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Molecular Plant 2022年第10期15卷 1506-1509页

作者： Zhi Luo Hui Xia Zhigui Bao Lei Wang Yu Feng Ting Zhang Jie Xiong Liang Chen Lijun Luo College of Plant Sciences&Technology Huazhong Agricultural UniversityWuhanChina Shanghai Agrobiological Gene Center ShanghaiChina Shenzhen Branch Guangdong Laboratory of Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization&Ecological Restoration and biodiversity Conservation Key Laboratory of Sichuan Province Chengdu Institute of BiologyChinese Academy of SciencesChengduChina Key Laboratory of Grain Crop Genetic Resources Evaluation and Utlization Ministry of Agriculture and Rural AffairsShanghaiChina Shanghai OE Biotech.Co. Ltd.ShanghaiChina School of Agriculture and Biology Shanghai Jiao Tong UniversityShanghaiChina

Dear Editor,Ensuring food security with finite resources and environmental impacts is a new challenge in sustainable agriculture(Yu et al.,2022).It is therefore essential to develop suitable rice varieties for resource-saving and environmentally friendly cultivation(Luo et al.,2019;Yu et al.,2022).Upland rice,which evolves many green characters for rice sustainable cultivation(e.g.,drought resistance,the usage efficiency of nitrate,the good capacity of direct seeding,etc.),is therefore an important germplasm in rice breeding(Luo et al.,2019).However,the origination and evolution of upland rice,as well as its green genetic resource,remain mysterious(Xia et al.,2019).

关键词： breeding drought upland

The evolving species concepts used for yeasts:from phenotypes and genomes to speciation networks

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Fungal Diversity 2021年第4期109卷 27-55页

作者： Teun Boekhout M.Catherine Aime Dominik Begerow Toni Gabaldón Joseph Heitman Martin Kemler Kantarawee Khayhan Marc-AndréLachance Edward J.Louis Sheng Sun Duong Vu Andrey Yurkov Westerdijk Fungal biodiversity Institute UtrechtThe Netherlands Institute of biodiversity and Ecosystem Dynamics(IBED) University of AmsterdamAmsterdamThe Netherlands Dept Botany and Plant Pathology College of AgriculturePurdue UniversityWest LafayetteIN 47907USA Evolution of Plants and Fungi Ruhr-University Bochum44801 BochumGermany Barcelona Supercomputing centre(BSC-CNS) Jordi Girona2908034 BarcelonaSpain Institute for Research in Biomedicine(IRB Barcelona) The Barcelona Institute of Science and TechnologyBaldiri Reixac1008028 BarcelonaSpain Catalan Institution for Research and Advanced Studies(ICREA) BarcelonaSpain Department of Molecular Genetics and Microbiology Duke University Medical CenterDurhamNC 27710USA Department of Microbiology and Parasitology Faculty of Medical SciencesUniversity of PhayaoPhayao 56000Thailand Department of Biology University of Western OntarioLondonON N6A 5B7Canada Department of Genetics and Genome Biology Genetic Architecture of Complex TraitsUniversity of LeicesterLeicester LE17RHUK German Collection of Microorganisms and Cell Cultures Leibniz Institute DSMZBrunswickGermany

Here we review how evolving species concepts have been applied to understand yeast ***,a phenotypic species concept was utilized taking into consideration morphological aspects of colonies and cells,and growth *** the biological species concept was added,which applied data from mating *** measurements of DNA similarity between isolates were an early measure that became more broadly applied with the advent of sequencing technology,leading to a sequence-based species concept using comparisons of parts of the ribosomal *** present phylogenetic species concepts that employ sequence data of rDNA and other genes are universally applied in fungal taxonomy,including yeasts,because various studies revealed a relatively good correlation between the biological species concept and sequence *** application of genome information is becoming increasingly common,and we strongly recommend the use of complete,rather than draft genomes to improve our understanding of species and their genome and genetic *** genomes allow in-depth comparisons on the evolvability of genomes and,consequently,of the species to which they *** seems a relatively common phenomenon and has been observed in all major fungal lineages that contain *** that hybrids may greatly differ in their post-hybridization *** in-depth studies,initially using some model species or complexes may shift the traditional species concept as isolated clusters of genetically compatible isolates to a cohesive speciation network in which such clusters are interconnected by genetic processes,such as hybridization.

