Studies in Mycology最新文献_第5页

Genera of phytopathogenic fungi: GOPHY 4. 植物病原真菌属：GOPHY 4.

IF 14.1 1区生物学

Studies in Mycology Pub Date : 2022-07-01 Epub Date: 2022-06-02 DOI: 10.3114/sim.2022.101.06

Q Chen, M Bakhshi, Y Balci, K D Broders, R Cheewangkoon, S F Chen, X L Fan, D Gramaje, F Halleen, M Horta Jung, N Jiang, T Jung, T Májek, S Marincowitz, I Milenković, L Mostert, C Nakashima, I Nurul Faziha, M Pan, M Raza, B Scanu, C F J Spies, L Suhaizan, H Suzuki, C M Tian, M Tomšovský, J R Úrbez-Torres, W Wang, B D Wingfield, M J Wingfield, Q Yang, X Yang, R Zare, P Zhao, J Z Groenewald, L Cai, P W Crous

{"title":"Genera of phytopathogenic fungi: GOPHY 4.","authors":"Q Chen, M Bakhshi, Y Balci, K D Broders, R Cheewangkoon, S F Chen, X L Fan, D Gramaje, F Halleen, M Horta Jung, N Jiang, T Jung, T Májek, S Marincowitz, I Milenković, L Mostert, C Nakashima, I Nurul Faziha, M Pan, M Raza, B Scanu, C F J Spies, L Suhaizan, H Suzuki, C M Tian, M Tomšovský, J R Úrbez-Torres, W Wang, B D Wingfield, M J Wingfield, Q Yang, X Yang, R Zare, P Zhao, J Z Groenewald, L Cai, P W Crous","doi":"10.3114/sim.2022.101.06","DOIUrl":"10.3114/sim.2022.101.06","url":null,"abstract":"This paper is the fourth contribution in the Genera of Phytopathogenic Fungi (GOPHY) series. The series provides morphological descriptions and information about the pathology, distribution, hosts and disease symptoms, as well as DNA barcodes for the taxa covered. Moreover, 12 whole-genome sequences for the type or new species in the treated genera are provided. The fourth paper in the GOPHY series covers 19 genera of phytopathogenic fungi and their relatives, including Ascochyta, Cadophora, Celoporthe, Cercospora, Coleophoma, Cytospora, Dendrostoma, Didymella, Endothia, Heterophaeomoniella, Leptosphaerulina, Melampsora, Nigrospora, Pezicula, Phaeomoniella, Pseudocercospora, Pteridopassalora, Zymoseptoria, and one genus of oomycetes, Phytophthora. This study includes two new genera, 30 new species, five new combinations, and 43 typifications of older names. Taxonomic novelties: New genera: Heterophaeomoniella L. Mostert, C.F.J. Spies, Halleen & Gramaje, Pteridopassalora C. Nakash. & Crous; New species: Ascochyta flava Qian Chen & L. Cai, Cadophora domestica L. Mostert, R. van der Merwe, Halleen & Gramaje, Cadophora rotunda L. Mostert, R. van der Merwe, Halleen & Gramaje, Cadophora vinacea J.R. Úrbez-Torres, D.T. O'Gorman & Gramaje, Cadophora vivarii L. Mostert, Havenga, Halleen & Gramaje, Celoporthe foliorum H. Suzuki, Marinc. & M.J. Wingf., Cercospora alyssopsidis M. Bakhshi, Zare & Crous, Dendrostoma elaeocarpi C.M. Tian & Q. Yang, Didymella chlamydospora Qian Chen & L. Cai, Didymella gei Qian Chen & L. Cai, Didymella ligulariae Qian Chen & L. Cai, Didymella qilianensis Qian Chen & L. Cai, Didymella uniseptata Qian Chen & L. Cai, Endothia cerciana W. Wang. & S.F. Chen, Leptosphaerulina miscanthi Qian Chen & L. Cai, Nigrospora covidalis M. Raza, Qian Chen & L. Cai, Nigrospora globospora M. Raza, Qian Chen & L. Cai, Nigrospora philosophiae-doctoris M. Raza, Qian Chen & L. Cai, Phytophthora transitoria I. Milenković, T. Májek & T. Jung, Phytophthora panamensis T. Jung, Y. Balci, K. Broders & I. Milenković, Phytophthora variabilis T. Jung, M. Horta Jung & I. Milenković, Pseudocercospora delonicicola C. Nakash., L. Suhaizan & I. Nurul Faziha, Pseudocercospora farfugii C. Nakash., I. Araki, & Ai Ito, Pseudocercospora hardenbergiae Crous & C. Nakash., Pseudocercospora kenyirana C. Nakash., L. Suhaizan & I. Nurul Faziha, Pseudocercospora perrottetiae Crous, C. Nakash. & C.Y. Chen, Pseudocercospora platyceriicola C. Nakash., Y. Hatt, L. Suhaizan & I. Nurul Faziha, Pseudocercospora stemonicola C. Nakash., Y. Hatt., L. Suhaizan & I. Nurul Faziha, Pseudocercospora terengganuensis C. Nakash., Y. Hatt., L. Su","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"101 ","pages":"417-564"},"PeriodicalIF":14.1,"publicationDate":"2022-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9365048/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40348350","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Multi-locus phylogeny unmasks hidden species within the specialised spider-parasitic fungus, Gibellula (Hypocreales, Cordycipitaceae) in Thailand. 多焦点系统发育揭示了泰国专门的蜘蛛寄生真菌 Gibellula（Hypocreales，Cordycipitaceae）中隐藏的物种。

