Modern taxonomy has developed towards the establishment of global authoritative lists of species that assume the standard-ized principles of species recognition,at least in a given taxonomic group.However,in fungi,spe...Modern taxonomy has developed towards the establishment of global authoritative lists of species that assume the standard-ized principles of species recognition,at least in a given taxonomic group.However,in fungi,species delimitation is fre-quently subjective because it depends on the choice of a species concept and the criteria selected by a taxonomist.Contrary to it,identification of fungal species is expected to be accurate and precise because it should predict the properties that are required for applications or that are relevant in pathology.The industrial and plant-beneficial fungi from the genus Tricho-derma(Hypocreales)offer a suitable model to address this collision between species delimitation and species identification.A few decades ago,Trichoderma diversity was limited to a few dozen species.The introduction of molecular evolutionary methods resulted in the exponential expansion of Trichoderma taxonomy,with up to 50 new species recognized per year.Here,we have reviewed the genus-wide taxonomy of Trichoderma and compiled a complete inventory of all Trichoderma species and DNA barcoding material deposited in public databases(the inventory is available at the website of the Interna-tional Subcommission on Taxonomy of Trichoderma www.trich oderm a.info).Among the 375 species with valid names as of July 2020,361(96%)have been cultivated in vitro and DNA barcoded.Thus,we have developed a protocol for molecular identification of Trichoderma that requires analysis of the three DNA barcodes(ITS,tef1,and rpb2),and it is supported by online tools that are available on www.trich okey.info.We then used all the whole-genome sequenced(WGS)Trichoderma strains that are available in public databases to provide versatile practical examples of molecular identification,reveal short-comings,and discuss possible ambiguities.Based on the Trichoderma example,this study shows why the identification of a fungal species is an intricate and laborious task that requires a background in mycology,molecular biological skills,training in molecular evolutionary analysis,and knowledge of taxonomic literature.We provide an in-depth discussion of species concepts that are applied in Trichoderma taxonomy,and conclude that these fungi are particularly suitable for the implementa-tion of a polyphasic approach that was first introduced in Trichoderma taxonomy by John Bissett(1948-2020),whose work inspired the current study.We also propose a regulatory and unifying role of international commissions on the taxonomy of particular fungal groups.An important outcome of this work is the demonstration of an urgent need for cooperation between Trichoderma researchers to get prepared to the efficient use of the upcoming wave of Trichoderma genomic data.展开更多
Species of Ophiognomonia are leaf-inhabiting endophytes,pathogens,and saprobes that infect plants in the families Betulaceae,Fagaceae,Juglandaceae,Lauraceae,Malvaceae,Platanaceae,Rosaceae,Salicaceae,and Sapindaceae.Ba...Species of Ophiognomonia are leaf-inhabiting endophytes,pathogens,and saprobes that infect plants in the families Betulaceae,Fagaceae,Juglandaceae,Lauraceae,Malvaceae,Platanaceae,Rosaceae,Salicaceae,and Sapindaceae.Based on extensive collecting,this speciesrich genus is now known to have a world wide distribution in primarily temperate areas,although some species are known from the subtropics.Analyses of DNA sequences from three markers including guanine nucleotide-binding protein subunit beta-like protein(MS204),translation elongation factor 1α(tef-1α),and the ITS region including ITS1,5.8 S rDNA and ITS2 regions(ITS)were used to define phylogenetic species in Ophiognomonia.Host plant association correlated with these species.Twenty-five new species of Ophiognomonia and two new combinations are proposed with descriptions and illustrations.In addition,descriptions and illustrations are provided for 12 other species of Ophiognomonia.A key is provided to the 45 currently accepted species of Ophiognomonia.The disposition of additional names in Ophiognomonia is also discussed.展开更多
