU227845 GU228237 GU228335 GU227943 GU228139 dematium
C. antirrhinicola CBS 102189* KM105180 KM105531 KM105250 KM105390 KM105460 destructivum
C. aotearoa ICMP 18537* JX010205 JX010005 JX009853 JX009854 JX010420 gloeosporioides
C. araceaerum CGMCC 3.14982* KX853166 KX893585   KX893577 KX893581 singleton
C. arboricola# CBS 144795* MH817944 MH817950   MH817956 MH817962 acutatum
C. artocarpicola# MFLUCC 18-1167* MN415991 MN435568 MN435569 MN435570 MN435567 gloeosporioides
C. arxii CBS 132511* KF687716 KF687843 KF687780 KF687802 KF687881 gigasporum
C. asianum# ICMP 18580* JX010196 JX010053 JX009867 JX009584 JX010406 gloeosporioides
C. atractylodicola CGMCC 3.18761* KR149280 KR259334 KR259333 KR132243 KU058178 destructivum
C. australe CBS 116478* JQ948455 JQ948786 JQ949116 JQ949776 JQ950106 acutatum
C. axonopodi IMI 279189/279189AA EU554086         singleton
C. beeveri CBS 128527* JQ005171 JQ005258 JQ005345 JQ005519 JQ005605 boninense
C. baltimorense BPI892771* JX076866         caudatum
C.bidentis COAD 1020* KF178481 KF178506 KF178530 KF178578 KF178602 orbiculare
C. bletillum CGMCC 3.15117* JX625178 KC843506   KC843542 JX625207 spaethianum
C. boninense# CBS 123755* JQ005153 JQ005240 JQ005327 JQ005501 JQ005588 boninense
C. brasiliense CBS 128501* JQ005235 JQ005322 JQ005409 JQ005583 JQ005669 boninense
C. brassicicola CBS 101059* JQ005172 JQ005259 JQ005346 JQ005520 JQ005606 boninense
C. brevisporum# BCC 38876* JN050238 JN050227   JN050216 JN050244 magnum
C. brisbaniense CBS 292.67* JQ948291 JQ948621 JQ948952 JQ949612 JQ949942 acutatum
C. bryoniicola CBS 109849* KM105181 KM105532 KM105251 KM105391 KM105461 destructivum
C. cacao# CBS 119297* MG600772 MG600832 MG600878 MG600976 MG601039 magnum
C. cairnsense# BRIP 63642* KU923672 KU923704 KU923710 KU923716 KU923688 acutatum
C. camelliae# CGMCC3.14925* KJ955081 KJ954782   KJ954363 KJ955230 gloeosporioides
C. camelliae-japonicae CGMCC3.18118* KX853165 KX893584   KX893576 KX893580 boninense
C. carthami# SAPA100011* AB696998       AB696992 acutatum
C. catinaense# CBS 142417* KY856400 KY856224 KY856136 KY855971 KY856482 boninense
C. cattleyicola CBS 170.49* MG600758 MG600819 MG600866 MG600963 MG601025 orchidearum
C. cariniferi MFLUCC 14-0100* MF448521       MH351274 singleton
C. caudatum CBS 131602* JX076860         caudatum
C. caudasporum CGMCC 3.15106* JX625162 KC843512   KC843526 JX625190 caudatum
C. cereale# CBS 129663* JQ005774   JQ005795 JQ005837 JQ005858 graminicola
C. changpingense# MFLUCC 15-0022* KP683152 KP852469 KP852449 KP683093 KP852490 gloeosporioides
C. chlorophyti# IMI 103806* GU227894 GU228286 GU228384 GU227992 GU228188 singleton
C. chiangraiense MFLUCC 14-0119* MF448522     MH376383 MH351275 gigapsorum
C. chrysanthemi# IMI 364540* JQ948273 JQ948603 JQ948934 JQ949594 JQ949924 acutatum
