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Divergence time calibrations for ancient lineages of Ascomycota classification based on a modern review of estimations

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fungal Diversity 2019年第3期96卷 285-346页

作者： Milan C.Samarakoon Kevin D.Hyde Sinang Hongsanan Eric H.C.McKenzie Hiran A.Ariyawansa Itthayakorn Promputtha Xiang-Yu Zeng Qing Tian Jian-Kui(Jack)Liu Center for Informational biology School of Life Science and TechnologyUniversity of Electronic Science and Technology of ChinaChengdu 611731People’s Republic of China Guizhou Key laboratory of Agricultural biotechnology Guizhou Academy of Agricultural SciencesGuiyang 550006People’s Republic of China Center of Excellence in fungal Research Mae Fah Luang UniversityChiang Rai 57100Thailand Department of biology Faculty of ScienceChiang Mai UniversityChiang Mai 50200Thailand Key laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of BotanyChinese Academy of ScienceKunming 650201YunnanPeople’s Republic of China Shenzhen Key laboratory of Microbial Genetic Engineering College of Life Sciences and OceanographyShenzhen UniversityShenzhenPeople’s Republic of China Manaaki Whenua Landcare Research Private Bag 92170AucklandNew Zealand Department of Plant Pathology and Microbiology College of Bio-Resources and AgricultureNational Taiwan UniversityNo.1Sec.4Roosevelt RoadTaipei 106TaiwanROC Environmental Science Research Center Faculty of ScienceChiang Mai UniversityChiang Mai 50200Thailand

Inaccurate taxonomic placement of fossils can lead to the accumulation of errors in molecular clock studies and their generated evolutionary *** are limited fossil data that can be used in divergence time ***,reliable morphological characterization and taxonomical identification of fossil fungi are extremely *** fossils of Dothideomycetes and Sordariomycetes are from the early Cenozoic(66-23 Mya),with fewer from the late Mesozoic(174-145 Mya).However,it is hard to distinguish some fossil descriptions as photographs and illustrations are unclear;thus,the validity of using these fossils in calibrations of molecular clocks is *** study brings scattered paleobiological data on selected fossil Ascomycota,using descriptions,fossil images and illustrations,coupled with recent age estimations,and taxonomic and phylogenetic affinity of extant *** an integrated approach,this study summarizes a historical fossil outline with a reliable minimum age for 16 calibrating points *** of Aigialus,Anzia,Aspergillus,Asterina,Calicium chlorosporum–***,Capnodiales,Chaenotheca,Colletotrichum,Diaporthales,Meliola,Ophiocordyceps,Microthyriales,Microthyrium,Muyocopron,Pezizomycotina and Stigmatomyces.A scheme of Ascomycota ancient lineages is also provided in order to improve divergence time estimations.

关键词： Fossil fungi Morphological characterization Phylogeny Taxonomy Two new combinations

Towards standardizing taxonomic ranks using divergence times-a case study for reconstruction of the Agaricus taxonomic system

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fungal Diversity 2016年第3期78卷 239-292页

作者： Rui-Lin Zhao Jun-Liang Zhou Jie Chen Simona Margaritescu Santiago Sánchez-Ramírez Kevin D Hyde Philippe Callac Luis A.Parra Guo-Jie Li Jean-Marc Moncalvo State Key laboratory of Mycology Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China Institute of Microbiology and Beijing Key laboratory for Forest Pest Control Beijing Forestry UniversityBeijing 100083China Center of Excellence in fungal Research Mae Fah LuangUniversityChiang Rai 57100Thailand School of Science Mae Fah Luang UniversityChiang Rai 57100Thailand Department of Natural History Royal Ontario MuseumTorontoON M5S 2C6Canada Department of Ecology and Evolutionary biology University of TorontoTorontoON M5S 3B2Canada Key laboratory of Economic Plants and biotechnology Kunming Institute of BotanyChinese Academy of Sciences132 Lanhei RoadKunming 650201China INRA-UR1264 Mycologie et Sécuritédes AlimentsCS 2003233882 Villenave d’Ornon cedexFrance Avda.Padre Claret n°7 5°G09400 Aranda de DueroBurgosSpain

