植物比較基因組學(xué)課件

植物比較基因組學(xué)研究ComparativeGenomics陳明生中國科學(xué)院遺傳發(fā)育所2006年10月20日植物比較基因組學(xué)研究陳明生1植物比較基因組學(xué)研究基因組物理圖譜和遺傳圖譜基因組加倍禾本科作物的人工馴化(Domestication)植物比較基因組學(xué)研究2植物比較基因組學(xué)研究基因組物理圖譜和遺傳圖譜基因組加倍禾本科作物的人工馴化(Domestication)植物比較基因組學(xué)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擬南芥

4800Mb

2800Mb

450Mb

140Mb

16000Mb植物基因組的大小

360Mb二穗短柄草水稻玉米大麥栽培小麥擬南芥4800Mb2800Mb450Mb7C-ValueParadox:VariationinGenomeSizeamongPlants

Species Mb/haploid pg/haploidArabidopsis 125

0.15Lily 100,000

100.00RepetitiveDNA重復(fù)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植物比較基因組學(xué)課件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反轉(zhuǎn)座子Theretrotransposonsinserted16PNAS95:1975(1998)PNAS95:1975(1998)17PNAS96:7409(1999)ColinearityandExceptionsinAdh1regionofmaizeandsorghumPNAS96:7409(1999)Colinearit18BarleyandRiceColinearRegionsBarleyandRiceColinearRegio19Zeingenefamilyinmaize,riceandsorghumgenomesZeingenefamilyinmaize,ric20禾本科植物具有很強的同線性禾本科植物具有很強的同線性21植物比較基因組學(xué)課件22植物比較基因組學(xué)課件23植物比較基因組學(xué)課件24植物比較基因組學(xué)課件25植物比較基因組學(xué)課件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野生稻的系統(tǒng)進化關(guān)系O.rufipogon 27植物比較基因組學(xué)課件28植物比較基因組學(xué)課件29植物比較基因組學(xué)課件30植物比較基因組學(xué)課件31植物比較基因組學(xué)課件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野生稻的系統(tǒng)進化關(guān)系O.rufipogon 34O.rufipogon AA 抗白葉枯病，細胞質(zhì)雄性不育，耐酸性硫酸 土O.nivara AA 抗草叢矮縮病O.meridionalis AA 耐旱O.longistaminata AA 抗白葉枯病O.glumaepatula AA 細胞質(zhì)雄性不育O.barthii AA 抗黑尾葉蟬、白葉枯病O.punctata BB 抗褐飛虱、白背飛虱、黑尾葉蟬O.officinalis CC 抗褐飛虱、白背飛虱、黑尾葉蟬、白葉枯病O.rhizomatis CC 根狀莖O.eichingeri CC 抗褐飛虱、白背飛虱、黑尾葉蟬、螟蟲、白 葉枯病O.schweinfurthiana BBCC 抗褐飛虱、白背飛虱O.minuta BBCC 抗褐飛虱、白背飛虱、稻瘟病、紋枯病、白 葉枯病野生稻蘊含的優(yōu)異基因資源O.rufipogon AA 抗白葉枯病，細胞質(zhì)雄性35O.sativaO.glaberrimaO.punctataO.officinalisO.australiensisO.granulate野生稻的比較基因組學(xué)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植物比較基因組學(xué)課件43植物比較基因組學(xué)課件44植物比較基因組學(xué)課件45植物比較基因組學(xué)課件46植物比較基因組學(xué)課件47ApplicationingenecloningGrassesasasinglegeneticsystemApplicationingenecloning48Theligularregionofnormalandlg1maizeleaves

A:Anormalleaf.b,blade;s,sheath;a,auricle;l,ligule;m,midrib.B:Alg1mutantleaf葉舌Theligularregionofnormala49Diversityofstructureatthesheath-bladeboundaryofleavesinthegrassfamily葉舌葉耳Diversityofstructureatthe50Syntenybetweenricechr04andmaizechr02and10Syntenybetweenricechr04and51AcommonsexdeterminationmechanismforpistilabortioninmaizeanditswildrelativeTripsacum鴨茅狀摩擦禾

