全球首次完成杨树全基因组测序

全球首次完成杨树全基因组测序由美国能源部启动并实施的杨树全基因组测序计划已圆满完成，并于2004年9月21日对公众开放了全序列数据库。南京林业大学科研人员尹佟明副教授参与了此项研究。杨树基因组的新闻发布及庆祝会定于12月6日在美国加州举行。该项研究可望使杨树这一重要树种的品种改良时间大大缩短，用区区几十年跨越千年关。研究的完成，使杨树成为继拟南芥和水稻之后，第三个测定全序列的植物，并且是第一个测定全基因组序列的多年生木本植物。杨树因此被广泛接受为研究多年生植物基因组的模式物种，这使该项工作具有重大的科学意义。杨树同时又是一种重要的工业用材树种，杨树全基因组计划实施，将为生物能源的开发提供知识贮备，具有重要的实际应用价值。目前，杨树的改良还处在一种半野生的初级改良阶段，在基因组研究的基础上，通过群体和数量遗传学的手段在杨树属不同树种间开发有用等位基因，并通过遗传工程的手段进行基因重组，可望在几十年的时间里完成一般作物几千年的改良历程。杨树全基因组全序列用“鸟枪法测定”，序列库中共含有7，649，993个序列片段，去除叶绿体基因组的污染，测得的序列大约为8x基因组长度。目前对序列拼接的组装已完成了483Mb,占杨树基因组物理全长的90%以上，基本上覆盖了杨树基因组常染色体的大部分。基于基因芯片和单核苷酸多态性检测技术，对小的序列拼接及序列间隙的填充工作正在进行中，预期这部分工作将于明年完成。南京林业大学尹佟明副教授自2001年以来一直参与此项研究，对杨树基因组的注释工作将于今年12月初完成。国际杨树基因组计划协作组的总负责人杰瑞先生认为，从世界范围来看，杨树在中国的林业生产中占有的比重是最大的，因此在杨树基因组信息的应用方面，中国在未来的研究中可能会居于世界前列。杨树全基因组计划的完成对我国从事林业及生物技术的科学家而言，提供了前所未有的机遇和挑战。Science15September2006:Vol.313.no.5793,pp.1596-1604DOI:10.1126/science.1128691RESEARCHARTICLESTheGenomeofBlackCottonwood,Populustrichocarpa(Torr.&Gray)G.A.Tuskan,1,3*S.DiFazio,1,4S.Jansson,5J.Bohlmann,6I.Grigoriev,9U.Sterck,10A.Aerts,9R.R.Bhalerao,5R.P.Bhalerao,12D.Blaudez,13W・Boerjan,10A.Brun,13A.Brunner,14V.Busov,15M.Campbell,16J.Carlson,17M.Chalot,13J.Chapman,9G.-L.Chen,2D.Cooper,6P.M.Coutinho,19J.Couturier,13S.Covert,20Q.Cronk,7R.Cunningham,1J.Davis,22S.Degroeve,10A.Dejardin,23C.dePamphilis,18J.Detter,9B.Dirks,24I.Dubchak,9,25S.Duplessis,13J.Ehlting,7B.Ellis,6K.Gendler,26D.Goodstein,9M.Gribskov,27J.Grimwood,28A.Groover,29L.Gunter,1B.Hamberger,7B.Heinze,30Y.Helariutta,12,31,33B.Henrissat,19D.Holligan,21R.Holt,11W.Huang,9N.Islam-Faridi,34S.Jones,11M.Jones-Rhoades,35R.Jorgensen,26C.Joshi,15J.Kangasjarvi,32J.Karlsson,5C.Kelleher,6R.Kirkpatrick,11M.Kirst,22A.

