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De novo assembly of a Tibetan genome and identification of novel structural variants associated with high-altitude adaptation

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National Science Review 2020年第2期7卷 391-402页

作者： Ouzhuluobu Yaoxi He Haiyi Lou Chaoying Cui Lian Deng Yang Gao Wangshan Zheng Yongbo Guo Xiaoji Wang Zhilin Ning Jun Li Bin Li Caijuan Bai Baimakangzhuo Gonggalanzi Dejiquzong Bianba Duojizhuoma Shiming Liu Tianyi Wu Shuhua Xu Xuebin Qi Bing Su High Altitude Medical research Center School of Medicine Tibetan University Fukang Obstetrics Gynecology and Children Branch Hospital Tibetan Fukang Hospital State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming College of Life Science University of Chinese Academy of Sciences Chinese Academy of sciences Key Laboratory of Computational Biology CAS-MPG Partner Institute for Computational Biology Shanghai Institute of Nutrition and Health Shanghai Institutes for Biological SciencesUniversity of Chinese Academy of Sciences School of Life Science and Technology Shanghai Tech University Center for Disease Control Tibet Autonomous Region National Key Laboratory of High Altitude Medicine High Altitude Medical Research Institute Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Collaborative Innovation Center of Genetics and Development

Structural variants(SVs) may play important roles in human adaptation to extreme environments such as high altitude but have been under-investigated. Here, combining long-read sequencing with multiple scaffolding techniques, we assembled a high-quality Tibetan genome(ZF1), with a contig N50 length of 24.57 mega-base pairs(Mb) and a scaffold N50 length of 58.80 Mb. The ZF1 assembly filled 80 remaining N-gaps(0.25 Mb in total length) in the reference human genome(GRCh38). Markedly, we detected17 900 SVs, among which the ZF1-specific SVs are enriched in GTPase activity that is required for activation of the hypoxic pathway. Further population analysis uncovered a 163-bp intronic deletion in the MKL1 gene showing large divergence between highland Tibetans and lowland Han Chinese. This deletion is significantly associated with lower systolic pulmonary arterial pressure, one of the key adaptive physiological traits in Tibetans. Moreover, with the use of the high-quality de novo assembly, we observed a much higher rate of genome-wide archaic hominid(Altai Neanderthal and Denisovan) shared non-reference sequences in ZF1(1.32%–1.53%) compared to other East Asian genomes(0.70%–0.98%),reflecting a unique genomic composition of Tibetans. One such archaic hominid shared sequence—a662-bp intronic insertion in the SCUBE2 gene—is enriched and associated with better lung function(the FEV1/FVC ratio) in Tibetans. Collectively, we generated the first high-resolution Tibetan reference genome, and the identified SVs may serve as valuable resources for future evolutionary and medical studies.

关键词： long-read sequencing Tibetan structural variants genetic adaptation reference genome

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Fungal diversity notes 603–708: taxonomic and phylogenetic notes on genera and species

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Fungal Diversity 2017年第6期87卷 1-235页