Inmaize,theprocessofpistilabortionrequiredtheactionofthetasselseed1andtasselseed2genes.Ts2hasbeenclonedandshowntoencodeashortchaindehydrogenase.Littleisknownaboutthegeneticsofunisexualityingamagrassexceptforaspontaneousrecessivemutationcalledgynomonoecioussexform1(gsf1).Thegsf1mutationblockspistilabortioninawaysimilartothets2mutantinmaize.Acommonsexdeterminationmec52TheinflorescencesofTripsacumWildtypegsf1mutantTheinflorescencesofTripsacu53Hordeum(barley)Secale(rye)Triticum(wheat)Avena(oats)OryzasativaZeamaysZealuxuriansZeadiploperennisTripsacumdactyloidesCoixlacryma-jobiSorghumbicolorPennisetumglaucumHordeum(barley)Secale(rye)Tr54植物比較基因組學(xué)課件55DeletionDeletion56Maize-gamagrasshybridsTs2orGsf1ts2/gsf1Maize-gamagrasshybridsTs2or57GAIGibberellinsgaiisasemidominantmutationofArabidopsis,whichconfersadarkgreen,dwarfphenotype.ThegaimutationisinsensitivetoexogenousGA,thereaffectsGAreceptionofsubsequentsignaltransduction.GAIGibberellins58植物比較基因組學(xué)課件59GAIMolecularcloningofGAIidentifiedanoveltranscriptionfactor.GAIisarepressorofGAresponses.Genes&Development11:3194(1997)GAIMolecularcloningofGAIid60“Greenrevolution”genesencodemutantgibberellinresponsemodulatorsNature400:256(1999)綠色革命“Greenrevolution”genesencod61植物比較基因組學(xué)課件62Nature400:256(1999)Nature400:256(1999)63植物比較基因組學(xué)研究基因組物理圖譜和遺傳圖譜基因組加倍禾本科作物的人工馴化(Domestication)植物比較基因組學(xué)研究64GeneticMap遺傳圖譜Recombination1cM=1%recombinationOrderofmarkersGeneticMap遺傳圖譜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物理圖譜KbMbDNA在染色體上的排列PhysicalMap物理圖譜67PhysicalMap/GeneticMapPhysicaldistance/GeneticdistanceKb/cMForexample,inrice1cM=250kbonaveragePhysicalMap/GeneticMap68植物比較基因組學(xué)課件69Recombination重組Hotspot:DistalendsofchromosomesGenicregions,suchasinbronzelocusofmaize14kb/cMRecombination重組70Recombination重組Coldspot:CentromericregionsHeterochromatinIntergenicregionsRecombination重組71Geneticdistancevs.Physicaldistance(cM/Mb)Physicaldistance(Mb)041.4CentromereGeneticdistancevs.Physical72基因組文庫-LargeinsertgenomicDNAlibraryBACBacterialArtificialChromosomeYACYeastArtificialChromosomeTACTransformation-competentArtificialChromosomePACP1ArtificialChromosome構(gòu)建物理圖譜的第一步-基因組文庫基因組文庫-LargeinsertgenomicDN73BAC–BacterialArtificialChromosomeInsertSize100–300Kb穩(wěn)定容易操作PhysicalMap:Rice,Human,ArabidopsisGenomeSequencingBAC–BacterialArtificialChr74BACcloningvectorBACcloningvector75Vectordigestion:HindIIIcompletedigestionGenomicDNApartialdigestion:HindIIIHindIIIrestrictionsite:5’-A^AGCTT-3’3’-TTCGA^A-5’46=4096bp100kb–300kbVectordigestion:HindIIIcom76植物比較基因組學(xué)課件77FingerprintingBACcloneDNAwasdigestedwithHindIII.Runthefragmentsonagrarosegels.ThefingerprintofeachclonewasformulatedwithIMAGEsoftware.WholegenomeassemblyusingFPC(FingerPrintedContig)software.構(gòu)建物理圖譜的第二步FingerprintingBACcloneDNAwa78Fingerprinting:High-throughputtechnologyDigesteveryclonewithHindIII:completedigestionFingerprinting:High-throughpu79植物比較基因組學(xué)課件80植物比較基因組學(xué)課件81Contig:疊加群Ricegenome:200-1000contigsHowtoorderthemonthechromosomes?Contig:疊加群82Integration:GeneticMapandPhysicalMapGeneticmap:DNAmarkersPhysicalMap:contigs構(gòu)建物理圖譜的第三步-物理圖譜和遺傳圖譜的整合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植物比較基因組學(xué)課件93植物比較基因組學(xué)課件94植物比較基因組學(xué)研究基因組物理圖譜和遺傳圖譜基因組加倍禾本科作物的人工馴化(Domestication)植物比較基因組學(xué)研究95AllplantsarepolyploidsAllopolyploidyordisomicpolyploidyCombingtwoormoredivergentgenomesWheatCottonCanolaA.suecicaTragopogonAutopolyploidyMultiplyingasinglegenomePotatoAlfalfaWatermelonBananaSugarcanePaleopolyploidyAncientor