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Taxa used for the phylogenetic analyses in this study. Ex-type/ex-epitype or reference strains are marked with an asterix (*). Sequence data obtained in this study are in bold.
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A new species, Colletotrichum artocarpicola, on Artocarpus heterophyllus from Chiang Rai, Thailand, is introduced using both morphological and molecular approaches. Combined phylogenetic analysis of ITS, GAPDH, CHS-1, ACT and TUB2 sequence data demonstrate that Colletotrichum artocarpicola is a distinct species within the gloeosporioides species co...
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Citations
... Among fungal pathogens, Colletotrichum species are the most important fungi responsible for the diseases of tropical and sub-tropical fruits [16]. Many Colletotrichum species have been reported from different hosts in Thailand such as C. aenigma [17], C. aeschynomenes [18], C. artocarpicola [19], C. asianum [20][21][22][23], C. boninense [18,24], C. brevisporum [16,[25][26][27], C. chiangraiense [24,28], C. cordylinicola [21,29,30], C. endophytica [31][32][33][34], C. orchidearum [24,25], C. orchidophilum [24], C. plurivorum [35], and C. siamense [16,21,24,36,37], majority belonging to gloeosporioides species complex. Colletotrichum fructicola is one of the most invasive species and has been reported as the causal agent of anthracnose, leaf spots and bitter rots in more than 90 plant species [38]. ...
Pineapple is one of the most economically important fruits in tropical countries, particularly in Thailand. Canned pineapple is currently Thailand's main exported commodity to many countries, including the United States, Russia, Germany, Poland, and Japan. Fungal diseases are considered a permanent threat to fruits in the pre-and post-harvest stages, leading to considerable economic losses. Fungal disease is one of the primary causes of massive yield losses in pineapples around the world. Colletotrichum species are the most common fungal pathogens affecting different tropical fruits. Although there are many reports regarding Colletotrichum species associated with pineapple, they do not have molecular data to confirm species identification. However, the occurrence of Colletotrichum species on pineapple has not been reported in Thailand so far. In this study, we isolated and identified Colletotrichum fructicola on pineapple in northern Thailand and have proven its pathogenicity to the host. This is the first report of the occurrence of Colletotrichum in pineapple, based on morpho-molecular approaches.
... Vários trabalhos retratam as limitações das características morfoculturais e o emprego de apenas uma região genômica na delimitação de espécies do gênero, especialmente da região ITS-rDNA HYDE et al., 2009;DAMM et al., 2009;CANNON et al., 2012;. Estudo realizado por Hyde et al. (2009) DAMM et al., 2013;CROUCH, 2014;DAMM et al., 2014;HYDE et al., 2014;LIU et al., 2014;LIU et al., 2015;HOU et al., 2016;JAYAWARDENA et al., 2016;BHUNJUN et al., 2019;JAYAWARDENA et al., 2021;BARONCELLI, 2021;LIU et al. 2022). No campo, os problemas ocasionados por fitopatógenos são comumente minimizados por meio do sistema convencional de produção agrícola (MARIANI et al., 2015;AMORIM et al., 2018). ...
... The colony of our isolate is white to grey, reverse dark grey at the centre with light yellow at the edge, and the conidia are 10-15 × 5-10 μm (x̄ =12 × 6 μm, n = 50). However, these variations might be possible with the interspecies diversity of C. endophytica as following the data shown in Bhunjun et al. (2019). Therefore, we introduce our two isolates as a new host record of C. endophytica from Acacia confusa (Farr & Rossman 2022). ...