C. chrysophillum URM7368* KX094252 KX094183 KX094083 KX093982 KX094285 gloeosporioides
C. ciggaro# ICMP 18539* JX010230 JX009966 JX009800 JX009523 JX010434 gloeosporioides
C. circinans CBS 221.81 GU227855 GU228247 GU228345 GU227953 GU228149 dematium
C. citri CBS 134233* KC293581 KC293741 KY856138 KY855973 KC293661 acutatum
C. citricola# CBS 134228* KC293576 KC293736 KC293792 KC293616 KC293656 boninense
C. clidemiae ICMP 18658* JX010265 JX009989 JX009877 JX009537 JX010438 gloeosporioides
C. cliviicola# CBS 125375* MG600733 MG600795 MG600850 MG600939 MG601000 orchidearum
C. cobbittiense BRIP 66219a* MH087016 MH094133 MH094135 MH094134 MH094137 gloeosporioides
C. coccodes# CBS 369.75* HM171679 HM171673 JQ005796 HM171667 JQ005859 singleton
C. coelogynes CBS 132504* MG600713 MG600776 MG600836 MG600920 MG600980 dracaenophilum
C. colombiense CBS 129818* JQ005174 JQ005261 JQ005348 JQ005522 JQ005608 boninense
C. condaoense CBS 134299* MH229914 MH229920 MH229926   MH229923 boninense
C. conoides# CAUG17* KP890168 KP890162 KP890156 KP890144 KP890174 gloeosporioides
C. constrictum CBS 128504* JQ005238 JQ005325 JQ005412 JQ005586 JQ005672 boninense
C. cordylinicola# MFU 09-0551* JX010226 JX009975 JX009864 HM470234 JX010440 gloeosporioides
C. cosmi CBS 853.73* JQ948274 JQ948604 JQ948935 JQ949595 JQ949925 acutatum
C. costaricense CBS 330.75* JQ948180 JQ948510 JQ948841 JQ949501 JQ949831 acutatum
C. curcumae# IMI 288937* GU227893 GU228285 GU228383 GU227991 GU228187 truncatum
C. cuscutae IMI 304802* JQ948195 JQ948525 JQ948856 JQ949516 JQ949846 acutatum
C. cymbidiicola# IMI 347923* JQ005166 JQ005253 JQ005340 JQ005514 JQ005600 boninense
C. dacrycarpi CBS 130241* JQ005236 JQ005323 JQ005410 JQ005584 JQ005670 boninense
C. dematium# CBS 125.25* GU227819 GU228211 GU228309 GU227917 GU228113 dematium
C. destructivum# CBS 136228* KM105207 KM105561 KM105277 KM105417 KM105487 destructivum
C. doitungense MFLUCC 14-0128* MF448524 MH049480   MH376385 MH351277 boninense
C. dracaenophilum# CBS 118199* JX519222 JX546707 JX519230 JX519238 JX519247 dracaenophilum
C. duyunensis CGMCC 3.15105* JX625160 KC843515   KC843530 JX625187 caudatum
C. echinochloae MAFF 511473* AB439811         graminicola
C. eleusines MAFF 511155* JX519218   JX519226 JX519234 JX519243 graminicola
C. endophytica# MFLUCC 13–0418* KC633854 KC832854   KF306258   gloeosporioides
C. endophytum CGMCC 3.15108 * JX625177 KC843521   KC843533 JX625206 graminicola
C. eremochloae# CBS 129661* JX519220   JX519228 JX519236 JX519245 graminicola
C. eriobotryae# GLMC 1935* MF772487 MF795423 MN191653 MN191648 MF795428 acutatum
C. eryngiicola MFLUCC 17-0318* KY792726 KY792723 KY792720 KY792717 KY792729 dematium
C. excelsum-altitudinum CGMCC 3.15130* HM751815 KC843502   KC843548 JX625211 dracaenophilum
C. euphorbiae CBS 134725* KF777146 KF777131 KF777128 KF777125 KF777247 singleton
