植物比较基因组学课件

植物比较基因组学研究ComparativeGenomics陈明生中国科学院遗传发育所2006年10月20日植物比较基因组学研究陈明生1植物比较基因组学研究基因组物理图谱和遗传图谱基因组加倍禾本科作物的人工驯化(Domestication)植物比较基因组学研究2植物比较基因组学研究基因组物理图谱和遗传图谱基因组加倍禾本科作物的人工驯化(Domestication)植物比较基因组学研究3ImpactsofComparativeGenomicsImproveannotationofgenomesEvaluatetheextentofsyntenybetweenspeciesAnalyzegenesandgenomeevolutionHelpincloningimportantgenesUnderstandcomparativebiologyandbiodiversityImpactsofComparativeGenomic4FamilyPoaceae(Gramineae)SubfamilyPooideaeEhrhartoideaeChloridoideaePanicoideaeTriticum(wheat)Secale(rye)Hordeum(barley)Avena(oats)Oryza(rice)Zizania(wildrice)Eleusine(fingermillet)Pennisetum(pearlmillet)Setaria(foxtailmillet)Zea(maize)TripsacumSorghumSaccharum(sugarcane)GenusExampleFamilyPoaceae(Gramineae)Subfa5AhnandTanksley(1993)PNASAhnandTanksley(1993)PNAS6拟南芥

4800Mb

2800Mb

450Mb

140Mb

16000Mb植物基因组的大小

360Mb二穗短柄草水稻玉米大麦栽培小麦拟南芥4800Mb2800Mb450Mb7C-ValueParadox:VariationinGenomeSizeamongPlants

Species Mb/haploid pg/haploidArabidopsis 125

0.15Lily 100,000

100.00RepetitiveDNA重复序列C-ValueParadox:8C-ValueParadox:VariationinGenomeSizeamongPlants

Species Mb/haploid Barley 5000 DiploidWheat 16000 HexaploidPolyploidy 倍性C-ValueParadox:9C-ValueParadox:HumanGenome 3000MbFuguFish 400MbRepetitiveDNAIntronSizeC-ValueParadox:10123456781223456782AB122345678AncestralSegment122345678122348567CD123456781223456782AB122345678A11植物比较基因组学课件12BSh2A1-aPSnPPPmSnCCCCCCBBBBBBXBXBSSXBXSsBgH5kbSh2A1SorghumRiceSSh2Maize

A1-bA1BSh2A1-aPSnPPPmSnCCCCCCBBBBBBX13

Sh2A1-aA1-bSoloLTRTTTTTSSRX1S-1S-2S-3Sorghum5kb

Sh2A1

EStSSRTTDWTSn-1Sn-2RiceX2X1X2Sh2A1-aA1-bSoloLTRTT14Science274:765(1996)NestedRetrotransposonsintheMaizeGenomeScience274:765(1996)Nested15Theretrotransposonsinsertedintothemaizegenome2to6millionyearsago,whichexpandedthemaizegenomebyafactorof2.Retrotransposon反转座子Theretrotransposonsinserted16PNAS95:1975(1998)PNAS95:1975(1998)17PNAS96:7409(1999)ColinearityandExceptionsinAdh1regionofmaizeandsorghumPNAS96:7409(1999)Colinearit18BarleyandRiceColinearRegionsBarleyandRiceColinearRegio19Zeingenefamilyinmaize,riceandsorghumgenomesZeingenefamilyinmaize,ric20禾本科植物具有很强的同线性禾本科植物具有很强的同线性21植物比较基因组学课件22植物比较基因组学课件23植物比较基因组学课件24植物比较基因组学课件25植物比较基因组学课件26O.rufipogon