关键词： Fungi Species concepts Comparative genomics Hybrids Nomenclature Taxonomy

Forecasting the number of species of asexually reproducing fungi(Ascomycota and Basidiomycota)

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Fungal Diversity 2022年第3期114卷 463-490页

作者： Nalin N.Wijayawardene Alan J.L.Phillips Diana Santos Pereira Dong-Qin Dai AndréAptroot Josiane S.Monteiro Irina S.Druzhinina Feng Cai Xinlei Fan Laura Selbmann Claudia Coleine Rafael F.Castañeda-Ruiz Martin Kukwa Adam Flakus Patricia Oliveira Fiuza Paul M.Kirk Kunhiraman C.Rajesh Kumar Ilesha S.leperuma Arachchi Nakarin Suwannarach Li-Zhou Tang Teun Boekhout Chen Shuhui Tan R.P.Prabath K.Jayasinghe Marco Thines centre for Yunnan Plateau Biological Resources Protection and Utilization College of Biological Resource and Food EngineeringQujing Normal UniversityQujing 655011YunnanPeople’s Republic of China Section of Genetics Institute for Research and Development in Health and Social CareNo:393/3Lily AvenueOff Robert Gunawardane MawathaBattaramulla 10120Sri Lanka Faculdade de Ciências Biosystems and Integrative Sciences Institute(BioISI)Universidade de LisboaCampo Grande1749-016 LisbonPortugal Laboratório de Botânica/Liquenologia Instituto de BiociênciasUniversidade Federal de Mato Grosso do SulAvenida Costa e Silva S/NBairro UniversitárioCampo GrandeMS CEP 79070-900Brazil Coordination of Botany Museu Paraense Emílio GoeldiBelémPA 66077830Brazil Fungal genomics Laboratory(FungiG) College of Resources and Environmental SciencesNanjing Agricultural UniversityWeigang 1Nanjing 210095JiangsuPeople’s Republic of China The Key Laboratory for Silviculture and Conservation of Ministry of Education Beijing Forestry UniversityBeijing 100083People’s Republic of China Department of Ecological and Biological Sciences University of TusciaViterboItaly Italian National Antarctic Museum(MNA) Mycological SectionGenoaItaly Alejandro de Humboldt’(INIFAT) Instituto de Investigaciones Fundamentales en AgriculturaTropicalSantiago de Las VegasHavanaCuba Department of Plant Taxonomy and Nature Conservation Faculty of BiologyUniversity of GdańskWita Stwosza 5980-308 GdańskPoland W.Szafer Institute of Botany Polish Academy of SciencesLubicz 4631-512 KrakowPoland Universidade Federal do Rio Grande do Norte(UFRN) Programa de Pós-Graduação em Sistemática e EvoluçãoCentro de BiociênciasCampus UniversitárioAv.Senador Salgado Filho3000Lagoa NovaNatalRN 59078-970Brazil biodiversity Informatics and Spatial Analysis Jodrell LaboratoryRoyal Botanic GardensKewRichmond TW93DSSurreyUK National Fungal Culture Collection of India(NFCCI) Biodiversity and Palaeobiology GroupMACS Agharkar Research InstituteG.G.