Kohler,13U.Kalluri,1F.Larimer,2J.Leebens-Mack,21J.-C.Leple,23P.Locascio,2Y.Lou,9S.Lucas,9F.Martin,13B.Montanini,13C.Napoli,26D.R.Nelson,36C.Nelson,37K.Nieminen,31O.Nilsson,12V.Pereda,13G.Peter,22R.Philippe,6G.Pilate,23A.Poliakov,25J.Razumovskaya,2P.Richardson,9C.Rinaldi,13K.Ritland,8P.Rouze,10D.Ryaboy,25J.Schmutz,28J.Schrader,38B.Segerman,5H.Shin,11A.Siddiqui,11F.S.Wessler,21G.Yang,21T.Yin,1C.Douglas,7M.Marra,11G.Sandberg,12Y.VandePeer,10D.Rokhsar9,24Wereportthedraftgenomeoftheblackcottonwoodtree,Populustrichocarpa.Integrationofshotgunsequenceassemblywithgeneticmappingenabledchromosome-scalereconstructionofthegenome.Morethan45,000putativeprotein-codinggeneswereidentified.Analysisoftheassembledgenomerevealedawhole-genomeduplicationevent;about8000pairsofduplicatedgenesfromthateventsurvivedinthePopulusgenome.Asecond,olderduplicationeventisindistinguishablycoincidentwiththedivergenceofthePopulusandArabidopsislineages.Nucleotidesubstitution,tandemgeneduplication,andgrosschromosomalrearrangementappeartoproceedsubstantiallymoreslowlyinPopulusthaninArabidopsis.Populushasmoreprotein-codinggenesthanArabidopsis,rangingonaveragefrom1.4to1.6putativePopulushomologsforeachArabidopsisgene.However,therelativefrequencyofproteindomainsinthetwogenomesissimilar.OverrepresentedexceptionsinPopulusincludegenesassociatedwithlignocellulosicwallbiosynthesis,meristemdevelopment,diseaseresistance,andmetabolitetransport.EnvironmentalSciencesDivision,OakRidgeNationalLaboratory,OakRidge,TN37831,USA.LifeSciencesDivision,OakRidgeNationalLaboratory,OakRidge,TN37831,USA.PlantSciencesDepartment,UniversityofTennessee,TN37996,USA.DepartmentofBiology,WestVirginiaUniversity,Morgantown,WV26506,USA.UmeaPlantScieneeCentre,DepartmentofPlantPhysiology,UmeaUniversity,SE-90187,Umea,Sweden.MichaelSmithLaboratories,UniversityofBritishColumbia,Vancouver,BCV6T1Z4,Canada.DepartmentofBotany,UniversityofBritishColumbia,Vancouver,BCV6T1Z4,Canada.DepartmentofForestSciences,UniversityofBritishColumbia,Vancouver,BCV6T1Z4,Canada.U.S.DepartmentofEnergy,JointGenomeInstitute,WalnutCreek,CA94598,USA.DepartmentofPlantSystemsBiology,FlandersInteruniversityInstituteforBiotechnology(VIB),GhentUniversity,B-9052Ghent,Belgium.GenomeSciencesCentre,100-570West7thAvenue,Vancouver,BCV5Z4S6,Canada.UmeaPlantScienceCentre,DepartmentofForestGeneticsandPlantPhysiology,SwedishUniversityofAgriculturalSciences,SE-90183Umea,Sweden.Tree-MicrobeInteractionsUnit,InstitutNationaldelaRechercheAgronomique(INRA)Universit©HenriPoinear©,INRA-Nancy,54280Champenoux,Franee.DepartmentofForestry,VirginiaPolytechnicInstituteandStateUniversity,Blacksburg,VA24061,USA.

BiotechnologyResearchCenter,SchoolofForestResourcesandEnvironmentalScience,MichiganTechnologicalUniversity,Houghton,MI49931,USA.DepartmentofCellandSystemsBiology,UniversityofToronto,25WillcocksStreet,Toronto,Ontario,M5S3B2Canada.SchoolofForestResourcesandHuckInstitutesoftheLifeSciences,ThePennsylvaniaStateUniversity,UniversityPark,PA16802,USA.DepartmentofBiology,InstituteofMolecularEvolutionaryGenetics,andHuckInstitutesofLifeSciences,ThePennsylvaniaStateUniversity,UniversityPark,PA16802,USA.ArchitectureetFonctiondesMacromoleculesBiologiques,UMR6098,CNRSandUniversitiesofAix-MarseilleIandII,case932,163avenuedeLuminy,13288Marseille,France.WarnellSchoolofForestResources,UniversityofGeorgia,Athens,GA30602,USA.DepartmentofPlantBiology,UniversityofGeorgia,Athens,GA30602,USA.SchoolofForestResourcesandConservation,GeneticsInstitute,andPlantMolecularandCellularBiologyProgram,UniversityofFlorida,Gainesville,FL32611,USA.INRA-Orleans,UnitofForestImprovement,GeneticsandPhysiology,45166OlivetCedex,France.CenterforIntegrativeGenomics,UniversityofCalifornia,Berkeley,CA94720,USA.GenomicsDivision,LawrenceBerkeleyNationalLaboratory,Berkeley,CA94720,USA.DepartmentofPlantSciences,UniversityofArizona,Tucson,AZ85721,USA.DepartmentofBiologicalSciences,PurdueUniversity,WestLafayette,IN47907,USA.TheStanfordHumanGenomeCenterandtheDepartmentofGenetics,StanfordUniversitySchoolofMedicine,PaloAlto,CA94305,USA.InstituteofForestGenetics,UnitedStatesDepartmentofAgriculture,ForestService,Davis,CA95616,USA.FederalResearchCentreforForests,Hauptstrasse7,A-1140Vienna,Austria.PlantMolecularBiologyLaboratory,InstituteofBiotechnology,UniversityofHelsinki,FI-00014Helsinki,Finland.DepartmentofBiologicalandEnvironmentalSciences,UniversityofHelsinki,FI-00014Helsinki,Finland.DepartmentofBiology,200014,UniversityofTurku,FI-20014Turku,Finland.SouthernInstituteofForestGenetics,UnitedStatesDepartmentofAgriculture,ForestServiceandDepartmentofForestScience,TexasA&M