This is the seventh in a series of Mycosphere notes in which we provide notes on the collection of fungi isolated from various hosts. In this set of notes, we introduce Pseudophialocephala as a new genus, nine new species, 27 new host or country records and five new combinations. The new species are Ceratosphaeria yunnanensis, Cytospora salicis-albae, Gymnopus bunerensis, Kalmusia cordylines, Leucoagaricus croceus, Leucoagaricus laosensis, Neopyrenochaeta shaoguanica, Pseudophialocephala cuneata and Robillarda aquatica. Pseudophialocephala humicola, Pseudophialocephala aquatica, Pseudophialocephala salinicola, Pseudophialocephala terricola and Pseudophialocephala xalapensis are introduced as new combinations. We provide new molecular data for 43 species belonging to two phyla, three classes and 15 orders. Updated phylogenetic trees for 22 families (Agaricaceae, Botryosphaeriaceae, Chaetosphaeriaceae, Coniochaetaceae, Didymosphaeriaceae, Gloeophyllaceae, Glomerellaceae, Hysteriaceae, Lophiostomataceae, Magnaporthaceae, Neopyrenochaetaceae, Omphalotacea, Phaeosphaeriaceae, Phyllostictaceae, Pleosporaceae, Saccotheciaceae, Savoryellaceae, Sporocadaceae, Stachybotryaceae, Torulaceae, Valsaceae, Physalacriaceae) and 32 genera (Alfaria, Aureobasidium, Ceratosphaeria, Collybiopsis, Colletotrichum, Comoclathris, Coniochaeta, Cytospora, Dothiorella, Gymnopus, Gymnopus, Heliocybe, Hysterium, Hysterobrevium, Kalmusia, Leptospora, Letendraea, Leucoagaricus, Mucidula, Neoleptosporella, Neopyrenochaeta, Paraleptospora, Phyllosticta, Pseudophialocephala, Rhytidhysteron, Robillarda, Savoryella, Sporocadus, Thozetella, Torula and Vaginatispora) are given.
... Most collections of Apiospora species have been found on Poaceae as this is the most frequently sampled host (Farr and Rossman 2021). Despite being found on a wide range of hosts and their ability to switch lifestyles, the number of Apiospora species is low as compared to other important pathogenic genera such as Colletotrichum which can also be found on a wide range of hosts and have been associated with different lifestyles (Bhunjun et al. 2019;Jayawardena et al. 2019bJayawardena et al. , 2021b. This suggest that a large number of species will be discovered in Apiospora with extensive sampling. ...
Fungi play vital roles in ecosystems as endophytes, pathogens and saprobes. The current estimate of fungal diversity is highly
uncertain, ranging from 1.5 to 12 million, but only around 150,000 species have been named and classified to date. Since
the introduction of DNA based methods for species identification, the number of newly described taxa has increased from
approximately 1000 to around 2000 yearly. This demonstrates the importance of DNA based methods to identify and distinguish species, especially cryptic species. Many novel species from recent studies have been found in historically understudied
regions and habitats, but these still represent only a small percentage of the estimated species. In this paper, we examine 16
genera from the top 40 most speciose genera as listed in Species Fungorum as case studies to examine the diversity of taxa in
each genus. The genera treated herein are Cercospora, Diaporthe, Meliola, Passalora, Phyllachora, Phyllosticta, Pseudocercospora, Ramularia (ascomycetes) and Cortinarius, Entoloma, Inocybe, Marasmius, Psathyrella, Puccinia, Russula, Uromyces
(basidiomycetes). We critically evaluate the number of species in these genera and correlate these numbers with the number
of entries in GenBank. We introduce 18 new species Apiospora multiloculata, Candolleomyces thailandensis, Cortinarius
acutoproximus, Cortinarius melleoalbus, Cortinarius pacificus, Cortinarius parvoacetosus, Diaporthe guizhouensis, Entoloma
pseudosubcorvinum, Inocybe meirensongia, Marasmius albulus, Marasmius obscuroaurantiacus, Meliola camporesii, Phyllachora siamensis, Phyllosticta doitungensis, Picipes yuxiensis, Pseudocercospora vignae, Puccinia maureanui and Russula
inornata. We also introduce a new record of Candolleomyces cladii-marisci and Inocybe iringolkavensis. We discuss the
genera Colletotrichum and Pleurotus that are speciose, but do not occur in the top 40. We hypothesize whether there might be
more species in these genera and discuss why these genera have some of the largest number of species.
... Colletotrichum artocarpicola Bhunjun, Jayawardena, Jeewon and K.D. Hyde, Phytotaxa 418: 273 (2019) Colletotrichum artocarpicola was collected as a saprobe from a dead root of jackfruit (Artocarpus heterophyllus, Moraceae) in Thailand in 2018 (Bhunjun et al. 2019). The pathological and conservation status of thus fungus remains to be investigated. ...