450

O.nivara448O.glaberrima

354

O.punctata423

O.minuta1124

O.officinalis

653

O.alta

1000

O.australiensis

960

O.coarctata

1283

O.brachyantha

338

O.ridleyi

1283

O.granulata

862

Mb野生稻的系统进化关系O.rufipogon 27植物比较基因组学课件28植物比较基因组学课件29植物比较基因组学课件30植物比较基因组学课件31植物比较基因组学课件32AAO.sativaO.glaberrimaO.barthiiO.glumaepatulaO.longstaminataO.meridionalisO.nivaraO.rufipogonO.spontaneaO.minutaO.punctataO.australiensisO.altaO.grandiglumisO.latifoliaO.schlechteriO.brachyanthaO.granulataO.meyerianaO.neocaledonicaO.longiglumisO.ridleyiBBCCBBCCCCDDO.punctataO.eichingeriO.officinalisO.rhizomatisEEFFGGHHJJHHKKAAO.sativaO.minutaO.austral33O.rufipogon

450

O.nivara448O.glaberrima

354

O.punctata423

O.minuta1124

O.officinalis

653

O.alta

1000

O.australiensis

960

O.coarctata

1283

O.brachyantha

338

O.ridleyi

1283

O.granulata

862

Mb野生稻的系统进化关系O.rufipogon 34O.rufipogon AA 抗白叶枯病，细胞质雄性不育，耐酸性硫酸 土O.nivara AA 抗草丛矮缩病O.meridionalis AA 耐旱O.longistaminata AA 抗白叶枯病O.glumaepatula AA 细胞质雄性不育O.barthii AA 抗黑尾叶蝉、白叶枯病O.punctata BB 抗褐飞虱、白背飞虱、黑尾叶蝉O.officinalis CC 抗褐飞虱、白背飞虱、黑尾叶蝉、白叶枯病O.rhizomatis CC 根状茎O.eichingeri CC 抗褐飞虱、白背飞虱、黑尾叶蝉、螟虫、白 叶枯病O.schweinfurthiana BBCC 抗褐飞虱、白背飞虱O.minuta BBCC 抗褐飞虱、白背飞虱、稻瘟病、纹枯病、白 叶枯病野生稻蕴含的优异基因资源O.rufipogon AA 抗白叶枯病，细胞质雄性35O.sativaO.glaberrimaO.punctataO.officinalisO.australiensisO.granulate野生稻的比较基因组学研究O.sativaO.glaberrimaO.punctat36japonicaAAindicaAAO.rufipogonAAO.nivaraAAO.glaberrimaAAjaponicaindicaO.rufipogonO.n37japonicaAAO.punctataBBjaponicaO.punctata38O.punctataBBO.minutaBBCC(BB)O.punctataO.minuta39O.minutaBBCC(CC)O.officinalisCCO.minutaO.officinalis40O.minutaBBCC(CC)O.minutaBBCC(BB)O.minutaO.minuta41O.punctataBBO.officinalisCCO.punctataO.officinalis42植物比较基因组学课件43植物比较基因组学课件44植物比较基因组学课件45植物比较基因组学课件46植物比较基因组学课件47ApplicationingenecloningGrassesasasinglegeneticsystemApplicationingenecloning48Theligularregionofnormalandlg1maizeleaves

A:Anormalleaf.b,blade;s,sheath;a,auricle;l,ligule;m,midrib.B:Alg1mutantleaf叶舌Theligularregionofnormala49Diversityofstructureatthesheath-bladeboundaryofleavesinthegrassfamily叶舌叶耳Diversityofstructureatthe50Syntenybetweenricechr04andmaizechr02and10Syntenybetweenricechr04and51AcommonsexdeterminationmechanismforpistilabortioninmaizeanditswildrelativeTripsacum鸭茅状摩擦禾