作者： Kevin D.Hyde Chada Norphanphoun Vanessa P.Abreu Anna Bazzicalupo K.W.Thilini Chethana Marco Clericuzio Monika C.Dayarathne Asha J.Dissanayake Anusha H.Ekanayaka Mao-Qiang He Sinang Hongsanan Shi-Ke Huang Subashini C.Jayasiri Ruvishika S.Jayawardena Anuruddha Karunarathna Sirinapa Konta Ivana Kusan Hyun Lee Junfu Li Chuan-Gen Lin Ning-Guo Liu Yong-Zhong Lu Zong-Long Luo Ishara S.Manawasinghe Ausana Mapook Rekhani H.Perera Rungtiwa Phookamsak Chayanard Phukhamsakda Igor Siedlecki Adriene Mayra Soares Danushka S.Tennakoon Qing Tian Saowaluck Tibpromma Dhanushka N.Wanasinghe Yuan-Pin Xiao Jing Yang Xiang-Yu Zeng Faten A.Abdel-Aziz Wen-Jing Li Indunil C.Senanayake Qiu-Ju Shang Dinushani A.Daranagama Nimali Ide Silva Kasun M.Thambugala Mohamed A.Abdel-Wahab Ali H.Bahkali Mary L.Berbee Saranyaphat Boonmee D.Jayarama Bhat Timur S.Bulgakov Bart Buyck Erio Camporesi Rafael F.Castaneda-Ruiz Putarak Chomnunti Minkwan Doilom Francesco Dovana Tatiana B.Gibertoni Margita Jadan Rajesh Jeewon E.B.Gareth Jones Ji-Chuan Kang Samantha C.Karunarathna Young Woon Lim Jian-Kui Liu Zuo-Yi Liu Helio Longoni Plautz Jr Saisamorn Lumyong Sajeewa S.N.Maharachchikumbura Neven Matocec Eric H.C.McKenzie Armin Mesic Daniel Miller Julia Pawłowska Olinto L.Pereira Itthayakorn Promputtha Andrea I.Romero Leif Ryvarden Hong-Yan Su Satinee Suetrong Zdenko Tkalcec Alfredo Vizzini Ting-Chi Wen Komsit Wisitrassameewong Marta Wrzosek Jian-Chu Xu Qi Zhao Rui-Lin Zhao Peter E.Mortimer Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of BotanyChinese Academy of ScienceKunming 650201YunnanPeople’s Republic of China Center of Excellence in Fungal research Mae Fah Luang UniversityChiang Rai 57100Thailand School of Science Mae Fah Luang UniversityChiang Rai 57100Thailand World Agroforestry centre East and Central AsiaKunming 650201YunnanPeople’s Republic of China Mushroom research Foundation 128 M.3 Ban Pa Deng T.Pa PaeA.Mae TaengChiang Mai 50150Thailand A.M.B Circolo Micologico“Giovanni Carini”C.P.314BresciaItaly A.M.B.Gruppo Micologico Forlivese“Antonio Cicognani”Via Roma 18Forlı`Italy centre of Mountain Ecosystem Studies Kunming Institute of BotanyChinese Academy of SciencesKunming 650201YunnanPeople’s Republic of China College of Agriculture and Biological sciences Dali UniversityDali 671003YunnanPeople’s Republic of China College of Life sciences University of Chinese Academy of SciencesHuairou DistrictBeijing 100408China Department of Biology Faculty of ScienceChiang Mai UniversityChiang Mai 50200Thailand Department of Botany University of British ColumbiaVancouverCanada Department of Botany and Microbiology College of ScienceKing Saud UniversityP.O.Box:2455Riyadh 1145Saudi Arabia Department of Botany and Microbiology Faculty of ScienceSohag UniversitySohag 82524Egypt Department of Crop sciences College of Agricultural and Marine SciencesSultan Qaboos UniversityP.O.Box 34123 Al-KhodOman Department of Entomology and Plant Pathology Faculty of AgricultureChiang Mai UniversityChiang Mai 50200Thailand Department of Health sciences Faculty of ScienceUniversity of MauritiusReduit 80837Mauritius Department of Molecular Phylogenetics and Evolution Faculty of BiologyBiological and Chemical Research CentreUniversity of Warsaw_Zwirki i Wigury 10102-089 WarsawPoland Departamento de Micologia Centro de BiocienciasUniversidade Federal de PernambucoAv.da Engenharia s/nRecifePernambuco 50760-600Brazil Dipartimento