The taxonomy of the genus Colletotrichum has undergone tremendous changes over the last decade, with over 200 species being currently recognised and species complexes being informally used to cluster those species. Many of these species are important plant pathogens, some rather polyphagous and others host-specific, but several occur seldomly and some may in fact be ecologically endangered. Based mainly on literature from the past decade, in this work we review the occurrence, geographic distribution and host spectrum of currently recognised Colletotrichum species under phylogenetic, pathological/agronomic and ecological perspectives, providing a list arranged by Colletotrichum species and species complexes. A total of 257 species are listed and grouped into 15 species complexes. In this work we have recorded 1353 unique host species-Colletotrichum species association records from 720 hosts, with the Fabaceae as the family with higher number of hosts (52 host species) but with the Rosaceae as the family with the highest number of host species-Colletotrichum species association records (118 association records). According to occurrence data, 88 species are common in nature, 128 were considered as data deficient and 41 are threatened, some of which are likely extinct from nature and preserved only in culture collections. Several species are relevant plant pathogens, in some cases geographically confined and thus of potential quarantine relevance. Based on the major changes that occurred on Colletotrichum taxonomy over the last decade, this work provides a comprehensive overview of occurrence data of Colletotrichum species, compiling host range and geographical distribution, with relevance for plant pathology and conservation mycology. The current taxonomic framework in Colletotrichum is revealing numerous species but poses challenges to the employment of standard criteria for the evaluation of biological conservation of these fungi. We advocate that conservation mycology and taxonomy should find common routes simultaneously enabling the correct delimitation of species of Colletotrichum and the implementation of feasible criteria for the evaluation of conservation. The employment of new technologies, such whole genome sequencing (WGS), will help and support the description of new species and to gain a better understanding of the genetic bases of speciation processes.
... Studies introducing new fungal pathogenic species usually include data on pathogenicity testing [13,74,75], but this has not been applied in all cases [76,77]. Inoculation of detached tissues allows disease assessment without destroying the whole plant, but it may not be reliable owing to the suppression of the host defence pathways [62]. ...
... Therefore, findings from detached inoculations should be regarded as preliminary findings that should be confirmed using the whole plant [62]. Another limitation of the detached method is difficulty in differentiating and describing the area of inoculation as the overall tissue changes colour after several days [74]. Different studies have used different scales in visual plant disease assessment, which is problematic for inter studies comparison. ...
... There is also a lack of replication in some studies, which can lead to biased results [79]. There is a lack of cross pathogenicity testing in some studies, which is an important indicator of the infection potential [74]. ...
Fungi are an essential component of any ecosystem, but they can also cause mild and
severe plant diseases. Plant diseases are caused by a wide array of fungal groups that affect a
diverse range of hosts with different tissue specificities. Fungi were previously named based only
on morphology and, in many cases, host association, which has led to superfluous species names
and synonyms. Morphology-based identification represents an important method for genus level
identification and molecular data are important to accurately identify species. Accurate identification
of fungal pathogens is vital as the scientific name links the knowledge concerning a species including
the biology, host range, distribution, and potential risk of the pathogen, which are vital for effective
control measures. Thus, in the modern era, a polyphasic approach is recommended when identifying
fungal pathogens. It is also important to determine if the organism is capable of causing host
damage, which usually relies on the application of Koch’s postulates for fungal plant pathogens.
The importance and the challenges of applying Koch’s postulates are discussed. Bradford Hill
criteria, which are generally used in establishing the cause of human disease, are briefly introduced.
We provide guidelines for pathogenicity testing based on the implementation of modified Koch’s
postulates incorporating biological gradient, consistency, and plausibility criteria from Bradford Hill.
We provide a set of protocols for fungal pathogenicity testing along with a severity score guide,
which takes into consideration the depth of lesions. The application of a standard protocol for fungal
pathogenicity testing and disease assessment in plants will enable inter-studies comparison, thus
improving accuracy. When introducing novel plant pathogenic fungal species without proving
the taxon is the causal agent using Koch’s postulates, we advise the use of the term associated with
the “disease symptoms” of “the host plant”. Where possible, details of disease symptoms should be
clearly articulated
... The placement was validated when phylogenetic data became available and Réblová et al. (2011) clarified the placement (Hyde et al. 2020a). Species in the Colletotrichum are wellknown pathogens on plants and humans (Jayawardena et al. 2017, Bhunjun et al. 2019, Jayawardena et al. 2021). The Species Fungorum database counts over 200 species names for Colletotrichum since August 2020 (http://www.speciesfungorum.org). ...