Inmaize,theprocessofpistilabortionrequiredtheactionofthetasselseed1andtasselseed2genes.Ts2hasbeenclonedandshowntoencodeashortchaindehydrogenase.Littleisknownaboutthegeneticsofunisexualityingamagrassexceptforaspontaneousrecessivemutationcalledgynomonoecioussexform1(gsf1).Thegsf1mutationblockspistilabortioninawaysimilartothets2mutantinmaize.Acommonsexdeterminationmec52TheinflorescencesofTripsacumWildtypegsf1mutantTheinflorescencesofTripsacu53Hordeum(barley)Secale(rye)Triticum(wheat)Avena(oats)OryzasativaZeamaysZealuxuriansZeadiploperennisTripsacumdactyloidesCoixlacryma-jobiSorghumbicolorPennisetumglaucumHordeum(barley)Secale(rye)Tr54植物比较基因组学课件55DeletionDeletion56Maize-gamagrasshybridsTs2orGsf1ts2/gsf1Maize-gamagrasshybridsTs2or57GAIGibberellinsgaiisasemidominantmutationofArabidopsis,whichconfersadarkgreen,dwarfphenotype.ThegaimutationisinsensitivetoexogenousGA,thereaffectsGAreceptionofsubsequentsignaltransduction.GAIGibberellins58植物比较基因组学课件59GAIMolecularcloningofGAIidentifiedanoveltranscriptionfactor.GAIisarepressorofGAresponses.Genes&Development11:3194(1997)GAIMolecularcloningofGAIid60“Greenrevolution”genesencodemutantgibberellinresponsemodulatorsNature400:256(1999)绿色革命“Greenrevolution”genesencod61植物比较基因组学课件62Nature400:256(1999)Nature400:256(1999)63植物比较基因组学研究基因组物理图谱和遗传图谱基因组加倍禾本科作物的人工驯化(Domestication)植物比较基因组学研究64GeneticMap遗传图谱Recombination1cM=1%recombinationOrderofmarkersGeneticMap遗传图谱653.8

SOG0510

6.2

SOG0091,SOG01757.7

SOG031110.8

SOG0087,SOG0509

14.6

SOG0483

24.6

SOG0059,SOG0060,SOG0177

30.0

SOG0417

34.6SOG0052,SOG0505

36.9

SOG0075,AEST157

39.2

SOG0108

40.8

SOG0060

46.2

SOG0034,SOG024556.2

SOG0094

75.4

SOG0154,SOG0273,SOG0274,SOG071085.4

SOG0462

95.4

SOG0004103.9

SOG0284

116.2

AEST31LinkagegroupB(Sorghum)CentromereTelomereTelomereShortArmLongArm3.8SOG05106.2SOG009166PhysicalMap物理图谱KbMbDNA在染色体上的排列PhysicalMap物理图谱67PhysicalMap/GeneticMapPhysicaldistance/GeneticdistanceKb/cMForexample,inrice1cM=250kbonaveragePhysicalMap/GeneticMap68植物比较基因组学课件69Recombination重组Hotspot:DistalendsofchromosomesGenicregions,suchasinbronzelocusofmaize14kb/cMRecombination重组70Recombination重组Coldspot:CentromericregionsHeterochromatinIntergenicregionsRecombination重组71Geneticdistancevs.Physicaldistance(cM/Mb)Physicaldistance(Mb)041.4CentromereGeneticdistancevs.Physical72基因组文库-LargeinsertgenomicDNAlibraryBACBacterialArtificialChromosomeYACYeastArtificialChromosomeTACTransformation-competentArtificialChromosomePACP1ArtificialChromosome构建物理图谱的第一步-基因组文库基因组文库-LargeinsertgenomicDN73BAC–BacterialArtificialChromosomeInsertSize100–300Kb稳定容易操作PhysicalMap:Rice,Human,ArabidopsisGenomeSequencingBAC–BacterialArtificialChr74BACcloningvectorBACcloningvector75Vectordigestion:HindIIIcompletedigestionGenomicDNApartialdigestion:HindIIIHindIIIrestrictionsite:5’-A^AGCTT-3’3’-TTCGA^A-5’46=4096bp100kb–300kbVectordigestion:HindIIIcom76植物比较基因组学课件77FingerprintingBACcloneDNAwasdigestedwithHindIII.Runthefragmentsonagrarosegels.ThefingerprintofeachclonewasformulatedwithIMAGEsoftware.WholegenomeassemblyusingFPC(FingerPrintedContig)software.构建物理图谱的第二步FingerprintingBACcloneDNAwa78Fingerprinting:High-throughputtechnologyDigesteveryclonewithHindIII:completedigestionFingerprinting:High-throughpu79植物比较基因组学课件80植物比较基因组学课件81Contig:叠加群Ricegenome:200-1000contigsHowtoorderthemonthechromosomes?Contig:叠加群82Integration:GeneticMapandPhysicalMapGeneticmap:DNAmarkersPhysicalMap:contigs构建物理图谱的第三步-物理图谱和遗传图谱的整合Integration:GeneticMapandP83

