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Journal ArticleDOI

Taxonomy and phylogeny of hyaline-spored coelomycetes

TL;DR: The present study revises the classification of the hyaline-spored coelomycetes and provides a modern taxonomic framework based on both morphology and phylogeny.
Abstract: Coelomycete is a general term used for asexual fungi which produce conidia in fruiting bodies: pycnidial, acervular, cupulate, pycnothyria or stromatic conidiomata. The group contains numerous plant pathogenic, saprobic and endophytic species associated with a wide range of hosts. Traditionally, morphological characters and host associations have been used as criteria to identify and classify coelomycetes, and this has resulted in a poor understanding of their generic and species boundaries. DNA based taxonomic studies have provided a better outlook of the phylogenetic and evolutionary trends in coelomycetes. However, the present outcomes represent only a preliminary step towards the understanding of coelomycetes. Many genera have not been revisited since they were first described. The present study revises the classification of the hyaline-spored coelomycetes and provides a modern taxonomic framework based on both morphology and phylogeny. In total, 248 genera were investigated, of which less than 100 are known to have sequence data. Multi-locus sequence data analyses of 28S nrDNA, 18S nrDNA, ITS, RNA polymerase II second largest subunit (rpb2), and part of the translation elongation factor 1-alpha gene (tef1) and β-tubulin (tub2) gene regions were analysed. As a result, three new genera and 23 new species are introduced. In addition, three new links between sexual and asexual genera are provided. There are 138 genera that lack sequence data, and these are treated as Ascomycota, genera incertae sedis. Line drawings and descriptions are provided based on the examination of types and fresh collections and on the literature.
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Journal ArticleDOI
10 Jul 2020
TL;DR: A conceptual framework for the identification of fungi is provided, encouraging the approach of integrative (polyphasic) taxonomy for species delimitation, i.e. the combination of genealogy, phenotype, and phenotype-based approaches to catalog the global diversity of fungi and establish initial species hypotheses.
Abstract: True fungi (Fungi) and fungus-like organisms (e.g. Mycetozoa, Oomycota) constitute the second largest group of organisms based on global richness estimates, with around 3 million predicted species. Compared to plants and animals, fungi have simple body plans with often morphologically and ecologically obscure structures. This poses challenges for accurate and precise identifications. Here we provide a conceptual framework for the identification of fungi, encouraging the approach of integrative (polyphasic) taxonomy for species delimitation, i.e. the combination of genealogy (phylogeny), phenotype (including autecology), and reproductive biology (when feasible). This allows objective evaluation of diagnostic characters, either phenotypic or molecular or both. Verification of identifications is crucial but often neglected. Because of clade-specific evolutionary histories, there is currently no single tool for the identification of fungi, although DNA barcoding using the internal transcribed spacer (ITS) remains a first diagnosis, particularly in metabarcoding studies. Secondary DNA barcodes are increasingly implemented for groups where ITS does not provide sufficient precision. Issues of pairwise sequence similarity-based identifications and OTU clustering are discussed, and multiple sequence alignment-based phylogenetic approaches with subsequent verification are recommended as more accurate alternatives. In metabarcoding approaches, the trade-off between speed and accuracy and precision of molecular identifications must be carefully considered. Intragenomic variation of the ITS and other barcoding markers should be properly documented, as phylotype diversity is not necessarily a proxy of species richness. Important strategies to improve molecular identification of fungi are: (1) broadly document intraspecific and intragenomic variation of barcoding markers; (2) substantially expand sequence repositories, focusing on undersampled clades and missing taxa; (3) improve curation of sequence labels in primary repositories and substantially increase the number of sequences based on verified material; (4) link sequence data to digital information of voucher specimens including imagery. In parallel, technological improvements to genome sequencing offer promising alternatives to DNA barcoding in the future. Despite the prevalence of DNA-based fungal taxonomy, phenotype-based approaches remain an important strategy to catalog the global diversity of fungi and establish initial species hypotheses.

191 citations


Cites background or methods from "Taxonomy and phylogeny of hyaline-s..."

  • ...Mating is inherently cryptic and often complex, involving the fusion of minute gametangial elements, an event rarely observed in nature or even in the laboratory (Kück and Pöggeler 2009; Ni et al. 2011; Ropars et al. 2016; Bruns et al. 2018; Nagel et al. 2018; Li et al. 2020a)....

