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A well-supported nuclear phylogeny of Poaceae and implications for the evolution of C4 photosynthesis

Molecular plant 2022年第4期15卷 755-777页

作者： Weichen Huang Lin Zhang jTravis Columbus Yi Hu Yiyong Zhao Lin Tang Zhenhua Guo Wenli Chen Michael McKain Madelaine bartlett Chien-Hsun Huang De-Zhu Li Song Ge Hong Ma Department of biology 510 Mueller LaboratoryHuck Institutes of the Life SciencesThe Pennsylvania State UniversityUniversity ParkState CollegePA 16802USA Ministry of Education Key Laboratory for biodiversity Science and Ecological Engineering and State Key Laboratory of Genetic Engineering Institute of Biodiversity Sciences and Institute of Plant BiologySchool of Life SciencesFudan University2005 Songhu RoadShanghai 200438China Rancho Santa Ana botanic Garden and Claremont Graduate University 1500 North College AvenueClaremontCA 91711USA College of Life Sciences Zhejiang UniversityHangzhouZhejiang 310058China plant Germplasm and Genomics Center Germplasm Bank of Wild SpeciesKunming Institute of BotanyChinese Academy of SciencesKunmingYunnan 650201 China State Key Laboratory of Systematic and Evolutionary botany Institute of BotanyChinese Academy of SciencesBeijing 100093China Department of biological Sciences University of Alabama411 Mary Harmon Bryant HallTuscaloosaAL 35487USA biology Department University of Massachusetts Amherst611 North Pleasant Street221 Morrill 3AmherstMA 01003 USA

Poaceae(the grasses)includes rice,maize,wheat,and other crops,and is the most economically important angiosperm *** is also one of the largest plant families,consisting of over 11000 species with a global distribution that contributes to diverse *** species are classified into 12 subfamilies,with generally strong phylogenetic support for their ***,many relationships within subfamilies,among tribes and/or subtribes,remain *** better resolve the Poaceae phylogeny,we generated 342 transcriptomic and seven genomic datasets;these were combined with other genomic and transcriptomic datasets to provide sequences for 357 Poaceae species in 231 genera,representing 45 tribes and all 12 *** 1200 low-copy nuclear genes were retrieved from these datasets,with several subsets obtained using additional criteria,and used for coalescent analyses to reconstruct a Poaceae *** results strongly support the monophyly of 11 subfamilies;however,the subfamily Puelioideae was separated into two non-sister clades,one for each of the two previously defined tribes,supporting a hypothesis that places each tribe in a separate *** clock analyses estimated the crown age of Poaceae to be101 million years *** character reconstruction of C3/C4 photosynthesis supports the hypothesis of multiple independent origins of C4 *** origins are further supported by phylogenetic analysis of the ppc gene family that encodes the phosphoenolpyruvate carboxylase,which suggests that members of three paralogous subclades(ppc-aL1a,ppc-aL1b,and ppcb2)were recruited as functional C4 ppc *** study provides valuable resources and a robust phylogenetic framework for evolutionary analyses of the grass family.

关键词： Gramineae transcriptome nuclear phylogeny molecular clock C4 photosynthesis ppc gene evolution

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Fungal diversity notes 1036-1150:taxonomic and phylogenetic contributions on genera and species of fungal taxa

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Fungal Diversity 2019年第3期96卷 1-242页