Markerhybridization

In

silicoanchoring:MonsantogenomesequenceSTCRGPgeneticmarkerGeneticmapPhysicalMapMarkerhybridizationMonsanto8419.9C47025.4G35943.2G31752.1C121158.1R171264.9S1501

103.7R2374116.5S2717118.9R1012123.5S1870124.8C137127.3

R1416129.3

C1282134.2

R758140.5

G370142.4R2125157.6

R2414167.2R503169.5

S10581176.3R117181.8C11212.2C307.0C16790.6C602**103.1G30273.1R596*123430456280781314151617181920212325262728293030191110124050.0C13577.9S91011.6S1088915.0S1400417.9G100319.0C42122.0G132725.8C293930.7C14931.7C36536.8C216842.4C98051.9Y2757L55.7S232858.4S10847A59.2C77781.7C49986.8R304189.9S107294.6S1112095.5

S1785101.2

S2287102.6R1381111.2L737118.1R3393126.4C92135.5C370143.6C1119150.5R3014A,152.7C379157.9C1470313236383940414243444748494575152525354555758333537461.1S1076013.3C72515.2S251420.3S276921.8S226424.7R321227.9R17628.5R247931.0C24536.1R201539.0R229341.9L76142.7S1380244.1C61446.9C60647.4S80447.7R411B50.8R315657.2R2906S61.9C58264.9R217069.7R298273.5C167785.2C8086.5R323990.3S146696.6S13580115.6C136120.4R2752A122.3R654127.4R2060137.6S770141.5G1015152.3C1484154.8R273164.4S15715960616865

66717273747576787980108828586876263647077835.1R18546.5S5925S6.8C567.1Y1065L10.1Y3635R10.7C94612.2E10326S16.7C70819.9S1118220.4R10729S52.6C97557.5C14062.1R9372.0R27872.3S1332274.5R89675.9R184976.8C79381.7R335183.0R278383.5R2370B94.4R73897.7S13536100.7R2785102.1R514107.9C600109.9R78111.3C55114.0R634114.3C1016122.9R1427123.8R2231128.5C1078990919697989910110210310410710510811011110967929394953.0C5974.6C56814.1S213617.9E1455S29.1S1244731.5R223232.5C61983S34.7E51274S37.2Y1060R40.6C24944.7R56945.8S1292848.3S1417749.4R56653.2C30954.6R205960.7C60228S66.1R331367.5R37270.5R143673.9R18878.2R272480.7R132087.4C62491.2L101394.5C12898.3C1402102.8C1018103.9L176107.4S2678110.4S10693112.4S974115.7S14121120.6S11036122.0C1230112113114118120122123124125126127561291311301321331151161171191281341351361371211234563.6S100689.8C108410.7R196211.5C76418.6L109232.7L68834.3Y2587L38.3C147840.2P12451.0S1114953.5R167964.9R53870.6R3273.2L24680.7R151981.8R295590.5R1559103.0R276105.1S1306S107.6L655113.4C1424115.6S14023117.0C69119.2R1782120.1R1479121.7R2614124.4S112391381391433241451461481491471501511521061531541551401411421442115697.1%90%86.9%96.1%93.1%92.4%19.9C47025.4G35943.2850.0E696S1.9C40013.4C39020.2R236724.9R228527.1R272335.7R297636.8R90238.8S209240.2R54445.4G101045.8R181348.8C48349.5S77950.5C110753.7C41158.4C62372.2E380280.4S1062286.7E2448S104.8S10655107.7C502108.2G56109.3S14003112.6S2314118.9C15392.2S4036S182184183188190191841921931951961971851861871891791940.0Y2769L2.1C11804S3.2S107094.4R116420.7R168730.6C145434.4S266035.2C117636.0S1392240.1C39741.0R4149.3R175154.2S207455.9S1974S62.4S180165.1R263868.2R156274.7C60979.1R333084.6C4790.4C50691.5R168392.1G29393.5S113020.8G361981992002042062072082092102112132012022032052120.0L7691.9S109063.9R230917.9C14821.8S3578S23.1S185626.1C96132.1C163341.6C67744.9R282548.8S1101453.3R187758.9C48871.4S1113183.0C23983.8C4056.3C4049.5S234811.4C1757S13.3S10020A15.2G112515.7S21221SA