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  • ...The data with imagery is also placed online in websites developed for specific groups (Jayawardena et al. 2019; Pem et al. 2019; Li et al. 2020b)....

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Journal ArticleDOI
TL;DR: It is not possible to detail all techniques for all fungi and thus, this paper emphasizes on microfungi, and general practices of phenotypic approaches are herein outlined.
Abstract: Traditionally, fungal taxonomy was based on observable phenotypic characters. Recent advances have driven taxonomic conclusions towards DNA-based approaches and these techniques have corresponding pros and cons. Species concepts must therefore rely on incorporated approaches of genotypic, phenotypic and physiological characters and chemotaxonomy. Examination and interpretation of morphological characters however vary from person to person. Standardized procedures are used in the taxonomic study of fungi and general practices of phenotypic approaches are herein outlined. It is not possible to detail all techniques for all fungi and thus, this paper emphasizes on microfungi. Specimen collection is the initial step in any Mycosphere 11(1): 2678–2754 (2020) www.mycosphere.org ISSN 2077 7019

176 citations

Journal ArticleDOI
Kevin D. Hyde, Yang Dong1, Rungtiwa Phookamsak, Rajesh Jeewon2, D. Jayarama Bhat, E. B. Gareth Jones3, E. B. Gareth Jones4, Ning-Guo Liu, Pranami D. Abeywickrama5, Ausana Mapook5, Ausana Mapook6, De-Ping Wei, Rekhani H. Perera7, Rekhani H. Perera5, Ishara S. Manawasinghe5, Dhandevi Pem5, Dhandevi Pem8, Digvijayini Bundhun4, Digvijayini Bundhun5, Anuruddha Karunarathna, Anusha H. Ekanayaka5, Anusha H. Ekanayaka9, Dan-Feng Bao10, Dan-Feng Bao5, Dan-Feng Bao4, Junfu Li, Milan C. Samarakoon, Napalai Chaiwan1, Napalai Chaiwan5, Chuan-Gen Lin5, Kunthida Phutthacharoen9, Kunthida Phutthacharoen5, Sheng-Nan Zhang4, Sheng-Nan Zhang5, Indunil C. Senanayake8, Ishani D. Goonasekara5, Kasun M. Thambugala11, Chayanard Phukhamsakda5, Danushka S. Tennakoon, Hong-Bo Jiang, Jing Yang, Ming Zeng, Naruemon Huanraluek5, Jian-Kui Liu12, Subodini N. Wijesinghe, Qing Tian5, Saowaluck Tibpromma13, Saowaluck Tibpromma9, Saowaluck Tibpromma14, Rashika S. Brahmanage5, Saranyaphat Boonmee5, Shi-Ke Huang, Vinodhini Thiyagaraja, Yong-Zhong Lu7, Ruvishika S. Jayawardena5, Wei Dong, Er-Fu Yang14, Er-Fu Yang9, Sanjay K. Singh15, Shiv Mohan Singh16, Shiwali Rana15, Sneha S. Lad15, Garima Anand17, B. Devadatha18, B. Devadatha5, M. Niranjan18, V. Venkateswara Sarma18, Kare Liimatainen19, Begoña Aguirre-Hudson19, Tuula Niskanen19, Andy Overall, Renato Lúcio Mendes Alvarenga20, Tatiana Baptista Gibertoni20, Walter P. Pfliegler21, Enikő Horváth21, Alexandra Imre21, Amanda Lucia Alves20, Ana Carla da Silva Santos20, Patricia Vieira Tiago20, Timur S. Bulgakov, Dhanushaka N. Wanasinghe13, Dhanushaka N. Wanasinghe14, Dhanushaka N. Wanasinghe9, Ali H. Bahkali3, Mingkwan Doilom13, Mingkwan Doilom9, Mingkwan Doilom14, Abdallah M. Elgorban3, Sajeewa S. N. Maharachchikumbura12, Kunhiraman C. Rajeshkumar15, Danny Haelewaters, Peter E. Mortimer9, Peter E. Mortimer14, Qi Zhao9, Saisamorn Lumyong22, Saisamorn Lumyong4, Jianchu Xu13, Jianchu Xu14, Jianchu Xu9, Jun Sheng1 
TL;DR: The present study describes two new families, 12 new genera, 82 new species, five new combinations and 25 new records on new hosts and new geographical distributions as well as sexual-asexual reports.