... Separate ITS, GAPDH, and ACT DNA sequences were subjected to the BLAST search engine of NCBI to verify and select taxa for phylogenetic analyses. Taxa used in the analyses were found from the latest publications (Bhunjun et al. 2019). ...
Padaruth OD, Pem D, Harishchandra DL, Jeewon R, Bulgakov TS, Jayawardena RS 2021-The first confirmed host record of Colletotrichum gloeosporioides on Citrus reticulata subsp. unshiu in the humid subtropics of Russia. Abstract A fresh collection of Colletotrichum gloeosporioides was recovered from Citrus reticulata Blanco in the humid subtropics of the Krasnodar region (Russia). Morphological examinations were performed and multi-loci phylogenies based on DNA sequences derived from actin (ACT), internal transcribed spacers (ITS), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), chitin synthase (CHS) and β-tubulin (TUB2) were generated to identify the species and investigate its evolutionary relationships to extant species. Our study provides the first confirmed host record of Colletotrichum gloeosporioides on Citrus reticulata Blanco subsp. unshiu in the humid subtropics of Russia. A brief introduction on Citrus reticulata and the impact of Colletotrichum gloeosporioides are discussed. Illustrations of the new host record are also provided.
... Cai et al. (2009) andHyde et al. (2009) proposed to use phylogeny, morphology, geographical and ecological information in order to resolve species boundaries in this genus. Recent studies have revealed 247 Colletotrichum species, which group in to 14 species complexes (Damm et al. 2018;Bhunjun et al. 2019). Tennakoon,C.H. Kuo & K.D. Hyde,sp. ...
... In addition, despite we were unable to obtain the GAPDH sequences for our species, the tree topology was Fig. 121 Results of the PHI test of related species using both LogDet transformation and splits decomposition. New species (MFLU 18-2615) described in this study are indicated in red similar to previous studies Bhunjun et al. 2019;Hyde et al. 2020c). Tennakoon -20 × 5-6.2 μm ( x = 17.8 × 5.5 μm, n = 20), hyaline, cylindrical or clavate, septate, branched, smooth-walled, simple, occurring in densely arranged clusters. ...
This article provides descriptions and illustrations of microfungi associated with the leaf litter of Celtis formosana, Ficus ampelas, F. septica, Macaranga tanarius and Morus australis collected from Taiwan. These host species are native to the island and Celtis formosana is an endemic tree species. The study revealed 95 species, consisting of two new families (Cylindrohyalosporaceae and Oblongohyalosporaceae), three new genera (Cylindrohyalospora, Neodictyosporium and Oblongohyalospora), 41 new species and 54 new host records. The newly described species are Acrocalymma ampeli (Acrocalymmaceae), Arthrinium mori (Apiosporaceae), Arxiella celtidis (Muyocopronaceae), Bertiella fici (Melanommataceae), Cercophora fici (Lasiosphaeriaceae), Colletotrichum celtidis, C. fici, C. fici-septicae (Glomerellaceae), Conidiocarpus fici-septicae (Capnodiaceae), Coniella fici (Schizoparmaceae), Cylindrohyalospora fici (Cylindrohyalosporaceae), Diaporthe celtidis, D. fici-septicae (Diaporthaceae), Diaporthosporella macarangae (Diaporthosporellaceae), Diplodia fici-septicae (Botryosphaeriaceae), Discosia celtidis, D. fici (Sporocadaceae), Leptodiscella sexualis (Muyocopronaceae), Leptospora macarangae (Phaeosphaeriaceae), Memnoniella alishanensis, M. celtidis, M. mori (Stachybotryaceae), Micropeltis fici, M. ficina (Micropeltidaceae), Microthyrium fici-septicae (Microthyriaceae), Muyocopron celtidis, M. ficinum, Mycoleptodiscus