2022年油菜基因组序列文件 .pdf

DOI: 10.1126/science.1253435, 950 (2014);345Science et al.Boulos Chalhouboilseed genomeBrassica napusEarly allopolyploid evolution in the post-Neolithic This copy is for your personal, non-commercial use only.clicking here.colleagues, clients, or customers by , you can order high-quality copies for yourIf you wish to distribute this article to othershere.following the guidelines can be obtained byPermission to republish or repurpose articles or portions of articles):August 22, 2014www.sciencemag.org (this information is current as ofThe following resources related to this article are available online athttp:/www.sciencemag.org/content/345/6199/950.full.htmlversion of this article at: including high-resolution figures, can be found in the onlineUpdated information and services, http:/www.sciencemag.org/content/suppl/2014/08/20/345.6199.950.DC1.html can be found at: Supporting Online Material http:/www.sciencemag.org/content/345/6199/950.full.html#ref-list-1, 51 of which can be accessed free:cites 138 articlesThis article http:/www.sciencemag.org/cgi/collection/geneticsGeneticshttp:/www.sciencemag.org/cgi/collection/botanyBotanysubject collections:This article appears in the following registered trademark of AAAS. is aScience2014 by the American Association for the Advancement of Science; all rights reserved. The title CopyrightAmerican Association for the Advancement of Science, 1200 New York Avenue NW, Washington, DC 20005. (print ISSN 0036-8075; online ISSN 1095-9203) is published weekly, except the last week in December, by theScience onAugust22,2014www.sciencemag.orgDownloadedfrom名师资料总结 - - -精品资料欢迎下载 - - - - - - - - - - - - - - - - - - 名师精心整理 - - - - - - - 第 1 页，共 5 页 - - - - - - - - - PLANTGENETICSEarly allopolyploid evolution in thepost-Neolithic Brassica napusoilseed genomeBoulosChalhoub,1* ? FranceDenoeud,2,3,4* ShengyiLiu,5* IsobelA. P. Parkin,6?HaibaoTang,7,8XiyinWang,9,10JulienChiquet,11HarryBelcram,1ChaoboTong,5BirgitSamans,12MargotCorr a,2CorinneDa Silva,2Jr myJust,1CyrilFalentin,13Chu ShinKoh,14IsabelleLe Clainche,1MariaBernard,2PascalBento,2BenjaminNoel,2KarineLabadie,2AdrianaAlberti,2MathieuCharles,15DominiqueArnaud,1HuiGuo,9ChristianDaviaud,16SalmanAlamery,17KamelJabbari,1,18MeixiaZhao,19PatrickP. Edger,20HoudaChelaifa,1DavidTack,21GillesLassalle,13ImenMestiri,1NicolasSchnel,13Marie-ChristineLe Paslier,15GuangyiFan,22VictorRenault,23PhilippeE. Bayer,17AgnieszkaA. Golicz,17SahanaManoli,17Tae-HoLee,9VinhHa DinhThi,1SmahaneChalabi,1QiongHu,5ChuchuanFan,24Reece Tollenaere,17YunhaiLu,1ChristopheBattail,2JinxiongShen,24ChristineH. D. Sidebottom,14XinfaWang,5Aurlie Canaguier,1Aurlie Chauveau,15Aurlie Brard,15Gwena?lleDeniot,13MeiGuan,25ZhongsongLiu,25FengmingSun,22YongPyo Lim,26EricLyons,27ChristopherD. Town,7IanBancroft,28XiaowuWang,29JinlingMeng,24JianxinMa,19J. ChrisPires,30GrahamJ. King,31DominiqueBrunel,15Rgine Delourme,13MichelRenard,13Jean-MarcAury,2KeithL.Adams,21JacquelineBatley,17,32Rod J. Snowdon,12JorgTost,16DavidEdwards,17,32? YongmingZhou,24? WeiHua,5?AndrewG. Sharpe,14? AndrewH. Paterson,9? ChunyunGuan,25? PatrickWincker2,3,4?Oilseedrape(BrassicanapusL.) was formed7500years ago by hybridizationbetweenB. rapa and B. oleracea , followedby chromosomedoubling,a processknownas allopolyploidy.Togetherwithmoreancientpolyploidizations,thisconferredan aggregate72 genomemultiplicationsincethe originof angiospermsand high gene content.We examinedtheB. napus genomeand the consequencesof its recentduplication.The constituentAnand Cnsubgenomesare engagedin subtlestructural,functional,and epigeneticcross-talk,withabundanthomeologousexchanges.Incipientgene loss and expressiondivergencehave begun.Selectionin B. napusoilseedtypeshas acceleratedthe loss of