作者： Kevin D.Hyde Danushka S.Tennakoon Rajesh jeewon Djayarama bhat Sajeewa S.N.Maharachchikumbura Walter Rossi Marco Leonardi Hyang burm Lee Hye Yeon Mun jos Houbraken Thuong T.T.Nguyen Sun jeong jeon jens Christian Frisvad Dhanushka N.Wanasinghe Robert Lucking Andre Aptroot Marcela E.S.Caceres Samantha C.Karunarathna Sinang Hongsanan Rungtiwa Phookamsak Nimali Ide Silva Kasun M.Thambugala Ruvishika S.jayawardena Indunil C.Senanayake Saranyaphat boonmee jie Chen Zong-Long Luo Chayanard Phukhamsakda Olinto L.Pereira Vanessa P.Abreu Andre Wilson Campos Rosado buyck bart Emile Randrianjohany Vale rie Hofstetter Tatiana b.Gibertoni Adriene Mayrada Silva Soares Helio Longoni Plautz jr Helen Maria Pontes Sotao William Kalhy Silva Xavier jadson Diogo Pereira bezerra Thays Gabrielle Linsde Oliveira Cristina Mariade Souza-Motta Oliane Maria Correia Magalhaes Digvijayini bundhun Dulanjalee Harishchandra Ishara S.Manawasinghe Wei Dong Sheng-Nan Zhang Dan-Feng bao Milan C.Samarakoon Dhandevi Pem Anuruddha Karunarathna Chuan-Gen Lin jing Yang Rekhani H.Perera Vinit Kumar Shi-Ke Huang Monika C.Dayarathne Anusha H.Ekanayaka Subashini C.jayasiri Yuanpin Xiao Sirinapa Konta Tuula Niskanen Kare Liimatainen Yu-Cheng Dai Xiao-Hong ji Xue-Mei Tian Armin Mesic Sanjay K.Singh Kunthida Phutthacharoen Lei Cai Touny Sorvongxay Vinodhini Thiyagaraja Chada Norphanphoun Napalai Chaiwan Yong-Zhong Lu Hong-bo jiang jin-Feng Zhang Pranami D.Abeywickrama janith V.S.Aluthmuhandiram Rashika S.brahmanage Ming Zeng Thilini Chethana Deping Wei Martina Reblova jacques Fournier jana Nekvindova Renan do Nascimento barbosa jose Ewerton Felintodos Santos Neiva Tintide Oliveira Guo-jie Li Damien Ertz Qiu-ju Shang Alan j.L.Phillips Chang-Hsin Kuo Erio Camporesi Timur S.bulgakov Saisamorn Lumyong E.b.Gareth jones Putarak Chomnunti Eleni Gentekaki Frank bungartz Xiang-Yu Zeng Sally Fryar Zdenko Tkalcec junmin Liang Guangshuo Li Ting-Chi Wen Paras Nath Singh Yusufjon Gafforov Itthayakorn Promputtha Erandi Yasanthika Ishani D.Goonasekara Rui-Lin Zhao Qi Zhao Paul M Key Laboratory for plant Diversity and biogeography of East Asia Kunming Institute of BotanyChinese Academy of ScienceKunming 650201YunnanPeople’s Republic of China School of Science Mae Fah Luang UniversityChiang Rai 57100Thailand Center of Excellence in Fungal Research Mae Fah Luang UniversityChiang Rai 57100Thailand East and Central Asia Regional Office World Agroforestry Centre(ICRAF)Kunming 650201YunnanPeople’s Republic of China Department of biology Faculty of ScienceChiang Mai UniversityChiang Mai 50200Thailand Mushroom Research Foundation 128 M.3 Ban Pa Deng T.Pa PaeA.Mae TaengChiang Mai 50150Thailand Department of plant Medicine National Chiayi University300 Syuefu RoadChiayi City 60004TaiwanPeople’s Republic of China Department of Health Sciences Faculty of ScienceUniversity of MauritiusReduitMauritius Formerly Department of botany Goa UniversityGoaIndia No.128/1-j Azad Housing SocietyCurcaGoa Velha 403108India Department of Crop Sciences College of Agricultural and Marine SciencesSultan Qaboos UniversityPO Box 8123 Al KhoudOman Sect.Environmental Sciences Dept.MeSVAUniversity of L’Aquila67100 CoppitoAQItaly Division of Food Technology Biotechnology&AgrochemistryCollege of Agriculture&Life SciencesChonnam National UniversityGwangju 61186Korea Fungal Resources Research Division NNIBRSangju-si 37242Korea Westerdijk Fungal biodiversity Institute Uppsalalaan 83584 CT UtrechtThe Netherlands Department of biotechnology and biomedicine DTUBioengineeringTechnical University of Denmark2800 Kongens LyngbyDenmark botanischer Garten und botanisches Museum berlin Freie Universitat BerlinKonigin-Luise-StraßBe 6-814195 BerlinGermany Laboratorio de botanica/Liquenologia Instituto de BiocienciasUniversidade Federal de Mato Grosso do SulAvenida Costa e Silva s/nBairro UniversitarioCampo GrandeMatto Grosso do Sul CEP 79070-900Brazil Departamento de biociencias Universidade Federal de SergipeItabaianaSergipe CEP:49500-000Brazil Shenzhen Key Laboratory of Microbial

This article is the tenth series of the Fungal Diversity Notes,where 114 taxa distributed in three phyla,ten classes,30 orders and 53 families are described and *** described in the present study include one new family(*** in Dothideomycetes),five new genera(Caatingomyces,Cryptoschizotrema,Neoacladium,Paramassaria and Trochilispora)and 71 new species,(*** thailandica,Amniculicola aquatica,***,Angustimassarina sylvatica,blackwellomyces lateris,boubovia gelatinosa,buellia viridula,Caatingomyces brasiliensis,Calophoma humuli,Camarosporidiella mori,Canalisporium dehongense,Cantharellus brunneopallidus,***,Castanediella meliponae,Coprinopsis psammophila,Cordyceps succavus,Cortinarius minusculus,***,Diaporthe italiana,***,Diatrypella delonicis,Dictyocheirospora aquadulcis,***,Digitodesmium chiangmaiense,Distoseptispora dehongensis,***,Dothiorella styphnolobii,Ellisembia aurea,Falciformispora aquatic,Fomitiporia carpinea,***,Grammothele aurantiaca,***,Hermatomyces bauhiniae,jahnula queenslandica,Kamalomyces mangrovei,Lecidella yunnanensis,Micarea squamulosa,Muriphaeosphaeria angustifoliae,Neoacladium indicum,Neodidymelliopsis sambuci,Neosetophoma miscanthi,***,Nodulosphaeria aquilegiae,***,Paramassaria samaneae,Penicillium circulare,***,***-pumilae,***,***,Phaeoisaria siamensis,Phaeopoacea asparagicola,Phaeosphaeria penniseti,Plectocarpon galapagoense,Porina sorediata,Pseudoberkleasmium chiangmaiense,Pyrenochaetopsis sinensis,Rhizophydium koreanum,Russula prasina,Sporoschisma chiangraiense,Stigmatomyces chamaemyiae,***,***,***,***,Thysanorea uniseptata,Torula breviconidiophora,***,Trochilispora schefflerae and Vaginatispora palmae).Further,twelve new combinations(*** cryptotrema,Prolixandromyces australi,***,***,***,P.