The recognition of taxonomic ranks in the Linnean classification system is largely *** authors have proposed the use of divergence time as a universally standardized ***(Agaricaceae,Agaricales)is a mushroom genus that contains many species of high commercial *** studies using ITS sequence data discovered 11 new phylogenetic lineages within the genus,however their taxonomic ranks were uncertain due to the lack of criteria to define them within traditional *** this study,we analyzed ITS sequence data from 745 collections(nearly 600 being newly generated)including 86 from type specimens of previously recognized subgenera and *** monophyletic groups were recognized,but most basal relationships were *** hundred and fourteen representatives of the identified ITS clades were selected in order to produce a multi-gene phylogeny based on combined LSU,tef-1α,and rpb2 sequence *** times within the multi-gene phylogeny were estimated using BEAST *** on phylogenetic relationships and with respect to morphology,we propose a revised taxonomic system for Agaricus that considers divergence time as a standardized criterion for establishing taxonomic *** propose to segregate Agaricus into five subgenera and 20 *** Pseudochitonia is substantially emended;circumscription of the subgenera Agaricus and Flavoagaricus is restricted to taxa of sections Agaricus and Arvenses,respectively;and two new subgenera(Minores and Spissicaules)are *** Pseudochitonia,sections Bivelares,Brunneopicti,Chitonioides,Nigrobrunnescentes,Sanguinolenti and Xanthodermatei are maintained,but the latter two are reduced because we raise subsection Bohusia to sectional rank and a clade within section Xanthodermatei is formally introduced as section Hondenses;and sections Rubricosi,Crassispori,Flocculenti,and Amoeni are *** Laeticolores is placed in the subgenus Minores and sections Rarolen

关键词： Agaricaceae Divergence times Multi-gene phylogenetics Systematics Taxonomy

Genomics homologous polygenes analysis of cultivars of Ganoderma sinense for molecular identification and new member of FIPs exploration

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Genomics homologous polygenes analysis of cultivars of Ganod...

Outline of Ascomycota: 2017

第十二届药用真菌学术研讨会

作者： Ti-Qiang Chen Xiao-Lan Xu Chi Yang Lin Yang Zheng-He Ying Xiao-Kun Shi Meng-Guang Ding Institute of Edible mushroom Fujian Academy of Agriculture Sciences National-Local Joint Engineering Research Center for Breeding and Cultivation of Featured Edible Mushroom Department of traditional Chinese medicine resources and bee products College of Animal Science(College of Bee Science) Fujian Agriculture and Forestry University Chengdu Jinxu biotechnology Co. Ltd

‘Zizhi S2' is a domesticated cultivar of Ganoderma sinense for commercial cultivation more than 18 years in southern China, which registered as Ganoderma sp. TQC-2021a strain Zizhi S2（NCBI: txid2816325）.Objectives To develop a genome-wide identification to verify the taxonomic status of this domesticated cultivars, and expect to explore novel gene（s） with important function. Methods The whole genome of Zizhi S2（56.76Mb, 16,681 genes） have been completed（DOI: 10.13560/***.1985.2021-1158）, and the assembled genome sequence and annotation information has been submitted to he Global Pharmacopoeia Herbal Genome Database with open download link（http://***/species/409）, 98.15% of complete BUSCOs were recovered in genome assembly, and the high-confidence annotation rate was accounted to 90.6%. Comparative genomics analysis and orthologous genes identification were analyzed by CD-HIT and OrthoMCL,collinearity analyses and Polygenetic sequence alignment were carry on by MUMmer and CLUSTAL *** software Phyml algorithm was applied to construct phylogenetic trees of 10 members of Ganoderma FIP gene family and two member of outgroup,3-D model were building on the SWISS-MODEL website together with the homologous FIPs. Results The collinearity exhibited the genome of ‘Zizhi S2' was 80.2% and 93.84% similar to reference genome of G. sinense ZZ0214-1 at the nucleotide and amino acid levels, respectively. And the core genes number between Zizhi S2 genome and reference genome of G. sinense ZZ0214-1 was 8,521 which presented 880 unique orthologous gene groups. Among that, at least seven highly conserved genes i.e. tef 1-α（translational elongation factor 1-alpha）, rpb2（RNA polymerase subunit 2）, β-tubulin（tubulin beta chain）, fip（fungal immunomodulatory protein）, CaM（Ca2+-binding protein）, Mn-SOD（manganese superoxide dismutase） and Ve A（velvet factor family protein）, which commonly used in phylogenetics) displaied high similarity to 99.27～100%.