17.1C51175SA2142152162222232242252272262282292172182192202302312322333640.0C5620.3G24A2.2C732A4.8R146628.6C47730.5R68232.1R231632.7L42833.4S271234.8G32054.3G4455.9R39156.2S790A57.3R189157.6C75464.2R72868.4G25779.9R334180.2C117285.7S72389.0S1092890.1C5090.6C691.4G40014.1C104B6.0S107928.1C2948.6R302310.3R291819.0S1031819.8C1350,S155920.3S10616A99.2G1465101.9G376104.9L833106.8C82110.1C950112.4Y2668LA112.9L1044116.2R1506117.9S10003234235236239242243245247248249250452372382402522542552562572582592612602412442462512537.1G19330.0R36739.7R337540.3S1052042.7E30009S47.0R61748.2S1090451.5R88751.8S1402555.1S13126S57.8S143661.6S82671.7C106073.0S254588.6C280895.1C8797.3C106999.7S8619.7C104A10.0R195726.0C13366.3R3266100.9L405103.1L714106.6R1684109.5C901262263264268270271272242732742752762652662672692772782792210.8S14082S1.9S141645.2C6158.8C2523S11.0C1023B24.2R56525.1R282926.0S1001235.7R240143.8E12196S44.4C67A46.5C63649.4Y2707L49.7Y2707R50.9C49251.2R178853.4C122655.9R43060.8S172370.8C90973.2C146775.6C100878.9R135781.4C43784.1R124592.0C141299.3R2658S102.3C1340105.7C596115.2C844117.4C924118.6C2131571581591631671681691701711731721751761781801811601611621641741776916516678910111286.6%93.5%94%93.8%94.7%83.3%0.0E696S1.9C4001386Geneticdistancevs.Physicaldistance(cM/Mb)Physicaldistance(Mb)041.4Geneticdistancevs.Physical87GenomeSequencingTwostrategies:Physicalmap-basedclone-by-cloneapproach:Human,Arabidopsis,RiceWholegenomeshotgunsequencing:Rice(Indica),Human,MouseGenomeSequencing88Wholegenomeshotgunsequencing:FastCheapIncompleteMissingimportantinformation,suchascentromere,repetitiveDNA,intergenicregions,etcWholegenomeshotgunsequenci89Physicalmap-basedclone-by-cloneapproach:MinimaltilingpathShotgunsequencingofeachBACcloneSlowExpensiveHighresolutionandaccurateContainingalmostallgenomeinformationPhysicalmap-basedclone-by-cl90BGIData10/2001,BeijingGenomicsInstitute(HuaDa)announcedadraftsequenceofindicavariety9311.Wholegenomeshotgunapproach.>120,000contigs.Freelyavailabletothepublic.PublishedonApril5th,2002issueofScience.BGIData10/2001,BeijingGenom91RiceGenomeSequencing1997,TheInternationalRiceGenomeSequencingProject(IRGSP):Japan,USA,China,Taiwan,Korea,India,France.Approach:Map-basedclone-by-clone(BAC/PAC-basedphysicalmap).Nature(2006)RiceGenomeSequencing1997,Th92植物比较基因组学课件93植物比较基因组学课件94植物比较基因组学研究基因组物理图谱和遗传图谱基因组加倍禾本科作物的人工驯化(Domestication)植物比较基因组学研究95AllplantsarepolyploidsAllopolyploidyordisomicpolyploidyCombingtwoormoredivergentgenomesWheatCottonCanolaA.suecicaTragopogonAutopolyploidyMultiplyingasinglegenomePotatoAlfalfaWatermelonBananaSugarcanePaleopolyploidyAncientor