Diaporthe is an important plant pathogenic genus,which also occurs as endophytes and saprobes.Many Diaporthe species that are morphologically similar proved to be genetically distinct.The current understanding of Diap...Diaporthe is an important plant pathogenic genus,which also occurs as endophytes and saprobes.Many Diaporthe species that are morphologically similar proved to be genetically distinct.The current understanding of Diaporthe taxonomy by applying morphological characters,host associations and multi-gene phylogeny are problematic leading to overestimation/underestimation of species numbers of this significant fungal pathogenic genus.Currently,there are no definite boundaries for the accepted species.Hence,the present study aims to re-structure the genus Diaporthe,based on single gene phylogenies(ITS,tef,tub,cal and his),multi-gene phylogeny justified by applying GCPSR(Genealogical Concordance Phylogenetic Species Recognition)methodology as well as the coalescence-based models(PTP-Poisson Tree Processes and mPTP-multi-rate Poisson Tree Processes).Considering all available type isolates of Diaporthe,the genus is divided into seven sections while boundaries for 13 species and 15 species-complexes are proposed.To support this re-assessment of the genus,82 Diaporthe isolates obtained from woody hosts in Guizhou Province in China were investigated and revealed the presence of two novel species and 17 previously known species.Synonymies are specified for 31 species based on molecular data and morphological studies.Dividing Diaporthe into several specific sections based on phylogenetic analyses can avoid the construction of lengthy phylogenetic trees of the entire genus in future taxonomic studies.In other words,when one con-ducts research related to the genus,only species from the appropriate section need to be selected for phylogenetic analysis.展开更多
基金the grants from the National Science Foundation of China(31801939)the Fundamental Research Funds for the Central Universities(KYXK202012).
文摘Modern taxonomy has developed towards the establishment of global authoritative lists of species that assume the standard-ized principles of species recognition,at least in a given taxonomic group.However,in fungi,species delimitation is fre-quently subjective because it depends on the choice of a species concept and the criteria selected by a taxonomist.Contrary to it,identification of fungal species is expected to be accurate and precise because it should predict the properties that are required for applications or that are relevant in pathology.The industrial and plant-beneficial fungi from the genus Tricho-derma(Hypocreales)offer a suitable model to address this collision between species delimitation and species identification.A few decades ago,Trichoderma diversity was limited to a few dozen species.The introduction of molecular evolutionary methods resulted in the exponential expansion of Trichoderma taxonomy,with up to 50 new species recognized per year.Here,we have reviewed the genus-wide taxonomy of Trichoderma and compiled a complete inventory of all Trichoderma species and DNA barcoding material deposited in public databases(the inventory is available at the website of the Interna-tional Subcommission on Taxonomy of Trichoderma www.trich oderm a.info).Among the 375 species with valid names as of July 2020,361(96%)have been cultivated in vitro and DNA barcoded.Thus,we have developed a protocol for molecular identification of Trichoderma that requires analysis of the three DNA barcodes(ITS,tef1,and rpb2),and it is supported by online tools that are available on www.trich okey.info.We then used all the whole-genome sequenced(WGS)Trichoderma strains that are available in public databases to provide versatile practical examples of molecular identification,reveal short-comings,and discuss possible ambiguities.Based on the Trichoderma example,this study shows why the identification of a fungal species is an intricate and laborious task that requires a background in mycology,molecular biological skills,training in molecular evolutionary analysis,and knowledge of taxonomic literature.We provide an in-depth discussion of species concepts that are applied in Trichoderma taxonomy,and conclude that these fungi are particularly suitable for the implementa-tion of a polyphasic approach that was first introduced in Trichoderma taxonomy by John Bissett(1948-2020),whose work inspired the current study.We also propose a regulatory and unifying role of international commissions on the taxonomy of particular fungal groups.An important outcome of this work is the demonstration of an urgent need for cooperation between Trichoderma researchers to get prepared to the efficient use of the upcoming wave of Trichoderma genomic data.