glucosinolategenes, whilepreservingexpansionof oil biosynthesisgenes. These processesprovideinsightsintoallopolyploidevolutionand its relationshipwithcropdomesticationand improvement.The Brassicaceaeare alargeeudicotfamily(1)and includethe modelplantArabi-dopsis thaliana.Brassicashaveapropen-sity for genomeduplications(Fig.1) andgenomemergers(2).Theyare majorcon-tributorstothe humandiet and wereamongthe earliestcultigens(3).B. napus(genomeAnAnCnCn)was formedbyrecentallopolyploidybetweenancestorsofB.oleracea(Mediterraneancabbage,genomeCoCo)andB. rapa(Asiancabbageorturnip,genomeArAr)and is polyphyletic(2,4), withspontaneousformationregardedby Darwinas an exampleofunconsciousselection(5).CultivationbeganinEuropeduringthe MiddleAgesand spreadworld-wide.Diversifyingselectiongaverise to oilseedrape(canola),rutabaga,fodder rape,andkale mor-photypesgrownfor oil, fodder,and food (4,6).Thehomozygous B. napusgenomeof Euro-peanwinteroilseedcultivarDarmor-bzh wasassembledwith long-read700basepairs(bp)454 GS-FLX+Titanium(Roche,Basel,Switzerland)and Sangersequence(tablesS1 to S5 and figs.S1 toS3) (7).Correctionand gap fillingused79 Gb ofIllumina(SanDiego,CA)HiSeq sequence.Afinalassemblyof 849.7Mb was obtainedwith SOAP(8)and Newbler(Roche),with 89%nongappedse-quence(tablesS2 and S3).Uniquemappingof5 nonassembled454 sequencesfromB.rapa(Chiifu)orB. oleracea(TO1000)assignedmostof the 20,702B. napusscaffoldsto eitherthe An(8294)or the Cn(9984)subgenomes(tablesS4 andS5 and fig. S3).The assemblycovers79%of the1130-Mbgenomeand includes95.6%ofBrassicaex-pressedsequencetags(ESTs)(7). A single-nucleotidepolymorphism(SNP)map (tablesS6 toS9 andfigs.S4 to S8) geneticallyanchored712.3Mb (84%)of the genomeassembly,yieldingpseudomoleculesforthe19 chromosomes(tableS10).The assembledCnsubgenome(525.8Mb) islargerthan the Ansubgenome(314.2Mb), con-sistentwith the relativesizesof the assembledCogenomeofB. oleracea(540 Mb, 85%of the630-Mbgenome)andtheArgenomeofB. rapa(312Mb, 59%of the 530-Mbgenome)(911). TheB. napusassemblycontains34.8%transposableelements(TEs),lessthan the 40%estimatedfromraw reads(tablesS11to S14)(7),with asymmetricdistributioninthe Anand Cnsubgenomes(tableS12)as in the progenitorgenomes(911). A smallTEfractionhas proliferatedsinceB. napusseparatedfromits progenitors(7), at lowerratesin theB.napussubgenomesthan the correspondingprogenitorgenomes(tableS14and figs. S9 andS10).TheB. napusgenomecontains101,040genemodelsestimatedfrom35.5Gb of RNAsequencing(RNA-seq)data (tablesS15and S16)incombina-tion with ab initiogeneprediction,proteinand ESTalignments,and transposonmasking(7). Of these,91,167wereconfirmedby matcheswithB. rapaand/orB.oleraceapredictedproteomes.Genesareabundantindistaleuchromatinbut sparsenearcentromericheterochromatin(Fig. 2). RNA-seqdatarevealedalternativesplicingin 48%of genes,with frequentintronretention(62%)and rare exonskipping(3%)(tablesS17and S18and fig. S11).TheB.napusAnand Cnsubgenomesare largelycolineartothe correspondingdiploidArand Co95022 AUGUST2014? VOL345ISSUE6199sciencemag.orgSCIENCE1Institut NationaldeRechercheAgronomique(INRA)/UniversitdEvryVal d Essone,Unit de RechercheenG nomiqueVgtale, UMR1165, Organizationand Evolutionof Plant Genomes,2 rue GastonCrmieux, 91057Evry,France.2Commissariat lEnergieAtomique(CEA),Institutde G nomique(IG), Genoscope,BP5706,91057Evry,France.3UniversitdEvry Vald Essone,UMR8030, CP5706,Evry,France.4CentreNationalde RechercheScientifique(CNRS),UMR8030, CP5706,Evry,France.5KeyLaboratoryofBiology and GeneticImprovementof OilCrops,Ministry ofAgriculture of People s Republicof China,Oil CropsResearchInstitute, ChineseAcademyof Agricultural Sciences,Wuhan430062, China.6Agriculture and Agri-FoodCanada,107SciencePlace,Saskatoon,SKS7N0X2, Canada.7J. CraigVenterInstitute, Rockville,MD20850, USA.8CenterforGenomicsand