C. falcatum# CBS 147945* JQ005772   JQ005793 JQ005835 JQ005856 graminicola
C. feijoicola CBS 144633 * MK876413 MK876475   MK876466 MK876507 boninense
C. fioriniae# CBS 128517* JQ948292 JQ948622 JQ948953 JQ949613 JQ949943 acutatum
C. fructi CBS 346.37* GU227844 GU228236 GU228334 GU227942 GU228138 dematium
C. fructicola# ICMP 18581* JX010165 JX010033 JX009866 FJ907426 JX010405 gloeosporioides
C. fructivorum# CBS 133125* JX145145       JX145196 gloeosporioides
C. fuscum# CBS 133701* KM105174 KM105524 KM105244 KM105384 KM105454 destructivum
C. fusiforme MFLU 13-0291* KT290266 KT290255 KT290253 KT290251 KT290256 truncatum
C. gigasporum# CBS 133266* KF687715 KF687822 KF687761   KF687866 gigasporum
C. gloeosporioides# CBS 112999* JQ005152 JQ005239 JQ005326 JQ005500 JQ005587 gloeosporioides
C. godetiae# CBS 133.44* JQ948402 JQ948733 JQ949063 JQ949723 JQ950053 acutatum
C. graminicola# M 1.001* JQ005767   JQ005788 JQ005830 JQ005851 graminicola
C. grevilleae CBS 132879* KC297078 KC297010 KC296987 KC296941 KC297102 gloeosporioides
C. grossum# CAUG7* KP890165  KP890159 KP890153 KP890141 KP890171 gloeosporioides
C. guajavae IMI 350839* JQ948270 JQ948600 JQ948931 JQ949591 JQ949921 acutatum
C. guizhouensis CGMCC 3.15112* JX625158 KC843507   KC843536 JX625185 spaethianum
C. hanaui MAFF 305404* JX519217   JX519225   JX519242 graminicola
C. hebeiense# MFLUCC13–0726* KF156863 KF377495 KF289008 KF377532 KF288975 gloeosporioides
C. hedericola MFLU 15-0689* MN631384   MN635794 MN635795   gloeosporioides
C. helleniense# CBS 142418* KY856446 KY856270 KY856186 KY856019 KY856528 gloeosporioides
C. henanense# CGMCC 3.17354* KJ955109 KJ954810   KM023257 KJ955257 gloeosporioides
C. hemerocallidis CDLG5 JQ400005 JQ400012 Q399998 JQ399991 JQ400019 dematium
C. higginsianum# IMI 349061* KM105184 KM105535 KM105254 KM105394 KM105464 destructivum
C. hippeastri CBS 125376* JQ005231 JQ005318 JQ005405 JQ005579 JQ005665 boninense
C. horii# NBRC 7478* GQ329690 GQ329681 JX009752 JX009438 JX010450 gloeosporioides
C. hystricis# CBS 142411* KY856450 KY856274 KY856190 KY856023 KY856532 gloeosporioides
C. hsienjenchang MAFF 243051 AB738855   AB738846 AB738845   singleton
C. incanum ATCC 64682* KC110789 KC110807   KC110825 KC110816 spaethianum
C. indonesiense CBS 127551* JQ948288 JQ948618 JQ948949 JQ949609 JQ949939 acutatum
C. insertae MFLU 15-1895* KX618686 KX618684 KX618683 KX618682 KX618685 dematium
C. jacksonii MAFF 305460* JX519216   JX519224 JX519233 JX519241 graminicola
C. jasminigenum CGMCC LLTX-01* HM131513 HM131499   HM131508 HM153770 truncatum
C. javanense# CBS 144963a* MH846576 MH846572 MH846573 MH846575 MH846574 acutatum
C. jiangxiense CGMCC 3.17363* KJ955201 KJ954902   KJ954471 KJ955348 gloeosporioides
C. jinshuiense# CGMCC 3.18903* MG748077 MG747995 MG747913 MG747767 MG748157 dematium