IF 3.784 1区生物学

Studies in Mycology Pub Date : 2022-07-01 Epub Date: 2022-04-29 DOI: 10.3114/sim.2022.101.04

W Kuephadungphan, B Petcharad, K Tasanathai, D Thanakitpipattana, N Kobmoo, A Khonsanit, R A Samson, J J Luangsa-Ard

{"title":"Multi-locus phylogeny unmasks hidden species within the specialised spider-parasitic fungus, Gibellula (Hypocreales, Cordycipitaceae) in Thailand.","authors":"W Kuephadungphan, B Petcharad, K Tasanathai, D Thanakitpipattana, N Kobmoo, A Khonsanit, R A Samson, J J Luangsa-Ard","doi":"10.3114/sim.2022.101.04","DOIUrl":"10.3114/sim.2022.101.04","url":null,"abstract":"Over 80 species of hypocrealean fungi are reported as pathogens of spiders and harvestmen. Among these fungi, the genus Gibellula is highly regarded as a specialised spider-killer that has never been reported to infect other arthropods. While more than 20 species of Gibellula are known, few attempts to identify the infected spiders have been made despite the fact that the host specificity can help identify the fungal species. Here, we morphologically describe and illustrate eight new species of Gibellula and three new records from Thailand of known species along with the multi-gene phylogeny that clearly showed the segregation among the proposed species. Examination of the Gibellula-infected spider hosts identified Oxyopidae, Uloboridae and, for the first time, the ant-mimicking genus Myrmarachne. Taxonomic novelties: New species: Gibellula brevistipitata Kuephadungphan, Tasanathai & Luangsa-ard, G. longicaudata Tasanathai, Kuephadungphan & Luangsa-ard, G. longispora Kuephadungphan & Luangsa-ard, G. nigelii Kuephadungphan, Tasanathai & Luangsa-ard, G. parvula Kuephadungphan, Tasanathai & Luangsa-ard, G. pilosa Kuephadungphan, Tasanathai & Luangsa-ard, G. solita Kuephadungphan, Tasanathai & Luangsa-ard, G. trimorpha Tasanathai, Khonsanit, Kuephadungphan & Luangsa-ard. Citation: Kuephadungphan W, Petcharad B, Tasanathai K, Thanakitpipattana D, Kobmoo N, Khonsanit A, Samson RA, Luangsa-ard JJ (2022). Multi-locus phylogeny unmasks hidden species within the specialised spider-parasitic fungus, Gibellula (Hypocreales, Cordycipitaceae) in Thailand. Studies in Mycology 101: 245-286. doi: 10.3114/sim.2022.101.04.","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"101 ","pages":"245-286"},"PeriodicalIF":3.784,"publicationDate":"2022-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9365043/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40348349","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Updating species diversity of Colletotrichum, with a phylogenomic overview. 炭疽菌的物种多样性更新及其系统基因组学综述。

IF 16.5 1区生物学

Studies in Mycology Pub Date : 2022-07-01 Epub Date: 2022-01-11 DOI: 10.3114/sim.2022.101.01