This is the sixth in a series of papers where we bring collaborating mycologists together to produce a set of notes of several taxa of *** this study we introduce a new family Fuscostagonosporaceae in *** also introduce the new ascomycete genera Acericola,Castellaniomyces,Dictyosporina and Longitudinalis and new species Acericola italica,Alternariaster trigonosporus,Amarenomyces dactylidis,Angustimassarina coryli,Astrocystis bambusicola,Castellaniomyces rosae,Chaetothyrina artocarpi,Chlamydotubeufia krabiensis,Colletotrichum lauri,Collodiscula chiangraiensis,Curvularia palmicola,Cytospora mali-sylvestris,Dictyocheirospora cheirospora,Dictyosporina ferruginea,Dothiora coronillae,Dothiora spartii,Dyfrolomyces phetchaburiensis,Epicoccum cedri,Epicoccum pruni,Fasciatispora calami,Fuscostagonospora cytisi,Grandibotrys hyalinus,Hermatomyces nabanheensis,Hongkongmyces thailandica,Hysterium rhizophorae,Jahnula guttulaspora,Kirschsteiniothelia rostrata,Koorchalomella salmonispora,Longitudinalis nabanheensis,Lophium zalerioides,Magnibotryascoma mali,Meliola clerodendri-infortunati,Microthyrium chinense,Neodidymelliopsis moricola,Neophaeocryptopus spartii,Nigrograna thymi,Ophiocordyceps cossidarum,Ophiocordyceps issidarum,Ophiosimulans plantaginis,Otidea pruinosa,Otidea stipitata,Paucispora kunmingense,Phaeoisaria microspora,Pleurothecium floriforme,Poaceascoma halophila,Periconia aquatica,Periconia submersa,Phaeosphaeria acaciae,Phaeopoacea muriformis,Pseudopithomyces kunmingnensis,Ramgea ozimecii,Sardiniella celtidis,Seimatosporium italicum,Setoseptoria scirpi,Torula gaodangensis and Vamsapriya *** also provide an amended account of Rhytidhysteron to include apothecial ascomata and a J?*** type species of Ascotrichella hawksworthii(Xylariales genera incertae sedis),Biciliopsis leptogiicola(Sordariomycetes genera incertae sedis),Brooksia tropicalis(Micropeltidaceae),Bryochiton monascus(Teratosphaeriaceae),Bryomyces scapaniae(Pseud

关键词： Ascomycota Basidiomycota Mucoromycota Phylogeny Taxonomy

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Fungal diversity notes 491–602: taxonomic and phylogenetic contributions to fungal taxa

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Fungal Diversity 2017年第2期83卷 1-261页