C. jishouense GMBC0209* MH482929 MH681658   MH708135 MH727473 gigasporum
C. johnstonii CBS 128532* JQ948444 JQ948775 JQ949105 JQ949765 JQ950095 acutatum
C. kahawae# IMI 319418* JX010231 JX010012 JX009813 JX009452 JX010444 gloeosporioides
C. kakivorum#  KCTC 46679* LC324781 LC324787 LC324783 LC324785 LC324791 dematium
C. karstii# CORCG6* HM585409 HM585391 HM582023 HM581995 HM585428 boninense
C. kinghornii CBS 198.35* JQ948454 JQ948785 JQ949115 JQ949775 JQ950105 acutatum
C. laticiphilum# CBS 112989* JQ948289 JQ948619 JQ948950 JQ949610 JQ949940 acutatum
C. lauri MFLUCC 17-0205* KY514347 KY514344 KY514341 KY514338 KY514350 acutatum
C. ledebouriae CBS 141284* KX228254     KX228357   singleton
C. lentis# CBS 127604* JQ005766 KM105597 JQ005787 JQ005829 JQ005850 destructivum
C. liaoningense# CGMCC 3.17616* KP890104 KP890135 KP890127 KP890097 KP890111 magnum
C. lilii CBS 109214/BBA 62147* GU227810 GU228202 GU228300 GU227908 GU228104 spaethianum
C. lini CBS 172.51* JQ005765 KM105581 JQ005786 JQ005828 JQ005849 destructivum
C. limetticola CBS 114.14* JQ948193 JQ948523 JQ948854 JQ949514 JQ949844 acutatum
C. limonicola# CBS 142410* KY856472 KY856296 KY856213 KY856045 KY856554 boninense
C. lindemuthianum# CBS 144.31* JQ005779 JX546712 JQ005800 JQ005842 JQ005863 orbiculare
C. lineola# CBS 125337* GU227829 GU228221 GU228319 GU227927 GU228123 dematium
C. liriopes# CBS 119444* GU227804 GU228196 GU228294 GU227902 GU228098 spaethianum
C. lobatum IMI 79736* MG600768 MG600828 MG600874 MG600972 MG601035 magnum
C. lupini# CBS 109225* JQ948155 JQ948485 JQ948816 JQ949476 JQ949806 acutatum
C. magnisporum CBS 398.84* KF687718 KF687842 KF687782 KF687803 KF687882 gigasporum
C. makassarense# CBS 143664a* MH728812 MH728820 MH805850 MH781480 MH846563 gloeosporioides
C. magnum CBS 519.97* MG600769 MG600829 MG600875 MG600973 MG601036 magnum
C. malvarum CBS 521.97*  KF178480 KF178504  KF178529 KF178577 KF178601 orbiculare
C. melonis# CBS 159.84* JQ948194 JQ948524 JQ948855 JQ949515 JQ949845 acutatum
C. menispermi MFLU 14-0625* KU242357 KU242356 KU242355 KU242353 KU242354 dematium
C. metake MAFF 244029 AB738859         singleton
C. merremiae CBS 124955* MG600765 MG600825 MG600872 MG600969 MG601032 magnum
C. miscanthi MAFF 510857* JX519221   JX519229 JX519237 JX519246 graminicola
C. musae# CBS 116870* HQ596292 HQ596299 JX009896 HQ596284 HQ596280 gloeosporioides
C. musicola# CBS 132885* MG600736 MG600798 MG600853 MG600942 MG601003 orchidearum
C. navitas CBS 125086* JQ005769   JQ005790 JQ005832 JQ005853 graminicola
C. neosansevieriae CPC 25127* KR476747 KR476791   KR476790 KR476797 singleton
C. nicholsonii MAFF 511115* JQ005770   JQ005791 JQ005833 JQ005854 graminicola
C. nigrum# CBS 169.49* JX546838 JX546742 JX546693 JX546646 JX546885 singleton
C. novae-zelandiae# CBS 128505* JQ005228 JQ005315 JQ005402 JQ005576 JQ005662 boninense