关键词： 71 new taxa Ascomycota basidiomycota Dothideomycetes Eurotiomycetes Lecanoromycetes Leotiomycetes Pezizomycetes Phylogeny Taxonomy

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Towards a natural classification and backbone tree for Sordariomycetes

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Fungal Diversity 2015年第3期72卷 199-301页

作者： Sajeewa S.N.Maharachchikumbura Kevin D.Hyde EbGareth jones Eric H.C.McKenzie Shi-Ke Huang Mohamed A.Abdel-Wahab Dinushani A.Daranagama Monika Dayarathne Melvina j.D’souza Ishani D.Goonasekara Sinang Hongsanan Ruvishika S.jayawardena Paul M.Kirk Sirinapa Konta jian-Kui Liu Zuo-Yi Liu Chada Norphanphoun Ka-Lai Pang Rekhani H.Perera Indunil C.Senanayake Qiuju Shang belle Damodara Shenoy Yuanpin Xiao Ali H.bahkali jichuan Kang Sayanh Somrothipol Satinee Suetrong Tingchi Wen jianchu Xu Guizhou Key Laboratory of Agricultural biotechnology Guizhou Academy of Agricultural SciencesGuiyang 550006GuizhouChina Key Laboratory for plant biodiversity and biogeography of East Asia(KLPb) Kunming Institute of BotanyChinese Academy of ScienceKunming 650201YunnanChina World Agroforestry Centre East and Central Asia132 Lanhei RoadKunming 650201China Institute of Excellence in Fungal Research and School of ScienceMae Fah Luang UniversityChiang Rai 57100Thailand Department of botany and Microbiology College of ScienceKing Saud UniversityP.O.Box 2455Riyadh 11451Kingdom of Saudi Arabia Manaaki Whenua Landcare Research Private Bag 92170AucklandNew Zealand The Engineering and Research Center for Southwest bio-Pharmaceutical Resources of National Education Ministry of China Guizhou UniversityGuiyang 550025Guizhou ProvincePeople’s Republic of China Department of botany Faculty of ScienceSohag UniversitySohag 82524Egypt Institute of Marine biology and Centre of Excellence for the Oceans Taiwan Ocean University2 Pei-Ning RoadKeelung 20224TaiwanRepublic of China Mycology Section Royal Botanic GardensKewLondonUK Microbe Interaction Laboratory(bMIT) National Center for Genetic Engineering and Biotechnology(BIOTEC)113 Thailand Science ParkPhahonyothin RoadKhlong NuengKhlong LuangPathum ThaniThailand Fungal Diversity Laboratory(bFbD) National Center for Genetic Engineering and Biotechnology(BIOTEC)113 Thailand Science ParkPhahonyothin RoadKhlong NuengKhlong LuangPathum ThaniThailand biological Oceanography Division CSIR-National Institute of OceanographyDona PaulaGoa 403004India Institute of plant and Environment Protection Beijing Academy of Agriculture and Forestry SciencesNo 9 of ShuGuangHuaYuanZhangLuHaidian DistrictBeijing 100097China

Sordariomycetes is one of the largest classes of Ascomycota and is characterised by perithecial ascomata and inoperculate unitunicate *** class includes many important plant pathogens,as well as endophytes,saprobes,epiphytes,and fungicolous,lichenized or lichenicolous *** class includes freshwater,marine and terrestrial taxa and has a worldwide *** paper provides an updated outline of the Sordariomycetes and a backbone tree incorporating asexual and sexual genera in the *** on phylogeny and morphology we introduced three subclasses;Diaporthomycetidae,Lulworthiomycetidae and Meliolomycetidae and five orders;Amplistromatales,Annulatascales,Falcocladiales,jobellisiales and *** outline is based on literature to the end of 2014 and the backbone tree published in this *** for 397 taxa with information,such as new family and genera novelties,novel molecular data published since the Outline of Ascomycota 2009,and new links between sexual and asexual genera and thus synonymies,are *** Sordariomycetes now comprises six subclasses,28 orders,90 families and 1344 *** addition a list of 829 genera with uncertain placement in Sordariomycetesis also provided.

关键词： boliniales Calosphaeriales Chaetosphaeriales Coniochaetales Coronophorales Diaporthales Glomerellales Hypocreomycetidae Hypocreales Koralionastetales Lulworthiales Magnaporthales Melanosporales Meliolales Microascales Molecular identification Nomenclature Ophiostomatales Phyllachorales Sordariales Sordariomycetidae Taxonomy Trichosphaeriales Type species Xylariales Xylariomycetidae

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Determination of the number of ψ(3686)events at bESⅢ

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Chinese Physics C 2018年第2期42卷 1-11页