F Liu, Z Y Ma, L W Hou, Y Z Diao, W P Wu, U Damm, S Song, L Cai

{"title":"Updating species diversity of Colletotrichum, with a phylogenomic overview.","authors":"F Liu, Z Y Ma, L W Hou, Y Z Diao, W P Wu, U Damm, S Song, L Cai","doi":"10.3114/sim.2022.101.01","DOIUrl":"https://doi.org/10.3114/sim.2022.101.01","url":null,"abstract":"The genus Colletotrichum includes important plant pathogens, endophytes, saprobes and human pathogens. Even though the polyphasic approach has facilitated Colletotrichum species identification, knowledge of the overall species diversity and host distribution is largely incomplete. To address this, we examined 952 Colletotrichum strains isolated from plants representing 322 species from 248 genera, or air and soil samples, from 87 locations in China, as well as 56 strains from Saudi Arabia, Thailand, Turkey, and the UK. Based on morphological characteristics and multi-locus phylogenetic analyses, the strains were assigned to 107 species, including 30 new species described in this paper and 18 new records for China. The currently most comprehensive backbone tree of Colletotrichum, comprising 16 species complexes (including a newly introduced C. bambusicola species complex) and 15 singleton species, is provided. Based on these analyses, 280 species with available molecular data are accepted in this genus, of which 139 have been reported in China, accounting for 49.6 % of the species. Colletotrichum siamense, C. karsti, C. fructicola, C. truncatum, C. fioriniae, and C. gloeosporioides were the most commonly detected species in China, as well as the species with the broadest host range. By contrast, 76 species were currently found to be associated with a single plant species or genus in China. To date, 33 Colletotrichum species have been exclusively reported as endophytes. Furthermore, we generated and assembled whole-genome sequences of the 30 new and a further 18 known species. The most comprehensive genome tree comprising 94 Colletotrichum species based on 1 893 single-copy orthologous genes was hence generated, with all nodes, except four, supported by 100 % bootstrap values. Collectively, this study represents the most comprehensive investigation of Colletotrichum diversity and host occurrence to date, and greatly enhances our understanding of the diversity and phylogenetic relationships in this genus. Taxonomic novelties: New species: Colletotrichum arecacearum F. Liu, Z.Y. Ma & L. Cai, Colletotrichum bicoloratum F. Liu, W.P. Wu & L. Cai, Colletotrichum bromeliacearum F. Liu & L. Cai, Colletotrichum buxi F. Liu, W.P. Wu & L. Cai, Colletotrichum chamaedoreae F. Liu, W.P. Wu & L. Cai, Colletotrichum crousii F. Liu, Z.Y. Ma & L. Cai, Colletotrichum danxiashanense F. Liu, W.P. Wu & L. Cai, Colletotrichum diversisporum F. Liu, W.P. Wu & L. Cai, Colletotrichum diversum F. Liu & L. Cai, Colletotrichum dolichoconidiophori F. Liu, W.P. Wu & L. Cai, Colletotrichum iris F. Liu & L. Cai, Colletotrichum monsterae F. Liu, W.P. Wu & L. Cai, Colletotrichum multiseptatum F. Liu, W.P. Wu & L. Cai, Colletotrichum nageiae F. Liu, W.P. Wu & L. Cai, Colletotr","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"101 ","pages":"1-56"},"PeriodicalIF":16.5,"publicationDate":"2022-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9365046/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40348347","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 42

Generic boundaries in the Ophiostomatales reconsidered and revised. 重新考虑和修订了蛇气孔门的属界。

IF 16.5 1区生物学

Studies in Mycology Pub Date : 2022-07-01 Epub Date: 2022-03-30 DOI: 10.3114/sim.2022.101.02