alishanensis (Muyocopronaceae), Neoanthostomella fici (Xylariales genera incertae sedis), Neodictyosporium macarangae (Sordariales genera incertae sedis), Neofusicoccum moracearum (Botryosphaeriaceae), Neophyllachora fici (Phyllachoraceae), Nigrospora macarangae (Apiosporaceae), Oblongohyalospora macarangae (Oblongohyalosporaceae), Ophioceras ficinum (Ophioceraceae), Parawiesneriomyces chiayiensis (Wiesneriomycetaceae), Periconia alishanica, P. celtidis (Periconiaceae), Pseudocercospora fici-septicae (Mycosphaerellaceae), Pseudoneottiospora cannabacearum (Chaetosphaeriaceae) and Pseudopithomyces mori (Didymosphaeriaceae). The new host records are Alternaria burnsii, A. pseudoeichhorniae (Pleosporaceae), Arthrinium hydei, A. malaysianum, A. paraphaeospermum, A. rasikravindrae, A. sacchari (Apiosporaceae), Bartalinia robillardoides (Sporocadaceae), Beltrania rhombica (Beltraniaceae), Cladosporium tenuissimum (Cladosporiaceae), Coniella quercicola (Schizoparmaceae), Dematiocladium celtidicola (Nectriaceae), Diaporthe limonicola, D. millettiae, D. pseudophoenicicola (Diaporthaceae), Dictyocheirospora garethjonesii (Dictyosporiaceae), Dimorphiseta acuta (Stachybotryaceae), Dinemasporium parastrigosum (Chaetosphaeriaceae), Discosia querci (Sporocadaceae), Fitzroyomyces cyperacearum (Stictidaceae), Gilmaniella bambusae (Ascomycota genera incertae sedis), Hermatomyces biconisporus (Hermatomycetaceae), Lasiodiplodia thailandica, L. theobromae (Botryosphaeriaceae), Memnoniella echinata (Stachybotryaceae), Muyocopron dipterocarpi, M. lithocarpi (Muyocopronaceae), Neopestalotiopsis asiatica, N. phangngaensis (Sporocadaceae), Ophioceras chiangdaoense (Ophioceraceae), Periconia byssoides (Periconiaceae), Pestalotiopsis dracaenea, P. formosana, P. neolitseae, P. papuana, P. parva, P. portugallica, P. trachycarpicola (Sporocadaceae), Phragmocapnias betle (Capnodiaceae), Phyllosticta capitalensis (Phyllostictaceae), Pseudopestalotiopsis camelliae-sinensis (Sporocadaceae), Pseudopithomyces chartarum, P. sacchari (Didymosphaeriaceae), Pseudorobillarda phragmitis (Pseudorobillardaceae), Robillarda roystoneae (Sporocadaceae), Sirastachys castanedae, S. pandanicola (Stachybotryaceae), Spegazzinia musae (Didymosphaeriaceae), Stachybotrys aloeticola, S. microspora (Stachybotryaceae), Strigula multiformis (Strigulaceae), Torula fici (Torulaceae), Wiesneriomyces laurinus (Wiesneriomycetaceae) and Yunnanomyces pandanicola (Sympoventuriaceae). The taxonomic placement of most taxa discussed in this study is based on morphological observation of specimens, coupled with multi-locus phylogenetic analyses of sequence data. In addition, this study provides a host-fungus database for future studies and increases knowledge of fungal diversity, as well as new fungal discoveries from the island.
... nicotianae Houttuynia cordata ITS, CAL [61] Nicotiana tabacum ITS, CAL [61] Cochliobolus heterostrophus Zea mays ITS, GAPDH, TEF [22] Cochliobolus setariae Imperata cylindrica ITS, GAPDH [22] Colletotrichum acidae Phyllanthus acidus ITS, ACT, CHS-1, GAPDH, TUB [14] Colletotrichum acutatum Fragaria sp. ITS, TUB [13] Capsicum annuum ITS, TUB [13,79] Colletotrichum aenigma Hylocereus undatus ITS [80] Colletotrichum aeschynomenes Manihot esculenta ITS [81] Colletotrichum artocarpicola Artocarpus heterophyllus ITS, ACT, CHS-1, GAPDH, TUB [82] Colletotrichum asianum Mangifera indica ITS, ACT, GAPDH, TUB [12] Coffea arabica ITS, ACT, CAL, GAPDH, GS, TUB [83] Colletotrichum boninense Manihot esculenta ITS [81] Dendrobium sp. ITS, ACT, GAPDH, TUB [84] Colletotrichum brevisporum Anthurium sp. ...