作者：麦迪娜 M.N.Achasov 艾小聪 D.j.Ambrose A.Amoroso 安芬芬安琪白景芝 R.baldini Ferroli 班勇 j.V.bennett M.bertani 边渐鸣 E.boger O.bonda renko I.boyko R.A.briere 蔡浩蔡啸 O.Cakir A.Calcaterra 曹国富 S.A.Cetin 常劲帆 G.Chelkov 陈刚陈和生陈江川陈玛丽陈申见谌炫陈旭荣陈元柏褚新坤初元萍 D.Cronin-Hennessy 代洪亮代建平 D.Dedovich 邓子艳 A.Denig I.Denysenko M.Destefanis 丁勇董超董静董燎原董明义杜书先范荆州方建房双世方易 L.Fava F.Feldbauer 封常青傅成栋高清高原宁 K.Goetzen 龚文煊 W.Gradl M.Greco 顾旻皓顾运厅管颖慧郭爱强郭玉萍韩艳良 F.A.Harris 何康林何苗 T.Held 衡月昆侯治龙胡海明胡涛黄光顺黄金书黄亮黄性涛 T.Hussain 纪全姬清平季晓斌季筱璐姜丽丽江晓山焦健斌焦铮金大鹏金山 T.johansson N.Kalantar-Nayestanaki 康晓琳康晓坤 M.Kavatsyuk b.Kloss b.Kopf M.Kornicer A.Kupsc W.Kuhn 赖蔚 j.S.Lange M.Lara P.Larin 李春花李澄李德民李飞李刚李海波李家才李康李科李蕾李培荣李秋菊李卫东李卫国李晓玲李小男李学潜李秀荣李志兵梁昊梁勇飞梁羽铁廖广睿林德旭刘北江刘春秀刘福虎刘芳刘峰刘宏邦刘怀民刘汇慧刘杰刘觉平刘凯刘魁勇刘倩刘树彬刘翔刘玉斌刘振安刘志强刘智青 H.Loehner 娄辛丑吕海江卢怀乐吕军光卢宇卢云鹏罗成林罗民兴 T.Luo 罗小兰吕蒙吕晓睿马凤才马海龙马秋梅马斯马天马骁妍 F.E.Maas M.Maggiora 冒亚军毛泽普 j.G.Messchendorp 闵建闵天觉 R.E.Mitchell 莫晓虎莫玉俊 C.Morales Morales K.Moriya N.Yu.Muchnoi H.Muramatsu Y.Nefedov I.b.Nikolaev 宁哲 S.Nisar 牛顺利牛讯伊马鹏欧阳群 S.Pacetti M.Pelizaeus 彭海平 K.Peters 平加伦平荣刚 R.Poling 祁鸣钱森乔从丰秦小帅秦中华邱进发 K.H.Rashid C.F.Redmer M.Ripka 荣刚 A.Sarantsev K.Schoenning 单葳邵明沈成平沈肖雁盛华义 M.R.Shepherd 宋维民宋欣颖 S.Sosio S.Spataro 孙功星孙俊峰孙胜森孙勇杰孙永昭孙志嘉唐昌建唐晓 I.Tapan E.H.Thorndike D.Toth I.Uman G.S.Varner 王斌王东王大勇王科王亮亮王灵淑王萌王平王佩良王庆娟王炜王雄飞 Y.D.Wang(Yadi) 王贻芳王亚乾王铮王志刚王至勇魏代会 P.Weidenkaff 文硕频 U.Wiedner M.Wolke 伍灵慧吴智夏力钢夏宇肖栋肖振军谢宇广修青磊许国发徐雷徐庆君徐庆年徐新平鄢文标颜永红杨洪勋杨迎杨永栩叶桦叶梅叶铭汉俞伯祥喻纯旭俞洁晟苑长征袁野 A.A.Zafar 曾云张丙新张炳云张长春张达华张宏浩章红宇张佳佳张敬庆张家文张建勇张景芝张磊张瑞张书华张晓杰张学尧张银鸿张瑶张正好张子平张振宇赵光赵京伟赵京周赵雷赵玲赵明刚赵强赵庆旺赵书俊赵天池赵豫斌赵政国 A.Zhemchugov 郑波郑建平郑阳恒钟彬周莉周详周晓康周小蓉周兴玉朱凯朱科军朱相雷朱莹春朱永生朱自安庄建邹冰松邹佳恒无 Institute of High Energy Physics Beijing 100049China beihang University Beijing 100191China beijing Institute of Petrochemical Technology Beijing 102617China bochum Ruhr-University D-44780 BochumGermany Carnegie Mellon University PittsburghPennsylvania 15213USA Central China Normal University Wuhan 430079China China Center of Advanced Science and Technology Beijing 100192China COMSATS Institute of Information Technology LahoreDefence RoadOff Raiwind Road54000 LahorePakistan G.I.budker Institute of Nuclear Physics Sb RAS(bINP) Novosibirsk 630090Russia GSI Helmholtzcentre for Heavy Ion Research GmbH D-64291 DarmstadtGermany Guangxi Normal University Guilin 541004China Guangxi University Nanning 530004China Hangzhou Normal University Hangzhou 310036China Helmholtz Institute Mainz Johann-Joachim-Becher-Weg 45D-55099 MainzGermany Henan Normal University Xinxiang 453007China Henan University of Science and Technology Luoyang 471003China Huangshan College Huangshan 245000China Hunan University Changsha 410082China Indiana University BloomingtonIndiana 47405USA INFN Laboratori Nazionali di Frascati 1-00044FrascatiItaly INFN and University of Perugia 1-06100PerugiaItaly INFN Sezione di Ferrara 1-44122FerraraItaly University of Ferrara 1-44122FerraraItaly johannes Gutenberg University of Mainz Johann-Joachim-Becher-Weg 45D-55099 MainzGermany joint Institute for Nuclear Research 141980 DubnaMoscow regionRussia justus-Liebig-Universitaet Giessen II.Physikalisches InstitutHeinrich-Buff-Ring 16D-35392 GiessenGermany KVI-CART University of GroningenNL-9747 AA GroningenThe Netherlands Lanzhou University Lanzhou 730000China Liaoning University Shenyang 110036China Nanjing Normal University Nanjing 210023China Nanjing University Nanjing 210093China Nankai University Tianjin 300071China Peking University Beijing 100871China Seoul National University Seoul151-747 Korea Shandong University Jinan 250100China Shanghai jiao Tong University Shanghai 200240China Shanxi University Taiyuan

The numbers of ψ（3686） events accumulated by the bESⅢ detector for the data taken during 2009 and 2012 are determined to be（107.0±0.8）×10^6 and（341.1±2.1）×10^6, respectively, by counting inclusive hadronic events,where the uncertainties are systematic and the statistical uncertainties are negligible. The number of events for the sample taken in 2009 is consistent with that of the previous measurement. The total number of ψ（3686） events for the two data taking periods is（448.1±2.9）×10^6.