Z W de Beer, M Procter, M J Wingfield, S Marincowitz, T A Duong

{"title":"Generic boundaries in the Ophiostomatales reconsidered and revised.","authors":"Z W de Beer, M Procter, M J Wingfield, S Marincowitz, T A Duong","doi":"10.3114/sim.2022.101.02","DOIUrl":"https://doi.org/10.3114/sim.2022.101.02","url":null,"abstract":"The Ophiostomatales was erected in 1980. Since that time, several of the genera have been redefined and others have been described. There are currently 14 accepted genera in the Order. They include species that are the causal agents of plant and human diseases and common associates of insects such as bark beetles. Well known examples include the Dutch elm disease fungi and the causal agents of sporotrichosis in humans and animals. The taxonomy of the Ophiostomatales was confused for many years, mainly due to the convergent evolution of morphological characters used to delimit unrelated fungal taxa. The emergence of DNA-based methods has resolved much of this confusion. However, the delineation of some genera and the placement of various species and smaller lineages remains inconclusive. In this study we reconsidered the generic boundaries within the Ophiostomatales. A phylogenomic framework constructed from genome-wide sequence data for 31 species representing the major genera in the Order was used as a guide to delineate genera. This framework also informed our choice of the best markers from the currently most commonly used gene regions for taxonomic studies of these fungi. DNA was amplified and sequenced for more than 200 species, representing all lineages in the Order. We constructed phylogenetic trees based on the different gene regions and assembled a concatenated data set utilising a suite of phylogenetic analyses. The results supported and confirmed the delineation of nine of the 14 currently accepted genera, i.e. Aureovirgo, Ceratocystiopsis, Esteya, Fragosphaeria, Graphilbum, Hawksworthiomyces, Ophiostoma, Raffaelea and Sporothrix. The two most recently described genera, Chrysosphaeria and Intubia, were not included in the multi-locus analyses. This was due to their high sequence divergence, which was shown to result in ambiguous taxonomic placement, even though the results of phylogenomic analysis supported their inclusion in the Ophiostomatales. In addition to the currently accepted genera in the Ophiostomatales, well-supported lineages emerged that were distinct from those genera. These are described as novel genera. Two lineages included the type species of Grosmannia and Dryadomyces and these genera are thus reinstated and their circumscriptions redefined. The descriptions of all genera in the Ophiostomatales were standardised and refined where this was required and 39 new combinations have been provided for species in the newly emerging genera and one new combination has been provided for Sporothrix. The placement of Afroraffaelea could not be confirmed using the available data and the genus has been treated as incertae sedis in the Ophiostomatales. Paleoambrosia was not included in this study, due to the absence of living material available for this monotypic fossil genus. Overall, this study has pro","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"101 ","pages":"57-120"},"PeriodicalIF":16.5,"publicationDate":"2022-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9365045/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40348345","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 32

Taxonomy, phylogeny and identification of Chaetomiaceae with emphasis on thermophilic species. Chaetomiaceae的分类、系统发育和鉴定，重点是嗜热物种。

IF 14.1 1区生物学

Studies in Mycology Pub Date : 2022-07-01 Epub Date: 2022-04-01 DOI: 10.3114/sim.2022.101.03

X W Wang, P J Han, F Y Bai, A Luo, K Bensch, M Meijer, Kraak B, D Y Han, B D Sun, P W Crous, J Houbraken

{"title":"Taxonomy, phylogeny and identification of Chaetomiaceae with emphasis on thermophilic species.","authors":"X W Wang, P J Han, F Y Bai, A Luo, K Bensch, M Meijer, Kraak B, D Y Han, B D Sun, P W Crous, J Houbraken","doi":"10.3114/sim.2022.101.03","DOIUrl":"10.3114/sim.2022.101.03","url":null,"abstract":"Chaetomiaceae comprises phenotypically diverse species, which impact biotechnology, the indoor environment and human health. Recent studies showed that most of the traditionally defined genera in Chaetomiaceae are highly polyphyletic. Many of these morphology-based genera, such as Chaetomium, Thielavia and Humicola, have been redefined using multigene phylogenetic analysis combined with morphology; however, a comprehensive taxonomic overview of the family is lacking. In addition, the phylogenetic relationship of thermophilic Chaetomiaceae species with non-thermophilic taxa in the family is largely unclear due to limited taxon sampling in previous studies. In this study, we provide an up-to-date overview on the taxonomy and phylogeny of genera and species belonging to Chaetomiaceae, including an extensive taxon sampling of thermophiles. A multigene phylogenetic analysis based on the ITS (internal transcribed spacers 1 and 2 including the 5.8S nrDNA), LSU (D1/D2 domains of the 28S nrDNA), rpb2 (partial RNA polymerase II second largest subunit gene) and tub2 (β-tubulin gene) sequences was performed on 345 strains representing Chaetomiaceae and 58 strains of other families in Sordariales. Divergence times based on the multi-gene phylogeny were estimated as aid to determine the genera in the family. Genera were delimited following the criteria that a genus must be a statistically well-supported monophyletic clade in both the multigene phylogeny and molecular dating analysis, fall within a divergence time of over 27 million years ago, and be supported by ecological preference or phenotypic traits. Based on the results of the phylogeny and molecular dating analyses, combined with morphological characters and temperature-growth characteristics, 50 genera and 275 species are accepted in Chaetomiaceae. Among them, six new genera, six new species, 45 new combinations and three new names are proposed. The results demonstrate that the thermophilic species fall into seven genera (Melanocarpus, Mycothermus, Remersonia, Thermocarpiscus gen. nov., Thermochaetoides gen. nov., Thermothelomyces and Thermothielavioides). These genera cluster in six separate lineages, suggesting that thermophiles independently evolved at least six times within the family. A list of accepted genera and species in Chaetomiaceae, together with information on their MycoBank numbers, living ex-type strains and GenBank accession numbers to ITS, LSU, rpb2 and tub2 sequences is provided. Furthermore, we provide suggestions how to describe and identify Chaetomiaceae species. Taxonomic novelties: new genera: Parvomelanocarpus X.Wei Wang & Houbraken, Pseudohumicola X.Wei Wang, P.J. Han, F.Y. Bai & Houbraken, Tengochaeta X.Wei Wang & Houbraken, Thermocarpiscus X.Wei Wang & Houb","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"101 ","pages":"121-243"},"PeriodicalIF":14.1,"publicationDate":"2022-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9365047/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40348346","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Species diversity, systematic revision and molecular phylogeny of Ganodermataceae (Polyporales, Basidiomycota) with an emphasis on Chinese collections. 灵芝科(多孢子门，担子菌门)的物种多样性、系统修订和分子系统发育——以中国标本为重点。