作者： Saowaluck Tibpromma Kevin D.Hyde Rajesh Jeewon Sajeewa S.N.Maharachchikumbura Jian-Kui Liu D.Jayarama Bhat E.B.Gareth Jones Eric H.C.McKenzie Erio Camporesi Timur S.Bulgakov Mingkwan Doilom AndreLuiz Cabral Monteiro de Azevedo Santiago Kanad Das Patinjareveettil Manimohan Tatiana B.Gibertoni Young Woon Lim Anusha Hasini Ekanayaka Benjarong Thongbai Hyang Burm Lee Jun-Bo Yang Paul M.Kirk Phongeun Sysouphanthong Sanjay K.Singh Saranyaphat Boonmee Wei Dong K.N.Anil Raj K.P.Deepna Latha Rungtiwa Phookamsak Chayanard Phukhamsakda Sirinapa Konta Subashini C.Jayasiri Chada Norphanphoun Danushka S.Tennakoon Junfu Li Monika C.Dayarathne Rekhani H.Perera Yuanpin Xiao Dhanushka N.Wanasinghe Indunil C.Senanayake Ishani D.Goonasekara N.Ide Silva Ausana Mapook Ruvishika S.Jayawardena Asha J.Dissanayake Ishara S.Manawasinghe K.W.Thilini Chethana Zong-Long Luo Kalani Kanchana Hapuarachchi Abhishek Baghela Adriene Mayra Soares Alfredo Vizzini Angelina Meiras-Ottoni Armin Mesic Arun Kumar Dutta Carlos Alberto Fragoso de Souza Christian Richter Chuan-Gen Lin Debasis Chakrabarty Dinushani A.Daranagama Diogo Xavier Lima Dyutiparna Chakraborty Enrico Ercole Fang Wu Giampaolo Simonini Gianrico Vasquez Gladstone Alves da Silva Helio Longoni Plautz Jr Hiran A.Ariyawansa Hyun Lee Ivana Kusan Jie Song Jingzu Sun Joydeep Karmakar Kaifeng Hu Kamal C.Semwal Kasun M.Thambugala Kerstin Voigt Krishnendu Acharya Kunhiraman C.Rajeshkumar Leif Ryvarden Margita Jadan MdIqbal Hosen Michal Miksık Milan C.Samarakoon Nalin N.Wijayawardene Nam Kyu Kim Neven Matocec Paras Nath Singh Qing Tian R.P.Bhatt Rafael JoseVilela de Oliveira Rodham E.Tulloss S.Aamir Saithong Kaewchai Sayali D.Marathe Sehroon Khan Sinang Hongsanan Sinchan Adhikari Tahir Mehmood Tapas Kumar Bandyopadhyay Tatyana YuSvetasheva Thi Thuong Thuong Nguyen Vladimır Antonın Wen-Jing Li Yong Wang Yuvraj Indoliya Zdenko Tkalcec Abdallah M.Elgorban Ali H.Bahkali Alvin M.C.Tang Hong-Yan Su Huang Zhang Itthayakorn Promputtha Jennifer Luangsa-ard Jianchu Xu Jiye Yan Kang Ji-Chuan Marc Stadler Pete Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of BotanyChinese Academy of ScienceKunming 650201YunnanPeople’s Republic of China Center of Excellence in Fungal research Mae Fah Luang UniversityChiang Rai 57100Thailand School of Science Mae Fah Luang UniversityChiang Rai 57100Thailand World Agroforestry centre East and Central AsiaKunming 650201YunnanPeople’s Republic of China Mushroom research Foundation 128 M.3 Ban Pa Deng T.Pa PaeA.Mae TaengChiang Mai 50150Thailand A.M.B.Gruppo Micologico Forlivese“Antonio Cicognani” Via Roma 18Forlı`Italy A.M.B.Circolo Micologico“Giovanni Carini” C.P.314BresciaItaly Societa`per gli Studi Naturalistici della Romagna C.P.144BagnacavalloRAItaly Formerly Department of Botany Goa UniversityTaleigaoGoaIndia No.128/1-J Azad Housing SocietyCurcaGoa VelhaIndia 33 B St.Edwards Road Southsea Hants Hampshire PO53DHUK Landcare research Manaaki Whenua Private Bag 92170AucklandNew Zealand Department of Biology Faculty of ScienceChiang Mai UniversityChiang Mai 50200Thailand Division of Applied Science College of International EducationThe Hong Kong Baptist UniversityHong Kong SARChina PostGraduate Program in Biology of Fungi Department of MycologyFederal University of PernambucoAv.Nelson Chavess/nRecifePE 50670-420Brazil Institute of Plant and Environment Protection Beijing Academy of Agriculture and Forestry SciencesBeijing 100097People’s Republic of China Environmental Microbiology Lab Division of Food TechnologyBiotechnology&AgrochemistryCollege of Agriculture and Life SciencesChonnam National UniversityYongbong-Dong 300Buk-GuGwangju 61186Korea Guizhou Key Laboratory of Agricultural Biotechnology Guizhou Academy of Agricultural SciencesGuiyang 550006GuizhouPeople’s Republic of China College of Agriculture and Biological sciences Dali UniversityDali 671003YunnanPeople’s Republic of China Yunnan Institute of Food Safety Kunming University of Science&TechnologyKunming 650500YunnanPeople’s Republic

This is a continuity of a series of taxonomic and phylogenetic papers on the fungi where materials were collected from many countries,examined and *** addition to extensive morphological descriptions and appropriate asexual and sexual connections,DNA sequence data are also analysed from concatenated datasets to infer phylogenetic relationships and substantiate systematic positions of taxa within appropriate ***ever new species or combinations are proposed,we apply an integrative approach using morphological and molecular data as well as ecological features wherever *** on 112 fungal taxa are compiled in this paper including Biatriosporaceae and Roussoellaceae,Didysimulans ***.,81 new species,18 new host records and new country records,five reference specimens,two new combinations,and three sexual and asexual morph *** new species are Amanita cornelii,***,Angustimassarina alni,***,***,***,***,Ascochyta italica,***,Austroboletus appendiculatus,Barriopsis thailandica,Berkleasmium ariense,Calophoma petasitis,Camarosporium laburnicola,***,***,***,***,Colletotrichum sambucicola,Coprinopsis cerkezii,Cytospora gelida,Dacrymyces chiangraiensis,Didysimulans italica,***,Entodesmium italica,Entoloma magnum,Evlachovaea indica,Exophiala italica,Favolus gracilisporus,Femsjonia monospora,Fomitopsis flabellata,***,Gongronella brasiliensis,Helvella crispoides,Hermatomyces chiangmaiensis,***nae,Hysterium centramurum,Inflatispora caryotae,Inocybe brunneosquamulosa,***,***,Keissleriella cirsii,Lepiota cylindrocystidia,***,***,Lophiotrema guttulata,Marasmius luculentus,Morenoina calamicola,Moelleriella thanathonensis,Mucor stercorarius,Myrmecridium fluviae,Myrothecium septentrionale,Neosetophoma garethjonesii,Nigrograna cangshanensis,Nodulosphaeria guttulatum,***tata,***,Panus subf