... Mangifera indica ITS, TUB [13] Manihot esculenta ITS [81] Artocarpus heterophyllus ITS, ACT, CHS-1, GAPDH, TUB [82] Fragaria sp. ITS [13] Capsicum annuum ITS, TUB [13] Colletotrichum graminicola Rottboellia cochinchinensis ITS [98] Colletotrichum lindemuthianum Manihot esculenta ITS [81] Colletotrichum musae Musa sp. ...
Thailand is rich in fungal diversity and new taxa are continuously introduced. In the last decade there has been a vast improvement on the taxonomy, phylogeny and classification of fungi, including in Thailand. Earlier studies were solely based on morphology while modern research uses morphology and molecular phylogeny. There is a huge gap between currently accepted species numbers and previously described species based on morphology. Hence, clarification of previously introduced species using molecular data and providing missing molecular data for those species, is as important as introducing novel taxa. Correct identification of fungi is important in plant pathology and for quarantine purposes. Some introduced fungal species have been discovered to be species complexes based on modern molecular phylogeny. The adoption of "one fungus one name" has necessitated the updating of previous classifications. There are also many taxa yet to be discovered from Thailand. Thus it is important to recollect, sequence, re-describe and resolve the taxonomic ambiguities. It is important to document all fungal taxa as well as provide information on their life modes and to update plant quarantine checklists. In this review we discuss the status of phytopathogenic fungal identification, evolution of the fungal studies through some well-known examples, modern technologies that can be used, and prospects. Most importantly we provide a checklist of plant associated fungi of Thailand, for which there is molecular data available.
... However, C. fructicola and C. siamense, which are common on the same hosts in other parts of the world, are not found in New Zealand. Colletotrichum artocarpicola was isolated as a saprobe from Artocarpus heterophyllus in Thailand (Bhunjun et al. 2019). When the authors conducted cross pathogenicity studies, they found out that this species can be a pathogen not only of Artocarpus heterophyllus, but also of Carica papaya and Capsicum sp. . ...
... The GCPSR as mentioned earlier is a pragmatic tool for the assessment of species limits, as the concordance of gene genealogies is a valuable criterion for evaluating the significance of gene flow between groups within an evolutionary timescale (Quaedvlieg et al. 2014). Many studies have conducted the PHI test using the GCPSR model to determine the recombination level between taxa when describing new Colletotrichum species (Crouch 2014, Liu et al. 2015a, 2016d, Jayawardena et al. 2016a, Bhunjun et al. 2019. Results of PHI below a 0.05 threshold (Фw < 0.05) indicate the presence of significant recombination. ...
Colletotrichum is an important plant pathogenic genus that has undergone tremendous taxonomic changes. Species of Colletotrichum also occur as endophytes, saprobes and rarely entomopathogens. The current understanding of Colletotrichum taxonomy and application of various techniques in defining species within the genus is discussed in this paper. Here we provide a review of lifestyles, infection mechanisms, life cycle, host-specificity, classification history and techniques defining Colletotrichum species and the relation to speciation. Misidentifications and mistakes during species introduction are discussed and recommendations are provided for valid species publication. We provide an account of 248 currently accepted species with molecular data, which falls into 14 species-complexes and 13 singleton species. An updated account of Colletotrichum species is provided. Species are listed alphabetically in each species complex and annotated with their habitat, host, geographic distribution, phylogenetic position and typification details. Tables of host specific (152 species) and geographically endemic Colletotrichum species (19 species) are provided. A table of 450 morpho-species is provided for the first time gathering all data to one place, allowing mycologists to check before publishing a new species. Phylogenetic trees are provided for the whole genus and each species complex. Genes and combinations of genes that can be used for the identification of the species complexes are suggested. Future directions for the advancement of this genus are discussed.