Abstract: Fungal diversity notes is one of the important journal series of fungal taxonomy that provide detailed descriptions and illustrations of new fungal taxa, as well as providing new information of fungal taxa worldwide. This article is the 11th contribution to the fungal diversity notes series, in which 126 taxa distributed in two phyla, six classes, 24 orders and 55 families are described and illustrated. Taxa in this study were mainly collected from Italy by Erio Camporesi and also collected from China, India and Thailand, as well as in some other European, North American and South American countries. Taxa described in the present study include two new families, 12 new genera, 82 new species, five new combinations and 25 new records on new hosts and new geographical distributions as well as sexual-asexual reports. The two new families are Eriomycetaceae (Dothideomycetes, family incertae sedis) and Fasciatisporaceae (Xylariales, Sordariomycetes). The twelve new genera comprise Bhagirathimyces (Phaeosphaeriaceae), Camporesiomyces (Tubeufiaceae), Eriocamporesia (Cryphonectriaceae), Eriomyces (Eriomycetaceae), Neomonodictys (Pleurotheciaceae), Paraloratospora (Phaeosphaeriaceae), Paramonodictys (Parabambusicolaceae), Pseudoconlarium (Diaporthomycetidae, genus incertae sedis), Pseudomurilentithecium (Lentitheciaceae), Setoapiospora (Muyocopronaceae), Srinivasanomyces (Vibrisseaceae) and Xenoanthostomella (Xylariales, genera incertae sedis). The 82 new species comprise Acremonium chiangraiense, Adustochaete nivea, Angustimassarina camporesii, Bhagirathimyces himalayensis, Brunneoclavispora camporesii, Camarosporidiella camporesii, Camporesiomyces mali, Camposporium appendiculatum, Camposporium multiseptatum, Camposporium septatum, Canalisporium aquaticium, Clonostachys eriocamporesiana, Clonostachys eriocamporesii, Colletotrichum hederiicola, Coniochaeta vineae, Conioscypha verrucosa, Cortinarius ainsworthii, Cortinarius aurae, Cortinarius britannicus, Cortinarius heatherae, Cortinarius scoticus, Cortinarius subsaniosus, Cytospora fusispora, Cytospora rosigena, Diaporthe camporesii, Diaporthe nigra, Diatrypella yunnanensis, Dictyosporium muriformis, Didymella camporesii, Diutina bernali, Diutina sipiczkii, Eriocamporesia aurantia, Eriomyces heveae, Ernakulamia tanakae, Falciformispora uttaraditensis, Fasciatispora cocoes, Foliophoma camporesii, Fuscostagonospora camporesii, Helvella subtinta, Kalmusia erioi, Keissleriella camporesiana, Keissleriella camporesii, Lanspora cylindrospora, Loratospora arezzoensis, Mariannaea atlantica, Melanographium phoenicis, Montagnula camporesii, Neodidymelliopsis camporesii, Neokalmusia kunmingensis, Neoleptosporella camporesiana, Neomonodictys muriformis, Neomyrmecridium guizhouense, Neosetophoma camporesii, Paraloratospora camporesii, Paramonodictys solitarius, Periconia palmicola, Plenodomus triseptatus, Pseudocamarosporium camporesii, Pseudocercospora maetaengensis, Pseudochaetosphaeronema kunmingense, Pseudoconlarium punctiforme, Pseudodactylaria camporesiana, Pseudomurilentithecium camporesii, Pseudotetraploa rajmachiensis, Pseudotruncatella camporesii, Rhexocercosporidium senecionis, Rhytidhysteron camporesii, Rhytidhysteron erioi, Septoriella camporesii, Setoapiospora thailandica, Srinivasanomyces kangrensis, Tetraploa dwibahubeeja, Tetraploa pseudoaristata, Tetraploa thrayabahubeeja, Torula camporesii, Tremateia camporesii, Tremateia lamiacearum, Uzbekistanica pruni, Verruconis mangrovei, Wilcoxina verruculosa, Xenoanthostomella chromolaenae and Xenodidymella camporesii. The five new combinations are Camporesiomyces patagoniensis, Camporesiomyces vaccinia, Camposporium lycopodiellae, Paraloratospora gahniae and Rhexocercosporidium microsporum. The 22 new records on host and geographical distribution comprise Arthrinium marii, Ascochyta medicaginicola, Ascochyta pisi, Astrocystis bambusicola, Camposporium pellucidum, Dendryphiella phitsanulokensis, Diaporthe foeniculina, Didymella macrostoma, Diplodia mutila, Diplodia seriata, Heterosphaeria patella, Hysterobrevium constrictum, Neodidymelliopsis ranunculi, Neovaginatispora fuckelii, Nothophoma quercina, Occultibambusa bambusae, Phaeosphaeria chinensis, Pseudopestalotiopsis theae, Pyxine berteriana, Tetraploa sasicola, Torula gaodangensis and Wojnowiciella dactylidis. In addition, the sexual morphs of Dissoconium eucalypti and Phaeosphaeriopsis pseudoagavacearum are reported from Laurus nobilis and Yucca gloriosa in Italy, respectively. The holomorph of Diaporthe cynaroidis is also reported for the first time.