基金This project was funded by the National Science Foundation Partnerships for Enhancing Expertise in Taxonomy(NSF 03-28364).Additional funding for field work by DMW was received through Rutgers University,New Brunswick,NJ,from the C.Reed Funk Student Award by the Department of Plant Biology and Pathology,also the Backus Award and Everett Lutrell Mentor Student Travel Award from the Mycological Society of America.DMW also thanks Jo Anne Crouch and Adam Bazinet for assistance with data analyses,Kentaro Hosaka,Shinobu Inoue,Takao Kobayashi,Tsuyoshi Hosoya,Yousuke Degawa for hosting a collecting trip to Japan and Yuuri Hirooka for coordinating the visit,Christian Feuillet and Drew Minnis for discussions about nomenclature,Ryan Vo and Tunesha Phipps for technical assistance,and Larissa Vasilyeva,Alain Gardiennet,Yannick Mourgues,Marc Chovillon,Jacques Fornier,and Mikhail Sogonov for collection of fresh specimens for examination.
文摘Species of Ophiognomonia are leaf-inhabiting endophytes,pathogens,and saprobes that infect plants in the families Betulaceae,Fagaceae,Juglandaceae,Lauraceae,Malvaceae,Platanaceae,Rosaceae,Salicaceae,and Sapindaceae.Based on extensive collecting,this speciesrich genus is now known to have a world wide distribution in primarily temperate areas,although some species are known from the subtropics.Analyses of DNA sequences from three markers including guanine nucleotide-binding protein subunit beta-like protein(MS204),translation elongation factor 1α(tef-1α),and the ITS region including ITS1,5.8 S rDNA and ITS2 regions(ITS)were used to define phylogenetic species in Ophiognomonia.Host plant association correlated with these species.Twenty-five new species of Ophiognomonia and two new combinations are proposed with descriptions and illustrations.In addition,descriptions and illustrations are provided for 12 other species of Ophiognomonia.A key is provided to the 45 currently accepted species of Ophiognomonia.The disposition of additional names in Ophiognomonia is also discussed.
基金supported by the National Natural Science Foundation of China(Grant No.32350410401)Joint Fund of the National Natural Science Foundation of China and the Karst Science Research Center of Guizhou Province(Grant No.U1812401)+1 种基金the Chinese Research Fund(project no E1644111K1)entitled“Flexible introduction of high-level expert program,Kunming Institute of Botany,Chinese Academy of Sciences and Major science and technology projects and key R&D plans/programs,Yunnan Province(202202AE090001)the High-level Talents in Zhongkai University of Agriculture and Engineering,grant no:J2201080102 and the Innovative team program of the Department of Education of Guangdong Province(2022KCXTD015 and 2022ZDJS020).
文摘Diaporthe is an important plant pathogenic genus,which also occurs as endophytes and saprobes.Many Diaporthe species that are morphologically similar proved to be genetically distinct.The current understanding of Diaporthe taxonomy by applying morphological characters,host associations and multi-gene phylogeny are problematic leading to overestimation/underestimation of species numbers of this significant fungal pathogenic genus.Currently,there are no definite boundaries for the accepted species.Hence,the present study aims to re-structure the genus Diaporthe,based on single gene phylogenies(ITS,tef,tub,cal and his),multi-gene phylogeny justified by applying GCPSR(Genealogical Concordance Phylogenetic Species Recognition)methodology as well as the coalescence-based models(PTP-Poisson Tree Processes and mPTP-multi-rate Poisson Tree Processes).Considering all available type isolates of Diaporthe,the genus is divided into seven sections while boundaries for 13 species and 15 species-complexes are proposed.To support this re-assessment of the genus,82 Diaporthe isolates obtained from woody hosts in Guizhou Province in China were investigated and revealed the presence of two novel species and 17 previously known species.Synonymies are specified for 31 species based on molecular data and morphological studies.Dividing Diaporthe into several specific sections based on phylogenetic analyses can avoid the construction of lengthy phylogenetic trees of the entire genus in future taxonomic studies.In other words,when one con-ducts research related to the genus,only species from the appropriate section need to be selected for phylogenetic analysis.