IF 16.5 1区生物学

Studies in Mycology Pub Date : 2022-07-01 Epub Date: 2022-05-20 DOI: 10.3114/sim.2022.101.05

Y-F Sun, J-H Xing, X-L He, D-M Wu, C-G Song, S Liu, J Vlasák, G Gates, T B Gibertoni, B-K Cui

{"title":"Species diversity, systematic revision and molecular phylogeny of Ganodermataceae (Polyporales, Basidiomycota) with an emphasis on Chinese collections.","authors":"Y-F Sun, J-H Xing, X-L He, D-M Wu, C-G Song, S Liu, J Vlasák, G Gates, T B Gibertoni, B-K Cui","doi":"10.3114/sim.2022.101.05","DOIUrl":"https://doi.org/10.3114/sim.2022.101.05","url":null,"abstract":"Ganodermataceae is one of the main families of macrofungi since species in the family are both ecologically and economically important. The double-walled basidiospores with ornamented endospore walls are the characteristic features of Ganodermataceae. It is a large and complex family; although many studies have focused on Ganodermataceae, the global diversity, geographic distribution, taxonomy and molecular phylogeny of Ganodermataceae still remained incompletely understood. In this work, taxonomic and phylogenetic studies on worldwide species of Ganodermataceae were carried out by morphological examination and molecular phylogenetic analyses inferred from six gene loci including the internal transcribed spacer regions (ITS), the large subunit of nuclear ribosomal RNA gene (nLSU), the second largest subunit of RNA polymerase II gene (rpb2), the translation elongation factor 1-α gene (tef1), the small subunit mitochondrial rRNA gene (mtSSU) and the small subunit nuclear ribosomal RNA gene (nSSU). A total of 1 382 sequences were used in the phylogenetic analyses, of which 817 were newly generated, including 132 sequences of ITS, 139 sequences of nLSU, 83 sequences of rpb2, 124 sequences of tef1, 150 sequences of mtSSU and 189 sequences of nSSU. The combined six-gene dataset included sequences from 391 specimens representing 146 taxa from Ganodermataceae. Based on morphological and phylogenetic analyses, 14 genera were confirmed in Ganodermataceae: Amauroderma, Amaurodermellus, Cristataspora, Foraminispora, Furtadoella, Ganoderma, Haddowia, Humphreya, Magoderna, Neoganoderma, Sanguinoderma, Sinoganoderma, Tomophagus and Trachydermella. Among these genera, Neoganoderma gen. nov. is proposed for Ganoderma neurosporum; Sinoganoderma gen. nov. is proposed for Ganoderma shandongense; Furtadoella gen. nov. is proposed to include taxa previously belonging to Furtadoa since Furtadoa is a homonym of a plant genus in the Araceae; Trachydermella gen. nov. is proposed to include Trachyderma tsunodae since Trachyderma is a homonym of a lichen genus in the Pannariaceae. Twenty-three new species, viz., Ganoderma acaciicola, G. acontextum, G. alpinum, G. bubalinomarginatum, G. castaneum, G. chuxiongense, G. cocoicola, G. fallax, G. guangxiense, G. puerense, G. subangustisporum, G. subellipsoideum, G. subflexipes, G. sublobatum, G. tongshanense, G. yunlingense, Haddowia macropora, Sanguinoderma guangdongense, Sa. infundibulare, Sa. longistipitum, Sa. melanocarpum, Sa. microsporum and Sa. tricolor are described. In addition, another 33 known ","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"101 ","pages":"287-415"},"PeriodicalIF":16.5,"publicationDate":"2022-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9365044/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40348348","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 26