C. nupharicola# CBS 470.96* JX010187 JX009972 JX009835 JX009437 JX010398 gloeosporioides
C. nymphaeae# CBS 515.78* JQ948197 JQ948527 JQ948858 JQ949518 JQ949848 acutatum
C. ocimi CBS 298.94* KM105222 KM105577 KM105292 KM105432 KM105502 destructivum
C. ochracea CGMCC 3.15104*  JX625156 KC843513   KC843527 JX625183 caudatum
C. okinawense# MAFF 240517* MG600767 MG600827   MG600971 MG601034 magnum
C. oncidii CBS 129828* JQ005169 JQ005256 JQ005343 JQ005517 JQ005603 boninense
C. orbiculare# CBS 570.97* KF178466 KF178490 KF178515 KF178563 KF178587 orbiculare
C. orchidearum# CBS 135131* MG600738 MG600800 MG600855 MG600944 MG601005 orchidearum
C. orchidophilum# CBS 632.80* JQ948151 JQ948481 JQ948812 JQ949472 JQ949802 singleton
C. orchidis MFLUCC 17-1302* MK502144 MK496857 MK496855 MK496853 MK496859 dematium
C. panacicola C08087* GU935869 GU935849   GU944758 GU935889 destructivum
C. pandanicola MFLUCC 17-0571* MG646967 MG646934 MG646931 MG646938 MG646926 gloeosporioides
C. panamense CBS 125386* MG600766 MG600826 MG600873 MG600970 MG601033 magnum
C. paranaense# CBS 134729* KC204992 KC205026 KC205043 KC205077 KC205060 acutatum
C. parallelophorum MFLUCC 14-0083* MF448525 MK165695     MH351280 singleton
C. parsonsiae CBS 128525* JQ005233 JQ005320 JQ005407 JQ005581 JQ005667 boninense
C. parthenocissicola MFLUCC 17-1098* MK629452 MK639362 MK639356 MK639358 MK639360 dematium
C. paspali MAFF 305403* JX519219   JX519227 JX519235 JX519244 graminicola
C. paxtonii IMI 165753* JQ948285 JQ948615 JQ948946 JQ949606 JQ949936 acutatum
C. petchii CBS 378.94* JQ005223 JQ005310 JQ005397 JQ005571 JQ005657 boninense
C. perseae# CBS 141365* KX620308 KX620242   KX620145 KX620341 gloeosporioides
C. phaseolorum# CBS 157.36 GU227896 GU228288 GU228386 GU227994 GU228190 dematium
C. phormii CBS 118194* JQ948446 JQ948777 JQ949107 JQ949767 JQ950097 acutatum
C. phyllanthi# CBS 175.67* JQ005221 JQ005308 JQ005395 JQ005569 JQ005655 boninense
C. piperis# IMI 71397* MG600760 MG600820 MG600867 MG600964 MG601027 orchidearum
C. pisicola CBS 724.97* KM105172 KM105522 KM105242 KM105382 KM105452 destructivum
C. plurivorum# CBS 125474* MG600718 MG600781 MG600841 MG600925 MG600985 orchidearum
C. pseudoacutatum# CBS 436.77* JQ948480 JQ948811 JQ949141 JQ949801 JQ950131 singleton
C. pseudomajus  CBS 571.88* KF687722 KF687826 KF687779 KF687801 KF687883 gigasporum
C. pseudotheobromicola# MFLUCC 18–1602* MH817395 MH853675 MH853678 MH853681 MH853684 gloeosporioides
C. psidii CBS 145.29* JX010219 JX009967 JX009901 JX009515 JX010443 gloeosporioides
C. proteae CBS 132882* KC297079 KC297009 KC296986 KC296940 KC297101 gloeosporioides
C. pyricola CBS 128531* JQ948445 JQ948776 JQ949106 JQ949766 JQ950096 acutatum
C. pyrifoliae# CGMCC 3.18902* MG748078 MG747996 MG747914 MG747768 MG748158 singleton
C. queenslandicum# ICMP 1778* JX010276 JX009934 JX009899 JX009447 JX010414 gloeosporioides