Asexually reproducing fungi play a significant role in essential processes in managed and wild ecosystems such as nutrients cycling and multitrophic interactions.A large number of such taxa are among the most notorious plant and animal *** addition,they have a key role in food production,biotechnology and *** without or rare sexual reproduction are distinguished based on their sporulating structures and conidiomata in traditional morphology-based *** number,variation and diversity of asexually reproducing taxa are insufficiently known,even though fungi capable of asexual reproduction may provide an untapped,rich biological resource for future ***,ca.30,000 asexual species belonging to ca.3800 genera have been reported(including 1388 coelomycetous and 2265 hyphomycetous genera).Recent reports(2017–2020)reiterate that the number of asexually producing fungi is higher than the number of frequently sexually-reproducing *** the advent of molecular tools and the abandonment of the dual nomenclature system for pleomorphic fungi,priority criteria were established and revisited in the latest outline of fungi and fungus-like ***,species numbers and taxonomic boundaries of pleomorphic taxa and their synanamorphs or synasexual morphs have yet to be *** number of species of speciose genera(***,Aspergillus,Cercospora,Fusarium,Phoma and Pseudocercospora),cryptic species,species of pleomorphic genera,less studied life modes(such as lichenicolous taxa,taxa from extreme environments)and species from biodiversity-rich areas still need evaluation to achieve more reliable estimates of their *** paper discusses the current knowledge on the matter,with diversity estimates,and potential obstacles in several chapters on(1)speciose genera;(2)pleomorphic genera;(3)cryptic species;(4)well-studied but insufficiently resolved taxa,*** inhabiting species,marine fungi,(5)less studied life modes,e.g.

关键词： Cryptic species DNA sequences Morphology Pleomorphism Speciose genera Species identificat

A near-complete assembly of the Houttuynia cordata genome provides insights into the regulatory mechanism of flavonoid biosynthesis in Yuxingcao

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Plant Communications 2024年第10期5卷 180-199页

作者： Zhengting Yang Fayin He Yingxiao Mai Sixian Fan Yin An Kun Li Fengqi Wu Ming Tang Hui Yu Jian-Xiang Liu Rui Xia Key Laboratory of State Forestry Administration on biodiversity Conservation in Karst Mountainous Areas of Southwestern China School of Life SciencesGuizhou Normal UniversityGuiyangGuizhou 550025China State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources College of HorticultureSouth China Agricultural UniversityGuangzhouGuangdong 510640China Lishui Innovation Center for Life and Health Zhejiang UniversityHangzhou 310027China

Houttuynia cordata,also known as Yuxingcao in Chinese,is a perennial herb in the Saururaceae *** is highly regarded for its medicinal properties,particularly in treating respiratory infections and inflammatory conditions,as well as boosting the human immune ***,a lack of genomic information has hindered research on the functional genomics and potential improvements of *** this study,we present a near-complete assembly of *** genome and investigate the biosynthetic pathway of flavonoids,specifically quercetin,using genomics,transcriptomics,and metabolomics *** genome of *** diverged from that of Saururus chinensis around 33.4 million years ago;it consists of 2.24 Gb with 76 chromosomes(4n=76)and has undergone three whole-genome duplication(WGD)*** WGDs played a crucial role in shaping the *** genome and influencing the gene families associated with its medicinal *** metabolomics and transcriptomics analyses,we identified key genes involved in the b-oxidation process for biosynthesis of houttuynin,one of the volatile oils responsible for the plant’s fishy *** addition,using the reference genome,we identified genes involved in flavonoid biosynthesis,particularly quercetin metabolism,in *** discovery has important implications for understanding the regulatory mechanisms that underlie production of active pharmaceutical ingredients in traditional Chinese ***,the high-quality genome assembly of *** serves as a valuable resource for future functional genomics research and provides a solid foundation for genetic improvement of *** for the benefit of human health.

关键词： Houttuynia cordata flavonoid biosynthesis genome assembly houttuynin quercetin whole-genome duplication

Systematics of the avian family Alaudidae using multilocus and genomic data

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Avian Research 2023年第2期14卷 137-152页