139 citations

Journal ArticleDOI
S. Hongsanan1, Kevin D. Hyde2, R. Phookamsak, Dhanushka N. Wanasinghe3, Eric H. C. McKenzie4, V. Venkateswara Sarma5, Saranyaphat Boonmee1, Robert Lücking6, Darbhe J. Bhat, Ning-Guo Liu7, Danushka S. Tennakoon1, Dhandevi Pem1, Anuruddha Karunarathna8, Shu-Hua Jiang3, E. B. G. Jones9, Alan J. L. Phillips10, Ishara S. Manawasinghe2, Saowaluck Tibpromma3, Subashini C. Jayasiri1, D. S. Sandamali1, Ruvishika S. Jayawardena1, Nalin N. Wijayawardene, Anusha H. Ekanayaka1, Rajesh Jeewon11, Yin Lu12, Asha J. Dissanayake13, Xiang Yu Zeng1, Zong-Long Luo14, Qing Tian1, Chayanard Phukhamsakda1, Kasun M. Thambugala15, Dong-Qin Dai, K. W. T. Chethana1, Milan C. Samarakoon1, Damien Ertz, Dan-Feng Bao1, Mingkwan Doilom3, Jian-Kui Liu13, Sergio Pérez-Ortega16, Ave Suija17, Chanokned Senwanna1, Subodini N. Wijesinghe1, Sirinapa Konta1, M. Niranjan18, S. N. Zhang1, Hiran A. Ariyawansa19, H. B. Jiang8, Junyan Zhang12, Chada Norphanphoun1, N. I. de Silva8, Vinodhini Thiyagaraja8, Haiyan Zhang12, Jadson D. P. Bezerra20, Ricardo Miranda-González21, André Aptroot22, Hiroyuki Kashiwadani, Dulanjalee Harishchandra1, Emmanuël Sérusiaux12, Janith V. S. Aluthmuhandiram1, Pranami D. Abeywickrama1, B. Devadatha1, Hai-Xia Wu, Kwang Hee Moon, Cécile Gueidan23, Felix Schumm, Digvijayini Bundhun1, Ausana Mapook1, Jutamart Monkai1, Putarak Chomnunti1, Satinee Suetrong24, N. Chaiwan8, Monika C. Dayarathne25, Jing Yang1, Achala R. Rathnayaka1, Chitrabhanu S. Bhunjun1, Jianchu Xu3, J. S. Zheng26, G. Liu26, Y. Feng25, Ning Xie26 
TL;DR: An overall phylogenetic tree of families in Dothideomycetes is provided based on combined analysis of LSU, SSU, rpb-2 and tef1 sequence data, and phylogenetic trees for each order in DothsideomyCetidae and PleosporomycETidae are provided.
Abstract: The class Dothideomycetes is the largest and most ecologically diverse class of fungi, comprising endophytes, epiphytes, saprobes, human and plant pathogens, lichens, and lichenicolous, nematode trapping and rock-inhabiting taxa. Members of this class are mainly characterized by bitunicate asci with fissitunicate dehiscence, and occur on broad range of hosts in aquatic and terrestrial habitats. Since the last monograph of families of Dothideomycetes in 2013, numerous novel species, genera, families and orders have been discovered. This has expanded information which has led to the modern classification in Dothideomycetes. In this paper, we provide a refined updated document on families of Dothideomycetes with emphasis on Dothideomycetidae and Pleosporomycetidae. We accept three orders with 25 families and four orders with 94 families in Dothideomycetidae and Pleosporomycetidae, respectively. The new family Paralophiostomataceae is introduced in Pleosporales. Each family is provided with an updated description, notes, including figures to represent the morphology, list of accepted genera, and economic and ecological significances. We also provide an overall phylogenetic tree of families in Dothideomycetes based on combined analysis of LSU, SSU, rpb-2 and tef1 sequence data, and phylogenetic trees for each order in Dothideomycetidae and Pleosporomycetidae. Familylevel trees are provided for the families which include several genera such as Mycosphaerellaceae and Teratosphaeriaceae. Two new genera (Ligninsphaeriopsis and Paralophiostoma) are introduced. Five new species (Biatrisopora borsei, Comoclathris galatellae, Ligninsphaeriopsis thailandica, Paralophiostoma hysterioides and Torula thailandica) are introduced based on morphology and phylogeny, together with nine new reports and seven new collections from