Biotechnology,FujianAgriculture andForestry,University,Fuzhou350002, FujianProvince,China.9PlantGenomeMappingLaboratory,University of Georgia,Athens, GA30602, USA.10Centerof GenomicsandComputationalBiology,Schoolof Life Sciences,HebeiUnitedUniversity,Tangshan,Hebei063000, China.11Laboratoirede Mathmatiques et Mod lisationdEvry UMR8071CNRS/Universit dEvry val dEssonne USCINRA,Evry,France.12Departmentof PlantBreeding,ResearchCenterforBiosystems,Land UseandNutrition, Justus Liebig University,Heinrich-Buff-Ring26-32,35392 Giessen,Germany.13INRA,Institut de G ntique, Environnementet ProtectiondesPlantes(IGEPP)UMR1349,BP35327,35653 LeRheuCedex,France.14NationalResearchCouncilCanada,110GymnasiumPlace,Saskatoon,SKS7N0W9,Canada.15INRA,EtudeduPolymorphismedesG nomes Vgtaux, US1279,CentreNational deG notypage,CEA IG,2 rue GastonCrmieux,91057Evry,France.16Laboratoryfor EpigeneticsandEnvironment,CentreNationaldeG notypage,CEA IG,2 rueGastonCrmieux, 91000 Evry,France.17AustralianCentrefor Plant FunctionalGenomics,SchoolofAgriculture andFood Sciences,Universityof Queensland,St. Lucia,QLD4072, Australia.18CologneCenterfor Genomics,UniversityofCologne,Weyertal115b,50931 K?ln,Germany.19Departmentof Agronomy,Purdue University,WSLRBuilding B018,WestLafayette,IN 47907, USA.20Departmentof Plant andMicrobial Biology,University of California,Berkeley,CA94720, USA.21Departmentof Botany, University of BritishColumbia,Vancouver,BC,Canada.22BeijingGenomeInstitute Shenzhen,Shenzhen518083,China.23FondationJean Dausset Centred tudedu PolymorphismeHumain,27 rue Juliette Dodu,75010Paris, France.24National KeyLaboratory of CropGeneticImprovement,HuazhongAgricultural University,Wuhan430070, China.25CollegeofAgronomy,HunanAgriculturalUniversity,Changsha410128,China.26MolecularGeneticsand GenomicsLaboratory,Departmentof Horticulture, ChungnamNationalUniversity,Daejeon-305764,SouthKorea.27Schoolof Plant Sciences,iPlant Collaborative,University of Arizona,Tucson,AZ,USA.28Departmentof Biology,Universityof York,Wentworth Way,Heslington,YorkYO105DD,UK.29Institute of Vegetablesand Flowers,ChineseAcademyofAgricultural Sciences,Beijing, China.30Divisionof BiologicalSciences,University ofMissouri, Columbia,MO 65211,USA.31SouthernCrossPlantScience,SouthernCrossUniversity,Lismore, NSW2480,Australia.32Schoolof PlantBiology,UniversityofWesternAustralia,WA6009, Australia.*These authors contributed equally to this work. ?Correspondingauthor. E-mail: chalhoubevry.inra.fr (B.C.); other e-mailaddressees are given in the supplementary materials.RESEARCH|REPORTS名师资料总结 - - -精品资料欢迎下载 - - - - - - - - - - - - - - - - - - 名师精心整理 - - - - - - - 第 2 页，共 5 页 - - - - - - - - - genomes, with asymmetricgenedistribution (42,320and 48,847,respectively)and 93% of the diploidgene space in orthologousblocks (fig. S12)(7).Weidentified 34,255and 38,661orthologous genepairs between the Anand Cnsubgenomes andtheir respective progenitorgenomes (fig. S13).Comparison ofAn-Arand Cn-Coorthologous genepairs suggested a divergence 7500 to 12,500years ago (fig. S14),indicatingformationof B.napus after this date. Synteny with Arabidopsis(table S19)confirmed the triplicatedmesoploidstructure (9 11 ) of the Anand Cnsubgenomes,with the recent allopolyploidyconferring on B.napus an aggregate 72genome multiplicationsince the origin of angiosperms(Fig. 1)(7).SCIENCEsciencemag.org22 AUGUST2014 ? VOL345ISSUE6199951Fig. 1.Recurrentgenome duplicationsin B. napus .Genomic alignments between the basal angiospermAmborella trichopoda(24), the basal eudicot Vitisvinifera (25), and the model crucifer A. thaliana , aswell as B. rapa (9), B. oleracea (10 , 11 ), and B. napus,are shown. A typical ancestral region in Amborellais expected