关键词： Agaricomycetes Ascomycota Basidiomycota Dacrymycetes Dothideomycetes Eurotiomycetes New combination Mucoromycotina New genus New records New species Pezizomycetes Phylogeny Sordariomycetes Taxonomy

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Fungal diversity notes 367-490:taxonomic and phylogenetic contributions to fungal taxa

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Fungal Diversity 2016年第5期80卷 1-270页

作者： Kevin D.Hyde Sinang Hongsanan Rajesh Jeewon D.Jayarama Bhat Eric H.C.McKenzie E.B.Gareth Jones Rungtiwa Phookamsak Hiran A.Ariyawansa Saranyaphat Boonmee Qi Zhao Faten Awad Abdel-Aziz Mohamed A.Abdel-Wahab Supharat Banmai Putarak Chomnunti Bao-Kai Cui Dinushani A.Daranagama Kanad Das Monika C.Dayarathne Nimali Ide Silva Asha J.Dissanayake Mingkwan Doilom Anusha H.Ekanayaka Tatiana Baptista Gibertoni Aristóteles Góes-Neto Shi-Ke Huang Subashini C.Jayasiri Ruvishika S.Jayawardena Sirinapa Konta Hyang Burm Lee Wen-Jing Li Chuan-Gen Lin Jian-Kui Liu Yong-Zhong Lu Zong-Long Luo Ishara S.Manawasinghe Patinjareveettil Manimohan Ausana Mapook Tuula Niskanen Chada Norphanphoun Moslem Papizadeh Rekhani H.Perera Chayanard Phukhamsakda Christian Richter AndréL.C.Mde A.Santiago E.Ricardo Drechsler-Santos Indunil C.Senanayake Kazuaki Tanaka T.M.D.S.Tennakoon Kasun M.Thambugala Qing Tian Saowaluck Tibpromma Benjarong Thongbai Alfredo Vizzini Dhanushka N.Wanasinghe Nalin N.Wijayawardene Hai-Xia Wu Jing Yang Xiang-Yu Zeng Huang Zhang Jin-Feng Zhang Timur S.Bulgakov Erio Camporesi Ali H.Bahkali Mohammad A.Amoozegar Lidia Silva Araujo-Neta Joseph F.Ammirati Abhishek Baghela R.P.Bhatt Dimitar Bojantchev Bart Buyck Gladstone Alves da Silva Catarina Letícia Ferreira de Lima Rafael JoséVilela de Oliveira Carlos Alberto Fragoso de Souza Yu-Cheng Dai Bálint Dima Tham Thi Duong Enrico Ercole Fernando Mafalda-Freire Aniket Ghosh Akira Hashimoto Sutakorn Kamolhan Ji-Chuan Kang Samantha C.Karunarathna Paul M.Kirk Ilkka Kytovuori Angela Lantieri Kare Liimatainen Zuo-Yi Liu Xing-Zhong Liu Robert Lücking Gianfranco Medardi Peter E.Mortimer Thi Thuong Thuong Nguyen Itthayakorn Promputtha K.N.Anil Raj Mateus A.Reck Saisamorn Lumyong Seyed Abolhassan Shahzadeh-Fazeli Marc Stadler Mohammad Reza Soudi Hong-Yan Su Takumasa Takahashi Narumon Tangthirasunun Priyanka Uniyal Yong Wang Ting-Chi Wen Jian-Chu Xu Zhong-Kai Zhang Yong-Chang Zhao Jun-Liang Zhou Lin Zhu Institute of Biotechnology and Germplasm Resources Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation Ministry of AgricultureYunnan Provincial Key Laboratory of Agricultural BiotechnologyYunnan Academy of Agricultural SciencesKunming 650223YunnanPeople’s Republic of China Key Laboratory of Plant Diversity and Biogeography of East Asia Kunming Institute of BotanyChinese Academy of SciencesKunming 650201YunnanPeople’s Republic of China Center of Excellence in Fungal research Mae Fah Luang University333 M.1T.ThasudMuangChiang Rai 57100Thailand State Key Laboratory of Mycology Institute of MicrobiologyChinese Academy of SciencesNo 31st West Beichen RoadChaoyang DistrictBeijing 100101People’s Republic of China Department of Botany and Microbiology College of ScienceKing Saud UniversityP.O.Box:2455Riyadh1145Saudi Arabia Department of Botany and Microbiology Faculty of ScienceSohag UniversitySohag 82524Egypt Faculty of Agriculture and Life sciences Hirosaki University3 Bunkyo-choHirosakiAomori 036-8561Japan The United Graduate School of Agricultural sciences Iwate University18-8 Ueda 3 ChomeMorioka 020-8550Japan Guizhou Key Laboratory of Agricultural Biotechnology Guizhou Academy of Agricultural SciencesXiaohe DistrictGuiyang CityGuizhou Province 550006People’s Republic of China School of Science Mae Fah Luang UniversityChiang Rai 57100Thailand Department of Plant Pathology College of AgricultureGuizhou UniversityGuiyang 550025GuizhouPeople’s Republic of China Department of Botany Goa UniversityTaleigãoGoaIndia No.128/1-J Azad Housing SocietyCurcaGoa Velha 403108India Department of Biology Faculty of ScienceChiang Mai UniversityChiang Mai 50200Thailand World Agroforestry centre East and Central AsiaKunming 650201YunnanPeople’s Republic of China centre of Mountain Ecosystem Studies Kunming Institute of BotanyChinese Academy of SciencesKunming 650201YunnanPeople’s Republic of China Department of Microbial Drugs Helmholtz Centre for Infection Res