Lessons on fruiting body morphogenesis from genomes and transcriptomes of Agaricomycetes 菌丝体基因组和转录组对子实体形态发生的启示

IF 16.5 1区生物学

Studies in Mycology Pub Date : 2021-12-10 DOI: 10.1101/2021.12.09.471732

L. Nagy, P. Vonk, M. Künzler, C. Földi, M. Virágh, R. Ohm, F. Hennicke, B. Bálint, Á. Csernetics, B. Hegedüs, Z. Hou, X. Liu, S. Nan, M. Pareek, N. Sahu, B. Szathmári, T. Varga, H. Wu, X. Yang, Z. Merényi

{"title":"Lessons on fruiting body morphogenesis from genomes and transcriptomes of Agaricomycetes","authors":"L. Nagy, P. Vonk, M. Künzler, C. Földi, M. Virágh, R. Ohm, F. Hennicke, B. Bálint, Á. Csernetics, B. Hegedüs, Z. Hou, X. Liu, S. Nan, M. Pareek, N. Sahu, B. Szathmári, T. Varga, H. Wu, X. Yang, Z. Merényi","doi":"10.1101/2021.12.09.471732","DOIUrl":"https://doi.org/10.1101/2021.12.09.471732","url":null,"abstract":"Fruiting bodies of mushroom-forming fungi (Agaricomycetes) are among the most complex structures produced by fungi. Unlike vegetative hyphae, fruiting bodies grow determinately and follow a genetically encoded developmental program that orchestrates tissue differentiation, growth and sexual sporulation. In spite of more than a century of research, our understanding of the molecular details of fruiting body morphogenesis is limited and a general synthesis on the genetics of this complex process is lacking. In this paper, we aim to comprehensively identify conserved genes related to fruiting body morphogenesis and distill novel functional hypotheses for functionally poorly characterized genes. As a result of this analysis, we report 921 conserved developmentally expressed gene families, only a few dozens of which have previously been reported in fruiting body development. Based on literature data, conserved expression patterns and functional annotations, we provide informed hypotheses on the potential role of these gene families in fruiting body development, yielding the most complete description of molecular processes in fruiting body morphogenesis to date. We discuss genes related to the initiation of fruiting, differentiation, growth, cell surface and cell wall, defense, transcriptional regulation as well as signal transduction. Based on these data we derive a general model of fruiting body development, which includes an early, proliferative phase that is mostly concerned with laying out the mushroom body plan (via cell division and differentiation), and a second phase of growth via cell expansion as well as meiotic events and sporulation. Altogether, our discussions cover 1480 genes of Coprinopsis cinerea, and their orthologs in Agaricus bisporus, Cyclocybe aegerita, Armillaria ostoyae, Auriculariopsis ampla, Laccaria bicolor, Lentinula edodes, Lentinus tigrinus, Mycena kentingensis, Phanerochaete chrysosporium, Pleurotus ostreatus, and Schizophyllum commune, providing functional hypotheses for ∼10% of genes in the genomes of these species. Although experimental evidence for the role of these genes will need to be established in the future, our data provide a roadmap for guiding functional analyses of fruiting related genes in the Agaricomycetes. We anticipate that the gene compendium presented here, combined with developments in functional genomics approaches will contribute to uncovering the genetic bases of one of the most spectacular multicellular developmental processes in fungi.","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"104 1","pages":"1 - 85"},"PeriodicalIF":16.5,"publicationDate":"2021-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43463552","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 8

Aspergillus fumigatus and aspergillosis: From basics to clinics 烟曲霉和曲霉病:从基础到临床

IF 16.5 1区生物学

Studies in Mycology Pub Date : 2021-09-01 DOI: 10.1016/j.simyco.2021.100115

A. Arastehfar , A. Carvalho , J. Houbraken , L. Lombardi , R. Garcia-Rubio , J.D. Jenks , O. Rivero-Menendez , R. Aljohani , I.D. Jacobsen , J. Berman , N. Osherov , M.T. Hedayati , M. Ilkit , D. Armstrong-James , T. Gabaldón , J. Meletiadis , M. Kostrzewa , W. Pan , C. Lass-Flörl , D.S. Perlin , M. Hoenigl