C. radicis CBS 529.93* KF687719  KF687825 KF687762 KF687785 KF687869 gigasporum
C. rhexiae CBS 133134* JX145128       JX145179 gloeosporioides
C. rhombiforme# CBS 129953* JQ948457 JQ948788 JQ949118 JQ949778 JQ950108 acutatum
C. riograndense ICMP 20083* KM655299 KM655298 KM655297 KM655295 KM655300 spaethianum
C. roseum CBS 145754 * MK903611 MK903603   MK903604 MK903607 acutatum
C. rusci CBS 119206* GU227818 GU228210 GU228308 GU227916 GU228112 singleton
C. salicis# CBS 607.94* JQ948460 JQ948791 JQ949121 JQ949781 JQ950111 acutatum
C. salsolae# ICMP 19051* JX010242 JX009916 JX009863 JX009562 JX010403 gloeosporioides
C. sambucicola MFLUCC 16–1388* KY098781 KY098780 KY098779 KY098778 KY098782 dematium
C. sansevieriae# MAFF 239721/Sa-1-2 LC179806 LC180130  LC180129 LC180127 LC180128 singleton
C. scovillei# CBS 126529* JQ948267 JQ948597 JQ948928 JQ949588 JQ949918 acutatum
C. sedi MFLUCC14-1002* KM974758 KM974755 KM974754 KM974756 KM974757 dematium
C. serranegrense COAD 2100a* KY400111   KY407894 KY407892 KY407896 gigasporum
C. shisoi# JCM 31818* MH660930 MH660931 MH660929 MH660928 MH660932 destructivum
C. siamense# MFU 090230* FJ972613 FJ972575 JX009865 FJ907423 FJ907438 gloeosporioides
C. sidae CBS 504.97* KF178472 KF178497 KF178521 KF178569 KF178593 orbiculare
C. simmondsii# CBS 122122* JQ948276 JQ948606 JQ948937 JQ949597 JQ949927 acutatum
C. sloanei IMI 364297* JQ948287 JQ948617 JQ948948 JQ949608 JQ949938 acutatum
C. somersetense CBS 131599* JX076862         caudatum
C. sonchicola MFLUCC 17-1299* KY962757 KY962754 KY962751 KY962748   dematium
C. sojae ATCC 62257* MG600749 MG600810 MG600860 MG600954 MG601016 orchidearum
C. spaethianum# CBS 167.49* GU227807 GU228199 GU228297 GU227905 GU228101 spaethianum
C. spinaciae# CBS 128.57 GU227847 GU228239 GU228337 GU227945 GU228141 dematium
C. spinosum CBS 515.97* KF178474 KF178498 KF178523 KF178571 KF178595 orbiculare
C. sublineola# CBS 131301* JQ005771   JQ005792 JQ005834 JQ005855 graminicola
C. sydowii CBS135819* KY263783 KY263785 KY263787 KY263791 KY263793 singleton
C. syzygiicola MFLUCC 10-0624* KF242094 KF242156    KF157801 KF254880 gloeosporioides
C. tabacum CPC 18945* KM105204 KM105557 KM105274 KM105414 KM105484 destructivum
C. tainanense CBS 143666a* MH728818 MH728823 MH805845 MH781475 MH846558 gloeosporioides
C. tanaceti# CBS 132693* JX218228 JX218243 JX259268 JX218238 JX218233 destructivum
C. tamarilloi# CBS 129814* JQ948184 JQ948514 JQ948845 JQ949505 JQ949835 acutatum
C. tebeesti CBS 522.97* KF178473 KF178505  KF178522 KF178570 KF178594 orbiculare
C. theobromicola# ICMP 18649* JX010294 JX010006 JX009869 JX009444 JX010447 gloeosporioides
C. temperatum CBS 133122* JX145159       JX145211 gloeosporioides
C. ti# ICMP 4832* JX010269 JX009952 JX009898 JX009520 JX010442 gloeosporioides