关键词： ψ(3686) inclusive process hadronic events bhabha process

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comLocal adaptation to distinct elevational cores contributes to current elevational divergence of two Aquilegia vulgaris subspecies

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journal of plant Ecology 2015年第3期8卷 273-283页

作者： jesús M.bastida Pedro j.Rey julio M.Alcántara Departamento de biología Animal Biología Vegetal y EcologíaUniversidad de JaénJaén E-23071Spain

Aims Phenotypic plasticity and local adaptation of populations at their distributional limits are crucial to understand species colonization and persistence in novel or marginal environments,as well as spe-cies divergence and niche width *** assess the contri-bution of these processes to shape current elevational limits and determine elevational phenotypic divergence between two subspe-cies of Aquilegia vulgaris(*** and nevadensis).Methods We conducted sowing and transplant experiments considering four elevations throughout the current elevational range of *** in southern Iberian *** were designed to explore,on the one hand,local adaptation through three components of performance(germination,survival and growth)and,on the other hand,the phenotypic differentiation and/or plasticity associated to local *** populations per subspecies(three from the elevational core and one from the elevational boundary)were used as seed *** of local adaptation and phenotypic differentiation are examined in the context of the‘centre-periphery’*** Findings Central populations of both subspecies performed better at their local elevations while marginal populations were maladapted,confirming the hypothesis and contributing to explain the current elevational segregation of these *** of glandular pubescence and germination timing seem to be related to local adaptation,through phenotypic differentiation between subspe-cies or *** widespread *** showed signals of adaptive plasticity in the timing of germination while it was not the case in the endemic ***.

关键词： Iberian Aquilegia local adaptation phenotypic plasticity centre-periphery hypothesis elevational divergence germination timing

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Chromosome-scale scaffolding of the black raspberry (Rubus occidentalis L.) genome based on chromatin interaction data

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Horticulture Research 2018年第1期5卷 868-878页

作者： Rubina jibran Helge Dzierzon Nahla bassil jill M.bushakra Patrick P.Edger Shawn Sullivan Chad E.Finn Michael Dossett Kelly j.Vining Robert Vanburen Todd C.Mockler Ivan Liachko Kevin M.Davies Toshi M.Foster David Chagné The New Zealand Institute for plant&Food Research Limited Private Bag 11600Palmerston North4474New Zealand USDA-ARS National Clonal Germplasm Repository 33447 Peoria RoadCorvallisOR97333USA Department of Horticulture Michigan State UniversityEast LansingMI48824-2604USA Phase Genomics SeattleWA98195USA USDA-ARS Horticultural Crops Research Unit CorvallisOR97330USA b.C.blueberry Council(in Partnership with Agriculture and Agri-Food Canada)Agassiz Food Research Centre AgassizBCV0M 1A0Canada The Donald Danforth plant Science Center St.LouisMO63132USA Department of Genome Sciences University of Washington School of MedicineSeattleWA98195USA

black raspberry(Rubus occidentalis L.)is a niche fruit crop valued for its flavor and potential health *** improvement of fruit and cane characteristics via molecular breeding technologies has been hindered by the lack of a high-quality reference *** recently released draft genome for black raspberry(ORUS 4115-3)lacks assembly of scaffolds to chromosome *** used high-throughput chromatin conformation capture(Hi-C)and Proximity-Guided Assembly(PGA)to cluster and order 9650 out of 11,936 contigs of this draft genome assembly into seven *** seven pseudo-chromosomes cover~97.2%of the total contig length(~223.8 Mb).Locating existing genetic markers on the physical map resolved multiple discrepancies in marker order on the genetic *** regions were inferred from recombination frequencies of genetic markers,alignment of 303 bp centromeric sequence with the PGA,and heat map showing the physical contact matrix over the entire *** demonstrate a high degree of synteny between each of the seven chromosomes of black raspberry and a high-quality reference genome for strawberry(Fragaria vesca L.)assembled using only Pacbio long-read *** conclude that PGA is a cost-effective and rapid method of generating chromosome-scale assemblies from Illumina short-read sequencing data.

关键词： breeding black interaction

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One stop shop Ⅱ:taxonomic update with molecular phylogeny for important phytopathogenic genera:26–50(2019)

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Fungal Diversity 2019年第1期 41-129页

作者： Ruvishika S.jayawardena Kevin D.Hyde Rajesh jeewon Masoomeh Ghobad-Nejhad Dhanushka N.Wanasinghe NingGuo Liu Alan j.L.Phillips jose Ribamar COliveira-Filho Gladstone Ada Silva Tatiana b.Gibertoni P.Abeywikrama L.M.Carris K.W.T.Chethana A.j.Dissanayake S.Hongsanan S.C.jayasiri A.R.McTaggart R.H.Perera K.Phutthacharoen K.G.Savchenko R.G.Shivas Naritsada Thongklang Wei Dong DePing Wei Nalin NWijayawardena ji-Chuan Kang The Engineering Research Center of Southwest biopharmaceutical Resources Ministry of EducationGuizhou UniversityGuiyang 550025People’s Republic of China Center of Excellence in Fungal Research Mae Fah Luang UniversityChiang RaiThailand Key Laboratory for plant Diversity and biogeography of East Asia Kunming Institute of BotanyChinese Academy of SciencesKunming 650201People’s Republic of China Department of Health Sciences Faculty of ScienceUniversity of MauritiusReduitMauritius Department of biotechnology Iranian Research Organization for Science and Technology(IROST)P.O.Box 15815-3538Tehran 15819Iran World Agroforestry Centre East and Central AsiaKunming 650201YunnanPeople’s Republic of China Universidade de Lisboa Faculdade de CienciasBiosystems and Integrative Sciences Institute(BioISI)Campo Grande1749-016 LisbonPortugal Departamento de Micologia Universidade Federal de PernambucoAvenida da EngenhariaS/N-Cidade UniversitariaRecifePE 50740-600Brazil beijing Key Laboratory of Environmet Friendly Management on Fruit Disease and Pests in North China Institute of Plant and Environment ProtectionBeijing Academy of Agriculture and Forestry SciencesBeijing 100097People’s Republic of China Department of plant Pathology Washington State UniversityPullmanWA 99164USA College of Life Science and Oceanography ShenZhen University1068Nanhai AvenueNanshanShenzhen 518055China Queensland Alliance for Agriculture and Food Innovation The University of QueenslandBrisbaneQLD 4001Australia Department of biological Sciences Butler UniversityIndianapolisIN 46208USA Centre for Crop Health University of Southern QueenslandToowoombaQLD 4350Australia Department of Entomology and plant Pathology Faculty of AgricultureChiang Mai UniversityChiang Mai 50200Thailand Faculty of Agriculture National Resources and EnvironmentNaresuan UniversityPhitsanulok 65000Thailand