作者： Per Alstrom Zeinolabedin Mohammadi Erik D.Enbody Martin Irestedt Derek Engelbrecht Pierre-Andre Crochet Alban Guillaumet Loïs Rancilhac B.Irene Tieleman Urban Olsson Paul F.Donald Martin Stervander Animal Ecology Department of Ecology and GeneticsEvolutionary Biology CentreUppsala UniversityNorbyvagen 18DSE-75236UppsalaSweden Key Laboratory of Zoological Systematics and Evolution Institute of ZoologyChinese Academy of SciencesBeijing100101China Department of Biology Faculty of SciencesGolestan UniversityGorganGolestanIran Department of Medical Biochemistry and Microbiology Uppsala University75123UppsalaSweden Department of Biomolecular Engineering University of CaliforniaSanta Cruz95060Santa CruzCAUSA Department of Bioinformatics and Genetics Swedish Museum of Natural HistoryP.O.Box 50007SE-10405StockholmSweden Department of biodiversity University of LimpopoPrivate Bag X1106Sovenga0727South Africa CEFE CNRSUniv MontpellierEPHEIRDMontpellierFrance Department of Biological&Environmental Sciences Troy UniversityTroyAL36082USA Groningen Institute for Evolutionary Life Sciences University of GroningenNijenborgh 79747 AGGroningenthe Netherlands Department of Biological and Environmental Sciences University of GothenburgP.O.Box 463SE-40530GothenburgSweden Gothenburg Global biodiversity centre P.O.Box 461SE-40530GothenburgSweden BirdLife International The David Attenborough BuildingPembroke StCambridgeCB23QZUK Department of Zoology University of CambridgeDowning StreetCambridgeCB23EJUK Bird Group Natural History MuseumAkeman StreetTringHertfordshireHP236APUnited Kingdom

The family Alaudidae,larks,comprises 93-100 species(depending on taxonomy)that are widely distributed across Africa and Eurasia,with single species extending their ranges to North and northernmost South America and Australia.A decade-old molecular phylogeny,comprising~80%of the species,revealed multiple cases of parallel evolution and large variation in rates of morphological evolution,which had misled taxonomists into creating many non-monophyletic ***,we reconstruct the phylogeny of the larks,using a dataset covering one mitochondrial and 16 nuclear loci and comprising all except one of the currently recognised species as well as several recently proposed new species(in total 133 taxa;not all loci available for all species).We provide additional support using genome-wide markers to infer a genus-level phylogeny based on near-complete generic sampling(in total 51 samples of 44 taxa across 40 species).Our results confirm the previous findings of rampant morphological convergence and divergence,and reveal new cases of paraphyletic *** propose a new subfamily classification,and also that the genus Mirafra is divided into four genera to produce a more balanced generic classification of the *** study supports recently proposed species splits as well as some recent lumps,while also questioning some of the *** comprehensive phylogeny will form an important basis for future studies,such as comparative studies of lark natural history,ecology,evolution and conservation.

关键词： Phylogeny Phylogenomics Multispecies coalescent Lark Paraphyly Taxonomy Subfamily description

Zebrafish as a Model for Human Ciliopathies

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Journal of Genetics and genomics 2016年第3期43卷 107-120页

作者： Zhu Song Xiaoli Zhang Shuo Jia Pamela C.Yelick Chengtian Zhao Institute of Evolution & Marine biodiversity College of Marine Life Science Ocean University of China Department of Orthodontics Division of Craniofacial and Molecular Genetics Tufts University Laboratory for Marine Biology and Biotechnology Qingdao National Laboratory for Marine Science and Technology

Cilia, microtubule-based structures found on the surface of almost all vertebrate cells, play an array of diverse biological functions. Abnormal ciliary axonemal structure and function can result in a class of genetic disorders that are collectively termed ciliopathies. Model organisms, including Chlamydomonas reinhardtii and Caenorhabditis elegans have been widely used to study the complex genetic basis of ciliopathies. Here, we review the advantages of the zebrafish as a vertebrate model for human ciliopathies. We summarize the features of zebrafish cilia, and the major findings and contributions of the zebrafish model in recent studies of human ciliopathies. We also discuss the new genome editing approaches being efficiently used in zebrafish, and the exciting prospects of these approaches in modeling human ciliopathies.