97 citations

01 Jan 2013
TL;DR: In this article, the diversity and distribution of the N. ribis-N. parvum species complex were analyzed using seven microsatellite markers and the global distribution of diversity was analyzed using sequence search results available in public and in their own databases.
Abstract: Aim: Cryptic species in the Neofusicoccum parvum-N. ribis species complex have only recently been described, invalidating previous interpretations on host and geographical distribution. This study aimed to characterize the diversity and distribution of these species and to understand the patterns of host association, likely origins and their patterns of spread. Location: Australia, Brazil, Cameroon, Chile, China, Colombia, Ethiopia, France, Greece, India, Indonesia, Iran, Italy, Japan, Kenya, Mexico, New Zealand, Panama, Portugal, Puerto Rico, South Africa, South Korea, Spain, Swaziland, Taiwan, Thailand, Uganda, United States of America, Uruguay, Zambia and Zimbabwe. Methods: Using the unique polymorphisms that separate species within the complex, we evaluated sequence search results available in public and in our own databases. In addition, the global distribution of diversity of N. parvum was analysed using seven microsatellite markers. Results: Neofusicoccum parvum is found in 90 hosts across six continents and 29 countries. Neofusicoccum kwambonambiense is found on four continents, six countries and on 14 hosts; N. occulatum is found on four continents, four countries and on 11 hosts; N. umdonicola is found on two continents, countries and hosts; N. cordaticola is found on three continents, countries and hosts; N. batangarum is found on two continents, three countries and three hosts; and N. ribis is found on one host in one country. Population genetic analysis of the global N. parvum population reflects admixture and repeat introductions. Main conclusions: This study illustrates the unfettered and frequent movement of latent pathogens across international borders. Amongst the species in the N. parvum-N. ribis complex, N. parvum is the most widespread and has been reported on the majority of the hosts studied. The current dispersal of N. parvum and its sister species is probably due to repeated introductions of plant material into new growing areas, with Eucalyptus and Vitis vinifera being two prominent candidates for material transfer.

84 citations

References
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Journal ArticleDOI
TL;DR: This version of MAFFT has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update.
Abstract: We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.

27,771 citations

Journal ArticleDOI
TL;DR: MrBayes 3 performs Bayesian phylogenetic analysis combining information from different data partitions or subsets evolving under different stochastic evolutionary models to analyze heterogeneous data sets and explore a wide variety of structured models mixing partition-unique and shared parameters.
Abstract: Summary: MrBayes 3 performs Bayesian phylogenetic analysis combining information from different data partitions or subsets evolving under different stochastic evolutionary models. This allows the user to analyze heterogeneous data sets consisting of different data types—e.g. morphological, nucleotide, and protein— and to explore a wide variety of structured models mixing partition-unique and shared parameters. The program employs MPI to parallelize Metropolis coupling on Macintosh or UNIX clusters.

25,931 citations


Additional excerpts

  • ...2010, 2012) using RAxML-HPC BlackBox v. 8.2.10 (Stamatakis 2014) and MrBayes onXSEDE v. 3.2.6 (Huelsenbeck and Ronquist 2001; Ronquist and Huelsenbeck 2003), respectively....

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