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fungal Diversity 2018年第1期88卷 167-263页

作者： Nalin N.Wijayawardene Kevin D.Hyde H.Thorsten Lumbsch Jian Kui Liu Sajeewa S.N.Maharachchikumbura Anusha H.Ekanayaka Qing Tian Rungtiwa Phookamsak Key laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of BotanyChinese Academy of ScienceKunming 650201YunnanPeople’s Republic of China Science&Education The Field Museum1400 S.Lake Shore DriveChicagoIL 60605USA Guizhou Institute of biotechnology Guizhou Academy of Agricultural SciencesGuiyang 550006People’s Republic of China Department of Crop Sciences College of Agricultural and Marine SciencesSultan Qaboos UniversityPO Box 34123 AlkhoudOman Center of Excellence in fungal Research Mae Fah Luang UniversityChiang Rai 57100Thailand

Taxonomic placement of genera have been changing rapidly as taxonomists widely use DNA sequence data in phylogenetic and evolutionary studies. It is essential to update existing databases/outlines based on recent studies, since thesesources are widely used as a foundation for other research. In this outline, we merge both asexual and sexual genera intoone outline. The phylum Ascomycota comprises of three subphyla viz. Pezizomycotina (including 13 classes, 124 ordersand 507 families), Saccharomycotina (including one class, one order and 13 families) and Taphrinomycotina (five classes,five orders and six families). Approximately, 6600 genera have been listed under different taxonomic ranks includingauxiliary (intermediate) taxonomic ranks.

关键词： Asexual genera Classification Sexual genera Systematic Taxonomic ranks

Identification of the novel recessive gene pi55(t) conferring resistance to Magnaporthe oryzae

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Science China(Life Sciences) 2012年第2期55卷 141-149页

作者： HE XiuYing LIU XinQiong WANG Li WANGLing LIN Fei CHENG YongSheng CHEN ZhaoMing LIAO YaoPing PAN QingHua State Key laboratory of Conservation and Utilization of Subtropical Agro-bioresources Laboratory of Plant Resistance and GeneticsCollege of Natural Resources and Environment SciencesSouth China Agricultural UniversityGuangzhou 510642China Rice Research Institute Guangdong Academy of Agricultural SciencesGuangzhou 510640China Key biotechnology laboratory of State Ethnic Affairs CommissionCollege of Life ScienceSouth-Central University for NationalitiesWuhan 43074China

The elite rice cultivar Yuejingsimiao 2 （YJ2） is characterized by a high level of grain quality and yield, and resistance against Magnaporthe oryzae. YJ2 showed 100% resistance to four fungal populations collected from Guangdong, Sichuan, Liaoning, and Heilongjiang Provinces, which is a higher frequency than that shown by the well-known resistance （R） gene donor culti- vats such as Sanhuangzhan 2 and 28zhan. Segregation analysis for resistance with F2 and F4 populations indicated the re- sistance of YJ2 was controlled by multiple genes that are dominant or recessive. The putative R genes of YJ2 were roughly tagged by SSR markers, located on chromosomes 2, 6, 8, and 12, in a hulked-segregant analysis using genome-wide selected SSR markers with F4 lines that segregated into 3 resistant （R）： 1 susceptible （S） or 1R：3S. The recessive R gene on chromosome 8 was further mapped to an interval ~1.9 cM/152 kb in length by linkage analysis with genomic position-ready markers in the mapping population derived from an F4 line that segregated into 1R：3S. Given that no major R gene was mapped to this inter- val, the novel R gene was designated as pi55（t）. Out of 26 candidate genes predicted in the region based on the reference genomic sequence of the cultivar Nipponbare, two genes that encode a leucine-rich repeat-containing protein and heavy-metalassociated domain-containing protein, respectively, were suggested as the most likely candidates for pi55（t）.

关键词： rice blast recessive resistance gene pi55 resistance inheritance gene mapping

Application of cDNA array for studying the gene expression profile of mature appressoria of Magnaporthe grisea

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Journal of Zhejiang University-Science B(Biomedicine & biotechnology) 2007年第2期8卷 88-97页

作者： JIN Qing-chao DONG Hai-tao PENG You-liang CHEN Bao-shan SHAO Jing DENG Ye DAI Cheng-en FANG Yong-qi LOU Yi-chun LI You-zhi LI De-bao Bioinformatics and Gene Network Research Group School of Agriculture and Biotechnology Zhejiang University Hangzhou 310029 China Key laboratory of Molecular Plant Pathology Ministry of Agriculture China Agricultural University Beijing 100094 China laboratory of Subtropical Bioresource Conservation and Utilization Guangxi University Nanning 530004 China

Appressorium is an infection structure of the phytopathogenic fungus Magnaporthe grisea. Analysis of gene expression profiles ofappressorium development provides insight into the molecular basis of pathogenicity and control of this fungal plant disease. A cDNA array representing 2927 unique genes based on a large EST （expressed sequence tag） database ofM. grisea strain Y34 was constructed and used to profile the gene expression patterns at mycelium and appressorium maturation stages. Compared with mycelia, 55 up-regulated and 22 down-regulated genes were identified in mature appressoria. Among 77 genes, 16 genes showed no similarity to the genome sequences of M. grisea. A novel homologue of peptidyl-prolyl cis-trans isomerase was found to be expressed at low-level in mature appressoria of M. grisea. The results indicated that the genes such as pyruvate carboxylase, phospholipid metabolism-related protein and glyceraldehyde 3-phosphate dehydrogenase involved in gluconeogenesis, lipid metabolism and glycolysis, showed differential expression in mature appressoria. Furthermore, genes such as PTHll, beta subunit of G protein and SGTI involved in cell signalling, were expressed differentially in mature appressoria. Northern blot analysis was used to confirm the cDNA array results.