{"title":"Aspergillus fumigatus and aspergillosis: From basics to clinics","authors":"A. Arastehfar , A. Carvalho , J. Houbraken , L. Lombardi , R. Garcia-Rubio , J.D. Jenks , O. Rivero-Menendez , R. Aljohani , I.D. Jacobsen , J. Berman , N. Osherov , M.T. Hedayati , M. Ilkit , D. Armstrong-James , T. Gabaldón , J. Meletiadis , M. Kostrzewa , W. Pan , C. Lass-Flörl , D.S. Perlin , M. Hoenigl","doi":"10.1016/j.simyco.2021.100115","DOIUrl":"https://doi.org/10.1016/j.simyco.2021.100115","url":null,"abstract":"<div>The airborne fungus Aspergillus fumigatus poses a serious health threat to humans by causing numerous invasive infections and a notable mortality in humans, especially in immunocompromised patients. Mould-active azoles are the frontline therapeutics employed to treat aspergillosis. The global emergence of azole-resistant A. fumigatus isolates in clinic and environment, however, notoriously limits the therapeutic options of mould-active antifungals and potentially can be attributed to a mortality rate reaching up to 100 %. Although specific mutations in CYP51A are the main cause of azole resistance, there is a new wave of azole-resistant isolates with wild-type CYP51A genotype challenging the efficacy of the current diagnostic tools. Therefore, applications of whole-genome sequencing are increasingly gaining popularity to overcome such challenges. Prominent echinocandin tolerance, as well as liver and kidney toxicity posed by amphotericin B, necessitate a continuous quest for novel antifungal drugs to combat emerging azole-resistant A. fumigatus isolates. Animal models and the tools used for genetic engineering require further refinement to facilitate a better understanding about the resistance mechanisms, virulence, and immune reactions orchestrated against A. fumigatus. This review paper comprehensively discusses the current clinical challenges caused by A. fumigatus and provides insights on how to address them.</div>","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"100 ","pages":"Article 100115"},"PeriodicalIF":16.5,"publicationDate":"2021-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.simyco.2021.100115","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"92099345","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 78

Trends in the molecular epidemiology and population genetics of emerging Sporothrix species 新发孢子丝菌的分子流行病学和群体遗传学趋势

IF 16.5 1区生物学

Studies in Mycology Pub Date : 2021-09-01 DOI: 10.1016/j.simyco.2021.100129

J.A. de Carvalho , M.A. Beale , F. Hagen , M.C. Fisher , R. Kano , A. Bonifaz , C. Toriello , R. Negroni , R.S. de M. Rego , I.D.F. Gremião , S.A. Pereira , Z.P. de Camargo , A.M. Rodrigues

{"title":"Trends in the molecular epidemiology and population genetics of emerging Sporothrix species","authors":"J.A. de Carvalho , M.A. Beale , F. Hagen , M.C. Fisher , R. Kano , A. Bonifaz , C. Toriello , R. Negroni , R.S. de M. Rego , I.D.F. Gremião , S.A. Pereira , Z.P. de Camargo , A.M. Rodrigues","doi":"10.1016/j.simyco.2021.100129","DOIUrl":"https://doi.org/10.1016/j.simyco.2021.100129","url":null,"abstract":"<div>Sporothrix (Ophiostomatales) comprises species that are pathogenic to humans and other mammals as well as environmental fungi. Developments in molecular phylogeny have changed our perceptions about the epidemiology, host-association, and virulence of Sporothrix. The classical agent of sporotrichosis, Sporothrix schenckii, now comprises several species nested in a clinical clade with S. brasiliensis, S. globosa, and S. luriei. To gain a more precise view of outbreaks dynamics, structure, and origin of genetic variation within and among populations of Sporothrix, we applied three sets of discriminatory AFLP markers (#3 EcoRI-GA/MseI-TT, #5 EcoRI-GA/MseI-AG, and #6 EcoRI-TA/MseI-AA) and mating-type analysis to a large collection of human, animal and environmental isolates spanning the major endemic areas. A total of 451 polymorphic loci were amplified in vitro from 188 samples, and revealed high polymorphism information content (PIC = 0.1765–0.2253), marker index (MI = 0.0001–0.0002), effective multiplex ratio (E = 15.1720–23.5591), resolving power (Rp = 26.1075–40.2795), discriminating power (D = 0.9766–0.9879), expected heterozygosity (H = 0.1957–0.2588), and mean heterozygosity (Havp = 0.000007–0.000009), demonstrating the effectiveness of AFLP markers to speciate Sporothrix. Analysis using the program structure indicated three genetic clusters matching S. brasiliensis (population 1), S. schenckii (population 2), and S. globosa (population 3), with the presence of patterns of admixture amongst all populations. AMOVA revealed highly structured clusters (PhiPT = 0.458–0.484, P < 0.0001), with roughly equivalent genetic variability within (46–48 %) and between (52–54 %) populations. Heterothallism was the exclusive mating strategy, and the distributions of MAT1-1 or MAT1-2 idiomorphs were not significantly skewed (1:1 ratio) for S. schenckii (χ2 = 2.522; P = 0.1122), supporting random mating. In contrast, skewed distributions were found for S. globosa (χ2 = 9.529; P = 0.0020) with a predominance of MAT1-1 isolates, and regional differences were highlighted for S. brasiliensis with the overwhelming occurrence of MAT1-2 in Rio de Janeiro (χ2 = 14.222; P = 0.0002) and Pernambuco (χ2 = 7.364; P = 0.0067), in comparison to a higher prevalence of MAT1-1 in the Rio Grande do Sul (χ2 = 7.364; P = 0.0067). Epidemiological trends reveal the geographic expansion of cat-transmitted sporotrichosis due to S. brasiliensis via founder effect. These data support Rio de Janeiro as the centre of origin that has led to the spread of this disease to other regions in Brazil","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"100 ","pages":"Article 100129"},"PeriodicalIF":16.5,"publicationDate":"2021-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0166061621000166/pdfft?md5=2d66cf749c8b6b116da997ac6b51cd53&pid=1-s2.0-S0166061621000166-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"92066454","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 21