This paper is the second in a series focused on providing a stable platform for the taxonomy of phytopathogenic *** focuses on 25 phytopathogenic genera:Alternaria,bipolaris,boeremia,botryosphaeria,Calonectria,Coniella,Corticiaceae,Curvularia,Elsinoe,Entyloma,Erythricium,Fomitiporia,Fulviformes,Laetisaria,Limonomyces,Neofabraea,Neofusicoccum,Phaeoacremonium,Phellinotus,Phyllosticta,Plenodomus,Pseudopyricularia,Tilletia,Venturia and Waitea,using recent molecular data,up to date names and the latest taxonomic *** each genus a taxonomic background,diversity aspects,species identification and classification based on molecular phylogeny and recommended genetic markers are *** this study,varieties of the genus boeremia have been elevated to species ***,bipolaris,Curvularia,Neofusicoccum and Phyllosticta that were included in the One Stop Shop 1 paper are provided with updated entries,as many new species have been introduced to these genera.

关键词： boeremia DNA barcodes Endophytes plant pathology Systematics Taxonomy

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FungalTraits:a user-friendly traits database of fungi and fungus-like stramenopiles

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Fungal Diversity 2020年第2期107卷 I0001-I0016页

作者： Sergei Põlme Kessy Abarenkov RHenrik Nilsson björn D.Lindahl Karina Engelbrecht Clemmensen Havard Kauserud Nhu Nguyen Rasmus Kjøller Scott T.bates Petr baldrian Tobias Guldberg Frøslev Kristjan Adojaan Alfredo Vizzini Ave Suija Donald Pfister Hans-Otto baral Helle järv Hugo Madrid jenni Nordén jian-Kui Liu julia Pawlowska Kadri Põldmaa Kadri Pärtel Kadri Runnel Karen Hansen Karl-Henrik Larsson Kevin David Hyde Marcelo Sandoval-Denis Matthew E.Smith Merje Toome-Heller Nalin N.Wijayawardene Nelson Menolli jr Nicole K.Reynolds Rein Drenkhan Sajeewa S.N.Maharachchikumbura Tatiana b.Gibertoni Thomas Læssøe William Davis Yuri Tokarev Adriana Corrales Adriene Mayra Soares Ahto Agan Alexandre Reis Machado Andrés Argüelles-Moyao Andrew Detheridge Angelina de Meiras-Ottoni Annemieke Verbeken Arun Kumar Dutta bao-Kai Cui C.K.Pradeep César Marín Daniel Stanton Daniyal Gohar Dhanushka N.Wanasinghe Eveli Otsing Farzad Aslani Gareth W.Griffith Thorsten H.Lumbsch Hans-Peter Grossart Hossein Masigol Ina Timling Inga Hiiesalu jane Oja john Y.Kupagme józsef Geml julieta Alvarez-Manjarrez Kai Ilves Kaire Loit Kalev Adamson Kazuhide Nara Kati Küngas Keilor Rojas-jimenez Krišs bitenieks Laszlo Irinyi LászlóGNagy Liina Soonvald Li-Wei Zhou Lysett Wagner M.Catherine Aime MaarjaÖpik María Isabel Mujica Martin Metsoja Martin Ryberg Martti Vasar Masao Murata Matthew PNelsen Michelle Cleary Milan C.Samarakoon Mingkwan Doilom Mohammad bahram Niloufar Hagh-Doust Olesya Dulya Peter johnston Petr Kohout Qian Chen Qing Tian Rajasree Nandi Rasekh Amiri Rekhani Hansika Perera Renata dos Santos Chikowski Renato L.Mendes-Alvarenga Roberto Garibay-Orijel Robin Gielen Rungtiwa Phookamsak Ruvishika S.jayawardena Saleh Rahimlou Samantha C.Karunarathna Saowaluck Tibpromma Shawn P.brown Siim-Kaarel Sepp Sunil Mundra Zhu-Hua Luo Tanay bose Tanel Vahter Tarquin Netherway Teng Yang Tom May Torda Varga Wei Li Victor Rafael Matos Coimbra Virton Rodrigo Targino de Oliveira Vitor Xavier de Lima Vladimir S.Mikryukov Yongzhong Lu Yosuke Matsuda Yumiko Miyamoto Urm Institute of Ecology and Earth Sciences University of Tartu14A Ravila50411 TartuEstonia Natural History Museum University of Tartu46 Vanemuise Str51003 TartuEstonia Gothenburg Global biodiversity Centre Box 46140530 GothenburgSweden Department of biological and Environmental Sciences University of GothenburgGothenburgSweden Department of Soil and Environment Swedish University of Agricultural SciencesBox 701475007 UppsalaSweden Department of Forest Mycology and plant Pathology Swedish University of Agricultural SciencesBox 702675007 UppsalaSweden Section for Genetics and Evolutionary biology(EvoGene) Department of BiosciencesUniversity of OsloP.O.Box 1066BlindernNO-0316 OsloNorway University of Hawaiʻi at Mānoa 3190 Maile WaySt.John 102HonoluluHIUSA Department of biology University of CopenhagenUniversitetsparken 152100 CopenhagenØDenmark Purdue University Northwest WestvilleIN 46391USA Institute of Microbiology Czech Academy of SciencesVidenska 108314220 Praha 4Czech Republic GLObE Institute University of CopenhagenØster Farimagsgade 5KH7.2.321353 CopenhagenDenmark Dipartimento di Scienze della Vita e biologia dei Sistemi Universitàdi TorinoViale Mattioli 2510125 TorinoItaly Department of Organismic and Evolutionary biology and Farlow Library and Herbarium Harvard University22 Divinity AveCambridgeMA 02138USA blaihofstr.42 72074 TübingenGermany SYNLAb Estonia Veerenni 53aTallinn 11313Estonia Escuela de Tecnología Médica Universidad Santo TomásLos Carreras 753OsornoChile Centro de Genómica y bioinformática Universidad MayorCamino La Pirámide 5750HuechurabaSantiagoChile Norwegian Institute for Nature Research(NINA) Sognsveien 680855 OsloNorway School of Life Science and Technology University of Electronic Science and Technology of ChinaChengdu 611731People’s Republic of China Evolutionary biology Faculty of BiologyBiological and Chemical Research CentreUniversity of Warsawul.Zwirki i Wigury 10102-089 WarsawPoland Department of botany Swedish Museum of