C. tofieldiae CBS 495.85* GU227801 GU228193 GU228291 GU227899 GU228095 spaethianum
C. tongrenense GZU_TRJ1-37/GMBC0209* MH482933 MH705332   MH717074 MH729805 dracaenophilum
C. torulosum CBS 128544* JQ005164 JQ005251 JQ005338 JQ005512 JQ005598 boninense
C. trichellum CBS 217.64* GU227812 GU228204 GU228302 GU227910 GU228106 singleton
C. trifolii# CBS 158.83* KF178478 KF178502 KF178527 KF178575 KF178599 orbiculare
C. tropicale# CBS 124949* JX010264 JX010007 JX009870 JX009489 JX010407 gloeosporioides
C. tropicicola BCC 38877* JN050240 JN050229   JN050218 JN050246 dracaenophilum
C. truncatum# CBS 151.35* GU227862 GU228254 GU228352 GU227960 GU228156 truncatum
C. utrechtense CBS 130243* KM105201 KM105554 KM105271 KM105411 KM105481 destructivum
C. verruculosum IMI 45525* GU227806 GU228198 GU228296 GU227904 GU228100 spaethianum
C. vietnamense LD16(L2)* KF687721 KF687832  KF687769 KF687792 KF687877 gigasporum
C. vignae CBS 501.97* KM105183 KM105534 KM105253 KM105393 KM105463 destructivum
C. viniferum# GZAAS5.08601* JN412804 JN412798   JN412795 JN412813 gloeosporioides
C. vittalense CBS 181.82* MG600734 MG600796 MG600851 MG600940 MG601001 orchidearum
C. walleri CBS 125472* JQ948275 JQ948605 JQ948936 JQ949596 JQ949926 acutatum
C. wanningense# CGMCC 3.18936* MG830462 MG830318 MG830302 MG830270 MG830286 acutatum
C. watphraense MFLUCC 14-0123* MF448523 MH049479   MH376384 MH351276 boninense
C. wuxiense# CGMCC 3.17894* KU251591 KU252045 KU251939 KU251672 KU252200 gloeosporioides
C. xanthorrhoeae BRIP 45094* JX010261 JX009927 JX009823 JX009478 JX010448 gloeosporioides
C. yulongense CFCC 50818* MH751507 MK108986 MH793605 MH777394 MK108987 gloeosporioides
C. yunnanense CBS 132135* JX546804 JX546706 JX519231 JX519239 JX519248 dracaenophilum
C. zoysiae MAFF238573* JX076871         caudatum

Fig. 2 Phylogram generated from MP analysis based on combined sequences of ITS, gapdh, chs, act and tub2 sequences of all species of Colletotrichum with molecular data. Related sequences were obtained from GenBank. Two hundred and fourty nine taxa are included in the analyses, which comprise 2296 characters including gaps, of which 868 characters are constant, 295 characters are parsimony-uninformative and 1133 characters parsimony-informative. The parsimony analysis of the data matrix resulted in the maximum of ten equally most parsimonious trees with a length of 10088 steps (CI = 0.283, RI=0.840, RC = 0.237, HI = 0.717) in the third tree. Single gene analyses were carried out and compared with each species, to compare the topology of the tree and clade stability. The tree was rooted with Monilochaetes infuscans (CBS 869.96) and M. populi (CBS 139623). MP bootstrap support value ≥50% and BYPP ≥0.9 are shown respectively near the nodes. Ex-type strains are in bold.

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