关键词： Cilia Zebrafish Ciliopathy Disease model

Dedicated population genomics for the silent world： the specific questions of marine population genetics

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Current Zoology 2016年第6期62卷 545-550页

作者： Nicolas BIERNE Francois BONHOMME Sophie ARNAUD-HAOND Universite de Montpellier Montpellier France UMR 5554 UM - CNRS - IRD - EPHE Station Marine OREME Sete France CNRS - Institut des Sciences de I'Evolution Montpellier UMR 5554 UM - CNRS - IRD - EPHE Station Marine OREME Sete France Ifremer - MARine biodiversity Exploitation and Conservation UMR 9190 IRD - IFREMER - UM - CNRS Sete France

Introduction The life cycle of most marine species is characterized by high fecundity, dispersal during a planktonic larval phase and a sessile or sedentary adult phase with large census population size （Figure 1 ）.... 详细信息

关键词：种群遗传学基因组学海洋人群世界

Plant and fungal species interactions differ between aboveground and belowground habitats in mountain forests of eastern China

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Science China(Life Sciences) 2023年第5期66卷 1134-1150页

作者： Teng Yang Leho Tedersoo Pamela S.Soltis Douglas E.Soltis Miao Sun Yuying Ma Yingying Ni Xu Liu Xiao Fu Yu Shi Han-Yang Lin Yun-Peng Zhao Chengxin Fu Chuan-Chao Dai Jack A.Gilbert Haiyan Chu State Key Laboratory of Soil and Sustainable Agriculture Institute of Soil ScienceChinese Academy of SciencesNanjing 210008China University of Chinese Academy of Sciences Beijing 100049China Mycology and Microbiology Center University of TartuTartu 50409Estonia College of Science King Saud UniversityRiyadh 11451Saudi Arabia Florida Museum of Natural History University of FloridaGainesville 32611USA College of Horticulture and Forestry Sciences Huazhong Agricultural UniversityWuhan 430070China State Key Laboratory of Crop Stress Adaptation and Improvement School of Life SciencesHenan UniversityKaifeng 475004China Systematic&Evolutionary Botany and biodiversity Group MOE Key Laboratory of Biosystems Homeostasis&ProtectionCollege of Life SciencesZhejiang UniversityHangzhou 310058China Jiangsu Key Laboratory for Microbes and Functional genomics College of Life SciencesNanjing Normal UniversityNanjing 210003China Department of Pediatrics School of MedicineUniversity of CaliforniaSan DiegoLa Jolla 92093USA

Plant and fungal species interactions drive many essential ecosystem properties and processes;however,how these interactions differ between aboveground and belowground habitats remains unclear at large spatial ***,we surveyed 494 pairwise fungal communities in leaves and soils by Illumina sequencing,which were associated with 55 woody plant species across more than 2,000-km span of mountain forests in eastern *** relative contributions of plant,climate,soil and space to the variation of fungal communities were assessed,and the plant-fungus network topologies were *** phylogeny was the strongest predictor for fungal community composition in leaves,accounting for 19.1%of the *** soils,plant phylogeny,climatic factors and soil properties explained 9.2%,9.0%and 8.7%of the variation in soil fungal community,*** plant-fungus networks in leaves exhibited significantly higher specialization,modularity and robustness(resistance to node loss),but less complicated topology(e.g.,significantly lower linkage density and mean number of links)than those in *** addition,host/fungus preference combinations and key species,such as hubs and connectors,in bipartite networks differed strikingly between aboveground and belowground *** findings provide novel insights into cross-kingdom(plant-fungus)species co-occurrence at large spatial *** data further suggest that community shifts of trees due to climate change or human activities will impair aboveground and belowground forest fungal diversity in different ways.

关键词： bipartite network analyses foliar endophytic fungi modularity mountain forests plant phylogeny effect soil fungi specialization stability

Trends in yeast diversity discovery

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Fungal Diversity 2022年第3期114卷 491-537页