The cryptic lifestyle of most fungi necessitates molecular identification of the guild in environmental *** the past decades,rapid development and affordability of molecular tools have tremendously improved insights of the fungal diversity in all ecosystems and ***,in spite of the progress of molecular methods,knowledge about functional properties of the fungal taxa is vague and interpretation of environmental studies in an ecologically meaningful manner remains *** order to facilitate functional assignments and ecological interpretation of environmental studies we introduce a user friendly traits and character database FungalTraits operating at genus and species hypothesis *** the information from previous efforts such as FUNGuild and FunFun together with involvement of expert knowledge,we reannotated 10,210 and 151 fungal and Stramenopila genera,*** resulted in a stand-alone spreadsheet dataset covering 17 lifestyle related traits of fungal and Stramenopila genera,designed for rapid functional assignments of environmental *** order to assign the trait states to fungal species hypotheses,the scientific community of experts manually categorised and assigned available trait information to 697,413 fungal ITS *** the basis of those sequences we were able to summarise trait and host information into 92,623 fungal species hypotheses at 1%dissimilarity threshold.

关键词： Fungal traits Trophic modes Function Guild bioinformatics High-throughput sequencing Community ecology

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Fungal diversity notes 111-252-taxonomic and phylogenetic contributions to fungal taxa

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Fungal Diversity 2015年第6期75卷 27-274页

作者： Hiran A.Ariyawansa Kevin D.Hyde Subashini C.jayasiri bart buyck K.W.Thilini Chethana Dong Qin Dai Yu Cheng Dai Dinushani A.Daranagama Ruvishika S.jayawardena Robert Lücking Masoomeh Ghobad-Nejhad Tuula Niskanen Kasun M.Thambugala Kerstin Voigt Rui Lin Zhao Guo-jie Li Mingkwan Doilom Saranyaphat boonmee Zhu L.Yang Qing Cai Yang-Yang Cui Ali H.bahkali jie Chen bao Kai Cui jia jia Chen Monika C.Dayarathne Asha j.Dissanayake Anusha H.Ekanayaka Akira Hashimoto Sinang Hongsanan E.b.Gareth jones Ellen Larsson Wen jing Li Qi-Rui Li jian Kui Liu Zong Long Luo Sajeewa S.N.Maharachchikumbura Ausana Mapook Eric H.C.McKenzie Chada Norphanphoun Sirinapa Konta Ka Lai Pang Rekhani H.Perera Rungtiwa Phookamsak Chayanard Phukhamsakda Umpava Pinruan Emile Randrianjohany Chonticha Singtripop Kazuaki Tanaka Cheng Ming Tian Saowaluck Tibpromma Mohamed A.Abdel-Wahab Dhanushka N.Wanasinghe Nalin N.Wijayawardene jin-Feng Zhang Huang Zhang Faten A.Abdel-Aziz Mats Wedin Martin Westberg joseph F.Ammirati Timur S.bulgakov Diogo X.Lima Tony M.Callaghan Philipp Callac Cheng-Hao Chang Luis F.Coca Manuela Dal-Forno Veronika Dollhofer Kateřina Fliegerová Katrin Greiner Gareth W.Griffith Hsiao-Man Ho Valerie Hofstetter Rajesh jeewon ji Chuan Kang Ting-Chi Wen Paul M.Kirk Ilkka Kytövuori james D.Lawrey jia Xing Hong Li Zou Yi Liu Xing Zhong Liu Kare Liimatainen H.Thorsten Lumbsch Misato Matsumura bibiana Moncada Salilaporn Nuankaew Sittiporn Parnmen AndréL.C.M.de Azevedo Santiago Sujinda Sommai Yu Song Carlos A.F.de Souza Cristina M.de Souza-Motta Hong Yan Su Satinee Suetrong Yong Wang Syuan-Fong Wei Ting Chi Wen Hai Sheng Yuan Li Wei Zhou Martina Réblová jacques Fournier Erio Camporesi j.jennifer Luangsa-ard Kanoksri Tasanathai Artit Khonsanit Donnaya Thanakitpipattana Sayanh Somrithipol Paul Diederich Ana M.Millanes Ralph S.Common Marc Stadler ji Ye Yan XingHong Li Hye Won Lee Thi T.T.Nguyen Hyang burm Lee Eliseo battistin Orlando Marsico Alfredo Vizzini jordi Vila Enrico Ercole Ursula Eberhardt Giampaolo Simonini Hua-An Wen Xin-Hua Chen Otto Mie Guizhou Key Laboratory of Agricultural biotechnology Guizhou Academy of Agricultural SciencesGuiyang 550006GuizhouChina Key Laboratory for plant Diversity and biogeography of East Asia Kunming Institute of BotanyChinese Academy of ScienceKunming 650201YunnanChina Centre of Excellence in Fungal Research Mae Fah Luang UniversityChiang Rai 57100Thailan Département Systématique et Evolution CP 39ISYEBUMR 7205 CNRS MNHN UPMC EPHEMuséum National d’Histoire Naturelle12 Rue BuffonF-75005 ParisFrance Institute of plant and Environment Protection Beijing Academy of Agriculture and Forestry SciencesNo.9 of Shu Guang Hua Yuan Zhong LuHaidian DistrictBeijing 10097China Microbial Drugs Helmholtz-Centre for Infection Research Inhoffenstrasse 738124 BraunschweigGermany Staatliches Museum für Naturkunde Stuttgart Rosenstein 1D-70191StuttgartGermany Institute of Microbiology Beijing Forestry UniversityPO Box 61Beijing 100083China State Key Laboratory of Mycology Institute of MicrobiologyChinese Academy of SciencesNo 31st West Beichen RoadChaoyang DistrictBeijing 100101China The Herbarium(ANDA) Universitas AndalasPadangSumatera Barat 25163Indonesia botanischer Garten&botanisches Museum berlin Freie Universität BerlinKönigin-Luise-Straße 6-814195 BerlinGermany Department of biotechnology Iranian Research Organization for Science and Technology(IROST)P.O.Box 3353-5111Tehran ***Iran jodrell Laboratory Royal Botanic GardensKew TW93DSUK Leibniz Institute for Natural Product Research and Infection biology Jena Microbial Resource CollectionAdolf-Reichwein-Strasse 2307745 JenaGermany Department of botany and Microbiology College of ScienceKing Saud UniversityP.O.Box:2455Riyadh 1145Saudi Arabia The United Graduate School of Agricultural Sciences Iwate University18-8 Ueda 3 ChomeMorioka 020-8550Japan Faculty of Agriculture and Life Sciences Hirosaki University3 Bunkyo-choHirosakiAomori 036-8561Japan Department of biological and Environmental Sciences University of GothenburgBox 461SE