关键词： Magnaporthe grisea Mature appressoria cDNA array Gene expression profile

Taxonomic studies of some often over-looked Diaporthomycetidae and Sordariomycetidae

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fungal Diversity 2021年第6期111卷 443-572页

作者： Shi-Ke Huang Kevin D.Hyde Ausana Mapook Sajeewa S.N.Maharachchikumbura Jayarama D.Bhat Eric H.C.McKenzie Rajesh Jeewon Ting-Chi Wen State Key laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering Key Laboratory of Green Pesticide and Agricultural BioengineeringMinistry of EducationGuizhou UniversityGuiyang 550025China The Engineering Research Center of Southwest Bio-Pharmaceutical Resources Ministry of EducationGuizhou UniversityGuiyang 550025Guizhou ProvinceChina Center of Excellence in fungal Research Mae Fah Luang UniversityChiang Rai 57100Thailand School of Science Mae Fah Luang UniversityChiang Rai 57100Thailand The mushroom Research Centre Guizhou UniversityGuiyang 550025China Institute of Plant Health Zhongkai University of Agriculture and EngineeringHaizhu DistrictGuangzhou 510225China School of Life Science and Technology University of Electronic Science and Technology of ChinaChengdu 611731China Department of Botany Goa UniversityGoaIndia Present Address:Goa Velha India Manaaki Whenua-Landcare Research Private Mail Bag 92170AucklandNew Zealand Department of Health Sciences Faculty of Medicine and Health SciencesUniversity of MauritiusReduitMauritius

Sordariomycetes is an earlier-introduced and one of the widely distributed class of *** class was initially clas-sified based on morphology in having inoperculate and unitunicate *** the development of DNA based phylogenetic analysis,several undetermined or polyphyletic members of Sordariomycetes were ***,not all species belonging to this class have been sequenced and *** are a number of species,especially those old and poorly studied ones which have never been sequenced before and not even recollected again for further taxonomic *** of the main objective in this study is to revise and update the taxonomy of several well-known early and poorly studied spe-cies whose classification are still ***,we re-examined the type materials and/or authentic specimens together to explore 74 relatively poorly-studied genera,which mainly belong to Boliniales,Calosphaeriales,Chaetosphaeriales,Jobellisiales,and Sordariales classified under Diaporthomycetidae and *** provide descriptions,notes,figures and/or drawings and discussed their phylogenetic *** a result,the monotypic Jobellisiales is transferred from Hypocreomycetidae to *** on phylogenetic analysis,the polyphyletic Lasiosphaeriaceae is divided into five families,Bombardiaceae(Apodospora,Bombardia,Bombardioidea,Fimetariella and Ramophialophora),Lasiosphaeriaceae(Anopodium,Bellojisia,Corylomyces,Lasiosphaeria,Mammaria and Zopfiella),Lasiosphaeridaceae(Lasiosphaeris),Strattoniaceae(Strattonia)and Zygospermellaceae(Episternus and Zygospermella).In addition,a new family Neoschizotheciaceae is established based on *** of the type species of Boothiella,Stel-latospora,Sulcatistroma and Tengiomyces placed them in Sordariaceae,Chaetomiaceae,Hypocreales and Coronophorales,*** classify the genera lacking molecular data based on their morphology and expect them to be recollected;that is

关键词： 43 new taxa Boliniales Calosphaeriales Helminthosphaeriaceae Jobellisiales Sordariales Sordariomycetes

Microfungi on Tamarix

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fungal Diversity 2017年第1期82卷 239-306页