This is a continuity of a series of taxonomic papers where materials are examined,described and novel combinations are proposed where necessary to improve our traditional species concepts and provide updates on their *** addition to extensive morphological descriptions and appropriate asexual and sexual connections,DNA sequence data are also analysed from concatenated datasets(rDNA,TEF-a,RBP2 and b-Tubulin)to infer phylogenetic relationships and substantiate systematic position of taxa within appropriate *** new species or combinations are being proposed,we apply an integrative approach(morphological and molecular data as well as ecological features wherever applicable).Notes on 125 fungal taxa are compiled in this paper,including eight new genera,101 new species,two new combinations,one neotype,four reference specimens,new host or distribution records for eight species and one alternative *** new genera introduced in this paper are Alloarthopyrenia,Arundellina,Camarosporioides,Neomassaria,Neomassarina,Neotruncatella,Paracapsulospora and *** new species are Alfaria spartii,Alloarthopyrenia italica,Anthostomella ravenna,***,Arthrinium paraphaeospermum,Arundellina typhae,Aspergillus koreanus,Asterina cynometrae,Bertiella ellipsoidea,Blastophorum aquaticum,Cainia globosa,Camarosporioides phragmitis,Ceramothyrium menglunense,Chaetosphaeronema achilleae,Chlamydotubeufia helicospora,Ciliochorella phanericola,Clavulinopsis aurantiaca,Colletotrichum insertae,Comoclathris italica,Coronophora myricoides,Cortinarius fulvescentoideus,***,***,***,Cunninghamella gigacellularis,Cyathus pyristriatus,Cytospora cotini,Dematiopleospora alliariae,***,Diaporthe aseana,***,Distoseptispora multiseptata,***,***,Dothiora buxi,Emericellopsis persica,Gloniopsis calami,Helicoma guttulatum,Helvella floriforma,***,Hermatomyces subiculosa,Ju

关键词： Ascomycota Basidiomycota Dothideomycetes Mortierellomycotina Mucoromycotina Pezizomycetes Phylogeny Taxonomy New genus New species New host records

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