to match up to 72 regions in B. napus(69 were detectedfor this specificregion).Graywedgesin thebackgroundhighlightconservedsyntenyblocks with more than 10 gene pairs.Fig. 2. The genome of the B. napus oilseed cul-tivar Darmor- bzh .The genome comprises 9 chro-mosomes belonging to the Cnsubgenomeand 10to the Ansubgenome,scaled on the basis of theirassembled lengths. Tracks displayed are ( A) genedensity (nonoverlapping,window size = 100 kb forall tracks). Positions showing loss of one or moreconsecutive genes are displayed (triangles)alongwith homeologous exchanges, detected as missinggenomic segments that have been replaced by du-plicates of correspondinghomeologoussegments(red rectangles).(B and C) Transcriptionstatesestimated by RNA-seq in leaves (B) and roots (C)(in nonoverlapping 100-kb windows). (D) DNA trans-poson density. (E) Retrotransposon density. (F) CpGmethylationin leaves (green) and roots (brown);both curves areoverlapping.(G) Centromeric repeats(densities exaggerated for visual clarity). Homeol-ogous relationshipsbetween Anand Cnchromo-somes are displayed with connecting lines coloredaccording to the Cnchromosomes.RESEARCH|REPORTS名师资料总结 - - -精品资料欢迎下载 - - - - - - - - - - - - - - - - - - 名师精心整理 - - - - - - - 第 3 页，共 5 页 - - - - - - - - - Most orthologousgene pairs in B. rapa andB.oleracea remain ashomeologous pairs in B.napus (tables S19to S25and figs. S12to S17)(7).DNA sequenceanalysis (7) confirmed the loss of112Anand 91Cngenesin B. napus Darmor-bzh(tablesS21to S26),2.6 times higher than the 41and37geneslost in B.rapa Chiifu and B.oleracea TO1000 respectively (tables S26and S27;c2testP = 5.3 10 14). Further analyses of a Brassicadiversity set showed that 47% of Darmor- bzhAnand 31%of Cndeleted genes were also de-leted in at leastone additional progenitor geno-type (tables S28 and S29),indicating that theirdeletion probably predated allopolyploidizationof B. napus (7). A high proportion (27% to 54%)of the remaining Darmor-bzh deleted geneswerealso deleted from diverse B. napus genotypes(tables S28and S29).Homeologousexchanges(HEs),including cross-overs and noncrossovers, are frequent betweenB. napus subgenomes and range in size fromlarge segments to single SNPs(7) (Fig. 3, figs. S17to S24,and tables S30to S39).At the chromosome segment level, HEs arecharacterized by replacement of a chromosomalregion with a duplicatedcopy from the corre-sponding homeologous subgenome (7). We iden-tified 17HEs, 14Cnto Anand 3 AntoCn(Fig.3,fig.S19,and tables S30 and S31).Sequencesfromseven diverse B. napus genotypes revealed bothshared and specific segmental HEs. These are ofvarying sizes and are most frequentbetweenchromosomesAn1-Cn1, An2-Cn2, and An9-Cn9(tableS32, Fig. 3, and fig. S19). Larger HEsfound in the synthetic B. napus H165 affect, forexample, most of chromosomesAn1-Cn1 andAn2-Cn2 (Fig. 3 and fig. S19). Functionalan-notationof genes withinHEs suggests somehave experienced selection, contributingto the95222 AUGUST2014? VOL345 ISSUE6199sciencemag.orgSCIENCEFig. 3. HEs betweenB. napus chromosomesAn2 and Cn2. (A) Coveragedepth obtained along the An2 chromosomeafter mappingIllumina sequencereads from seven natural and one resynthesized B. napus genotypes (named onthe right) to the reference genome of B. napus Darmor- bzh. (B and C) Coveragedepth obtained for Ar2 and Co2 chromosomes, respectively, after mapping 21genome-equivalents of Illumina sequence reads from B. napus Darmor -bzh onthe B. rapa and B. oleracea genome assemblies concatenated together. (D) Simi-lar to (A), where the Cn2 chromosome of Darmor-bzh is displayed. SegmentalHEs are revealed based on sequence read coverage analysis, where a duplication(red) is revealed by significantly greater coverage for a given segment t