This paper is a compilation of notes on 142 fungal taxa,including five new families,20 new genera,and 100 new species,representing a wide taxonomic and geographic *** new families,Ascocylindricaceae,Caryosporaceae and Wicklowiaceae(Ascomycota)are introduced based on their distinct lineages and unique *** new Dothideomycete genera Pseudomassariosphaeria(Amniculicolaceae),Heracleicola,Neodidymella and Pseudomicrosphaeriopsis(Didymellaceae),Pseudopithomyces(Didymosphaeriaceae),brunneoclavispora,Neolophiostoma and Sulcosporium(Halotthiaceae),Lophiohelichrysum(Lophiostomataceae),Galliicola,Populocrescentia and Vagicola(Phaeosphaeriaceae),Ascocylindrica(Ascocylindricaceae),Elongatopedicellata(Roussoellaceae),Pseudoasteromassaria(Latoruaceae)and Pseudomonodictys(Macrodiplodiopsidaceae)are *** newly described species of Dothideomycetes(Ascomycota)are Pseudomassariosphaeria bromicola(Amniculicolaceae),Flammeascoma lignicola(Anteagloniaceae),Ascocylindrica marina(Ascocylindricaceae),Lembosia xyliae(Asterinaceae),Diplodia crataegicola and Diplodia galiicola(botryosphaeriaceae),Caryospora aquatica(Caryosporaceae),Heracleicola premilcurensis and Neodidymella thailandicum(Didymellaceae),Pseudopithomyces palmicola(Didymosphaeriaceae),Floricola viticola(Floricolaceae),brunneoclavispora bambusae,Neolophiostoma pigmentatum and Sulcosporium thailandica(Halotthiaceae),Pseudoasteromassaria fagi(Latoruaceae),Keissleriella dactylidicola(Lentitheciaceae),Lophiohelichrysum helichrysi(Lophiostomataceae),Aquasubmersa japonica(Lophiotremataceae),Pseudomonodictys tectonae(Macrodiplodiopsidaceae),Microthyrium buxicola and Tumidispora shoreae(Microthyriaceae),Alloleptosphaeria clematidis,Allophaeosphaeria cytisi,Allophaeosphaeria subcylindrospora,Dematiopleospora luzulae,Entodesmium artemisiae,Galiicola pseudophaeosphaeria,Loratospora luzulae,Nodulosphaeria senecionis,Ophiosphaerella aquaticus,Populocrescentia forlicesenensis and Vagicola vagans(Phaeosphaeriaceae),Elon

关键词： Fungi Taxonomy New genus New species Phylogeny

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Osmotic Regulation and Viability during Storage of Potato Microtubers Obtained in Vitro

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journal of Environmental Science and Engineering(b) 2020年第3期9卷 108-113页

作者： j.Gerardo Ortiz-Montiel M.Teresa Ortiz-Melo Yolanda Pozos-Ruiz Rocio Reyero-Saavedra Manuel Mandujano-Piña Miguel Verastegui-Vidal plant Tissue Culture Laboratory Morphology and Function UnitFacultad de Estudios Superiores IztacalaUNAM.Los Reyes Iztacala 54090México

Dehydration,viability,proline,sucrose and glucose concentrations were evaluated on green and white microtubers during storage at two different *** 10 months at 4℃,the green and white microtubers showed shrinkage with a dry weight loss of 3.91%and 3.15%.both,the green and white microtubers at 4℃ presented an enhanced sprouting after *** 23℃,the green microtubers lost the lowest quantity in dry weight(0.8%)and white microtubers lost 2.2%.This behavior is possibly related to the increase in the thickness of the peridermis observed in green microtubers or to the osmotic regulation mediated principally by the observed concentrations of proline and glucose but not *** best storage conditions for potato microtubers obtained in vitro were at 4℃ for green or white microtubers for up to 10 months with little loss of viability.

关键词： Osmolite peridermis Solanum tuberosum suberization tuberization

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