全球首次完成楊樹全基因組測序

全球首次完成楊樹全基因組測序由美國能源部啟動(dòng)并實(shí)施的楊樹全基因組測序計(jì)劃已圓滿完成，并于2004年9月21日對公眾開放了全序列數(shù)據(jù)庫。南京林業(yè)大學(xué)科研人員尹佟明副教授參與了此項(xiàng)研究。楊樹基因組的新聞發(fā)布及慶祝會(huì)定于12月6日在美國加州舉行。該項(xiàng)研究可望使楊樹這一重要樹種的品種改良時(shí)間大大縮短，用區(qū)區(qū)幾十年跨越千年關(guān)。研究的完成，使楊樹成為繼擬南芥和水稻之后，第三個(gè)測定全序列的植物，并且是第一個(gè)測定全基因組序列的多年生木本植物。楊樹因此被廣泛接受為研究多年生植物基因組的模式物種，這使該項(xiàng)工作具有重大的科學(xué)意義。楊樹同時(shí)又是一種重要的工業(yè)用材樹種，楊樹全基因組計(jì)劃實(shí)施，將為生物能源的開發(fā)提供知識貯備，具有重要的實(shí)際應(yīng)用價(jià)值。目前，楊樹的改良還處在一種半野生的初級改良階段，在基因組研究的基礎(chǔ)上，通過群體和數(shù)量遺傳學(xué)的手段在楊樹屬不同樹種間開發(fā)有用等位基因，并通過遺傳工程的手段進(jìn)行基因重組，可望在幾十年的時(shí)間里完成一般作物幾千年的改良?xì)v程。楊樹全基因組全序列用“鳥槍法測定”，序列庫中共含有7，649，993個(gè)序列片段，去除葉綠體基因組的污染，測得的序列大約為8x基因組長度。目前對序列拼接的組裝已完成了483Mb,占楊樹基因組物理全長的90%以上，基本上覆蓋了楊樹基因組常染色體的大部分?；诨蛐酒蛦魏塑账岫鄳B(tài)性檢測技術(shù)，對小的序列拼接及序列間隙的填充工作正在進(jìn)行中，預(yù)期這部分工作將于明年完成。南京林業(yè)大學(xué)尹佟明副教授自2001年以來一直參與此項(xiàng)研究，對楊樹基因組的注釋工作將于今年12月初完成。國際楊樹基因組計(jì)劃協(xié)作組的總負(fù)責(zé)人杰瑞先生認(rèn)為，從世界范圍來看，楊樹在中國的林業(yè)生產(chǎn)中占有的比重是最大的，因此在楊樹基因組信息的應(yīng)用方面，中國在未來的研究中可能會(huì)居于世界前列。楊樹全基因組計(jì)劃的完成對我國從事林業(yè)及生物技術(shù)的科學(xué)家而言，提供了前所未有的機(jī)遇和挑戰(zhàn)。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