作者： Kasun M.Thambugala Dinushani A.Daranagama Alan J.L.Phillips Timur S.Bulgakov Darbhe J.Bhat Erio Camporesi Ali H.Bahkali Prapassorn D.Eungwanichayapant Zuo-Yi Liu Kevin D.Hyde Guizhou Key laboratory of Agricultural biotechnology Guizhou Academy of Agricultural SciencesGuiyang 550006GuizhouPeople’s Republic of China Centre of Excellence in fungal Research Mae Fah Luang UniversityChiang Rai 57100Thailand School of Science Mae Fah Luang UniversityChiang Rai 57100Thailand State Key laboratory of Mycology Institute of MicrobiologyChinese Academy of SciencesNo 31st West Beichen RoadChaoyang DistrictBeijing 100101People’s Republic of China Faculty of Sciences Biosystems and Integrative Sciences Institute(BioISI)University of LisbonCampo Grande1749-016 LisbonPortugal Academy of biology and biotechnology Southern Federal UniversityRostov-on-Don344090 Rostov RegionRussia Formerly Department of Botany Goa UniversityGoaIndia Curca No.128/1–JAzad Housing SocietyGoa VelhaIndia A.M.B.Gruppo Micologico ForliveseBAntonio Cicognani^ Via Roma 18ForlìItaly A.M.B.Circolo Micologico BGiovanni Carini^ C.P.314BresciaItaly Department of Botany and Microbiology College of ScienceKing Saud UniversityP.O.Box:2455Riyadh 1145Saudi Arabia

Tamarix species are small trees that grow in various natural habitats and have a wide geographic *** species previously found on Tamarix and recently collected in Italy and Russia were identified based on morphological characters and analyses of gene sequence *** sexual morph of the coelomycetous genus Homortomyces was collected for the first time and is described and illustrated.A new family,Homortomycetaceae(Dothideomycetes,families incertae sedis)is introduced to accommodate *** new genera Neomicrosphaeropsis(Didymellaceae)and Tamaricicola(Pleosporaceae)are introduced in this *** tamaricicola was recollected and is placed in Neomicrosphaeropsis based on morphology and molecular *** new species,Cytospora italica,***,Diaporthe ravennica,Eutypella tamaricis,Neomicrosphaeropsis italica,***,***,Keissleriella tamaricicola,Paracamarosporium tamaricis and Tamaricicola muriformis are introduced,while Alternaria tenuissima,Dothiorella sarmentorum,Neofusicoccum luteum,Paraepicoccum amazonense,Pleospora herbarum and Pseudocamarosporium propinquum are reported for the first time on Tamarix *** descriptions and ***-gene analyses show that Paraepicoccum amazonense should be placed in Pleosporineae,Pleosporales,where it is closely related to Camarosporium sensu *** herbarium specimens were studied to illustrate other fungal species recorded on Tamarix species.A comprehensive account of microfungi on Tamarix is provided,which includes a list with data from the literature,as well as those identified in the present *** taxonomic placement of most taxa discussed in this study is based on a modern taxonomic framework based on analysis of multi-gene sequence data.

关键词： Dothideomycetes Homortomycetaceae Incertae sedis New species Phylogeny Pleosporales Sordariomycetes Tamaricaceae Taxonomy

Agaricus blazei Murill polysaccharides alleviate oxidative stress and inflammatory responses against liver and lung injury

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Food Bioscience 2022年第3期47卷 534-543页

作者： Wenshuai Wang Min Liu Mengyu Zhang Wenxue Sun Jianjun Zhang Le Jia College of Life Science Shandong Agricultural UniversityTaian271018PR China Department of Animal Science & Technology Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and PreventionShandong Agricultural UniversityTaian271018PR China

As a kind of well-known edible mushroom,the medicinal values of Agaricus blazei Murill also have been well *** is no efficient treatment strategy for multiple organ dysfunction syndrome (MODS) so far,a crucial cause of clinical *** present work was designed to evaluate the beneficially protective effects of Agaricus blazei Murill polysaccharides (ABMP) on liver and lung against zymosan (ZY)-induced MODS related *** MODS mice were successfully established by given one-time injection of zymosan solution (500 mg/kg) *** in vivo results demonstrated that ABMP could improve the 10-day survival rate,ease abnormal physiological behavior and alleviate tissues oxidative stress in MODS ***,ABMP showed potential effects on attenuating the functional impairments of liver and ***,ABMP effectively inhibited the activation of NF-κB signaling pathway and reduced the expressions of inflammatory cytokines,including TNF-α,IL-1β,IL-6,COX-2 and ***,the structural characterizations showed that the significant function of ABMP was possibly related with the β-pyranose configuration with a triple-helical structure composing of glucose mainly with the proper molecular weights of 12.26 *** findings demonstrated that ABMP exhibited potential protections against liver and lung damages in the ZY-induced MODS mice,providing more theoretical basis and reference significance for the exploration of biological activity of *** Murill.

关键词： Agaricus blazei Murill polysaccharides Antioxidation Inflammation Liver and lung injury NF-κB signaling pathway