Comparative genomic analysis of clinical Candida glabrata isolates identifies multiple polymorphic loci that can improve existing multilocus sequence typing strategy 临床光假丝酵母分离株的比较基因组分析鉴定出多个多态性位点，可以改进现有的多位点序列分型策略

IF 16.5 1区生物学

Studies in Mycology Pub Date : 2021-09-01 DOI: 10.1016/j.simyco.2021.100133

A. Arastehfar , M. Marcet-Houben , F. Daneshnia , S.J. Taj-Aldeen , D. Batra , S.R. Lockhart , E. Shor , T. Gabaldón , D.S. Perlin

{"title":"Comparative genomic analysis of clinical Candida glabrata isolates identifies multiple polymorphic loci that can improve existing multilocus sequence typing strategy","authors":"A. Arastehfar , M. Marcet-Houben , F. Daneshnia , S.J. Taj-Aldeen , D. Batra , S.R. Lockhart , E. Shor , T. Gabaldón , D.S. Perlin","doi":"10.1016/j.simyco.2021.100133","DOIUrl":"https://doi.org/10.1016/j.simyco.2021.100133","url":null,"abstract":"<div>Candida glabrata is the second leading cause of candidemia in many countries and is one of the most concerning yeast species of nosocomial importance due to its increasing rate of antifungal drug resistance and emerging multidrug-resistant isolates. Application of multilocus sequence typing (MLST) to clinical C. glabrata isolates revealed an association of certain sequence types (STs) with drug resistance and mortality. The current C. glabrata MLST scheme is based on single nucleotide polymorphisms (SNPs) at six loci and is therefore relatively laborious and costly. Furthermore, only a few high-quality C. glabrata reference genomes are available, limiting rapid analysis of clinical isolates by whole genome sequencing. In this study we provide long-read based assemblies for seven additional clinical strains belonging to three different STs and use this information to simplify the C. glabrata MLST scheme. Specifically, a comparison of these genomes identified highly polymorphic loci (HPL) defined by frequent insertions and deletions (indels), two of which proved to be highly resolutive for ST. When challenged with 53 additional isolates, a combination of TRP1 (a component of the current MLST scheme) with either of the two HPL fully recapitulated ST identification. Therefore, our comparative genomic analysis identified a new typing approach combining SNPs and indels and based on only two loci, thus significantly simplifying ST identification in C. glabrata. Because typing tools are instrumental in addressing numerous clinical and biological questions, our new MLST scheme can be used for high throughput typing of C. glabrata in clinical and research settings.</div>","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"100 ","pages":"Article 100133"},"PeriodicalIF":16.5,"publicationDate":"2021-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0166061621000208/pdfft?md5=7511e85e8764997b464763fdf771e7f5&pid=1-s2.0-S0166061621000208-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"92066237","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3