作者： Teun Boekhout Anthony S.Amend Fouad El Baidouri Toni Gabaldón József Geml Moritz Mittelbach Vincent Robert Chen Shuhui Tan Benedetta Turchetti Duong Vu Qi-Ming Wang Andrey Yurkov Westerdijk Institute of Fungal biodiversity Uppsalalaan 83584CT UtrechtThe Netherlands Institute of biodiversity and Ecosystems Dynamics(IBED) University of AmsterdamSciencepark 9041098 XH AmsterdamThe Netherlands School of Life Sciences University of Hawaii at Manoa2538 McCarthy MallEdmonson 216HonoluluHI 96822USA Barcelona Supercomputing centre(BSC-CNS) Jordi Girona2908034 BarcelonaSpain Institute for Research in Biomedicine(IRB Barcelona) The Barcelona Institute of Science and TechnologyBaldiri Reixac1008028 BarcelonaSpain Catalan Institution for Research and Advanced Studies(ICREA) BarcelonaSpain MTA-EKE Lendület Environmental Microbiome Research Group Eszterházy Károly UniversityLeányka u.6.3300 EgerHungary Senate Department for the Environment Transport and Climate ProtectionBerlinGermany The Yeasts Foundation UtrechtThe Netherlands Department of Agriculture Food and Environmental SciencesUniversity of PerugiaPerugiaItaly Industrial Yeasts Collection DBVPG University of PerugiaPerugiaItaly College of Life Sciences Institute of Life Sciences and Green DevelopmentHebei UniversityBaoding 071002HebeiChina Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures BrunswickGermany

Yeasts,usually defined as unicellular fungi,occur in various fungal ***,they are not a taxonomic unit,but rather represent a fungal lifestyle shared by several unrelated *** the discovery of new yeast species occurs at an increasing speed,at the current rate it will likely take hundreds of years,if ever,before they will all be *** parts of the earth,including many threatened habitats,remain unsampled for yeasts and many others are only superficially *** habitats,such as glaciers,are home to a specific community of cold-adapted yeasts,and,hence,there is some urgency to study such environments at locations where they might disappear soon due to anthropogenic climate *** same is true for yeast communities in various natural forests that are impacted by deforestation and forest *** countries of the so-called Global South have not been sampled for yeasts,despite their economic ***,extensive research activity in Asia,especially China,has yielded many taxonomic *** genomics stud-ies have demonstrated the presence of yeast species with a hybrid origin,many of them isolated from clinical or industrial ***-metabarcoding studies have demonstrated the prevalence,and in some cases dominance,of yeast species in soils and marine waters worldwide,including some surprising distributions,such as the unexpected and likely common presence of Malassezia yeasts in marine habitats.

关键词： Yeasts Ascomycota Basidiomycota Diversity CBD Nagoya protocol Soil DNA-metabarcoding Marine Malassezia Cold environments China

Genome sequencing and population genomics modeling provide insights into the local adaptation of weeping forsythia

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Horticulture Research 2020年第1期7卷 1173-1184页

作者： Lin-Feng Li Samuel ACushman Yan-Xia He Yong Li Innovation Platform of Molecular Biology College of ForestryHenan Agricultural UniversityZhengzhouChina Ministry of Education Key Laboratory for biodiversity Science and Ecological Engineering School of Life SciencesFudan UniversityShanghai 200438China U.S.Forest Service Rocky Mountain Research Station2500 S.Pine Knoll Dr.FlagstaffArizonaUSA School of Life Sciences Henan UniversityKaifengChina

Understanding the genetic basis underlying the local adaptation of nonmodel species is a fundamental goal in evolutionary *** this study,we explored the genetic mechanisms of the local adaptation of Forsythia suspensa using genome sequence and population genomics data obtained from specific-locus amplified fragment *** assembled a high-quality reference genome of weeping forsythia(Scaffold N50=7.3 Mb)using ultralong Nanopore ***,genome-wide comparative analysis was performed for 15 natural populations of weeping forsythia across its current distribution *** results revealed that candidate genes associated with local adaptation are functionally correlated with solar radiation,temperature and water variables across heterogeneous environmental *** particular,solar radiation during the period of fruit development and seed drying after ripening,cold,and drought significantly contributed to the adaptive differentiation of *** selection exerted by environmental factors contributed substantially to the population genetic structure of *** results supported the hypothesis that adaptive differentiation should be highly pronounced in the genes involved in signal crosstalk between different environmental *** population genomics study of *** provides insights into the fundamental genetic mechanisms of the local adaptation of plant species to climatic gradients.

关键词： local adaptation drought