比较基因组学应用PPT课件.ppt

比较基因组学应用 1 Jian HongXuALEBuildingA365jhxu0571 88982406ResearchInterested Molecularevolutionofgenes genefamiliesandgenomesinplantsExpressionandregulationofseedstorageproteinsinplantsMobileElementsandtheirregulationsEpigeneticsandsmallRNAs LaboratoryofPlantGenomicsandGeneticBreeding 2 基因组 Genome 泛指一个细胞或者生物体的全部遗传物质 包括全套基因和间隔序列 非编码DNA 在真核生物中 是指一套完整的染色体 单倍体 序列 基因组学 Genomics 是研究生物基因组和如何利用基因的一门学科 通过应用重组DNA DNA测序方法和生物信息学对基因组进行测序 组装并对其结构和功能分析 3 结构基因组学 StructuralGenomics 基因组的遗传制图 物理制图及DNA测序功能基因组学 FunctionalGenomics 认识 分析基因组所包含的基因 非基因序列及功能比较基因组学 ComparativeGenomics 比较不同的基因组 增强对各个基因组功能及发育相关性的认识 基因组学的三个领域 4 比较基因组学 Comparativegenomics 是基于基因组图谱和测序技术基础上 对已知的基因和基因组结构进行比较以了解基因的功能 表达调控机制以及物种进化过程的学科 比较基因组学的定义 基因和基因组结构功能进化 DNA和蛋白质序列 5 比较基因组学研究 种间比较基因组学全基因组的比较系统发生的进化关系分析种内比较基因组学单核苷酸多态性 SNP 拷贝数多态性 6 Threemodelsofevolution 7 8 序列的比对分析 相似性 similarity 同源性 homology 基因组序列的进化关系 共线性 synteny 基因组结构的分析 转座 插入和缺失 染色体重排 比较基因组学的方法与思路 9 Hardison2010 10 揭示非编码功能序列发现新基因发现功能性SNP阐述物种的进化史 比较基因组学的应用 11 tb1 teosintebranched1 controlregion58 69kb 12 Zhouetal CellResearch2011 Studeretal NatureGenetics2011 13 FuandDooner PNAS2002 Laietal PNAS2005 Geneduplicationmodel 14 Rice Wheat Maize Genefinding mis annotation 15 Jiaoetal 2010 Miuraetal 2010 OsSPL14 16 Genefamily 低拷贝或少数几个物种 可以用简单的blast多拷贝或多物种 借助于一些软件 17 SeedStorageProtein 清蛋白 Albumins 胚乳球蛋白 Globulins 胚与糊粉层醇溶蛋白 Prolamins 胚乳谷蛋白 Glutenins Glutelins 胚乳 18 DistributionofSeedStorageProtein 19 Rice Oryzasativa Poaceae Grass Panicoideae Andropogoneae Maize Zeamays Sorghum Sorghumbicolor Paniceae FoxtailMillet Setariaitalica Pooideae Brachypodieae Brachypodium Brachypodiumdistachyon Triticeae Wheat Triticumaestivum Ehrhartoideae Oryzeae TaxonomicFamily Subfamily Tribe Species 20 Rice Oryzasativa Panicoideae Andropogoneae Maize Zeamays Sorghum Sorghumbicolor Paniceae FoxtailMillet Setariaitalica Pooideae Brachypodieae Brachypodium Brachypodiumdistachyon Triticeae Wheat Triticumaestivum Ehrhartoideae Oryzeae Poaceae Grass TaxonomicFamily Subfamily Tribe Species 21 Rice Oryzasativa Panicoideae Andropogoneae Maize Zeamays Sorghum Sorghumbicolor Paniceae FoxtailMillet Setariaitalica Pooideae Brachypodieae Brachypodium Brachypodiumdistachyon Triticeae Wheat Triticumaestivum Ehrhartoideae Oryzeae oryzein 10 13 16 kDa Brachypodin Bra1 Bra2 Bra3 glutenin gliadin S rich S poor HMW zein kafirin d b Poaceae Grass setarin d b TaxonomicFamily Subfamily Tribe Species GeneFamilySubfamily 22 Rice Oryzasativa Panicoideae Andropogoneae Maize Zeamays Sorghum Sorghumbicolor Paniceae FoxtailMillet Setariaitalica Pooideae Brachypodieae Brachypodium Brachypodiumdistachyon Triticeae Wheat Triticumaestivum Ehrhartoideae Oryzeae oryzein 10 13 16 kDa Brachypodin Bra1 Bra2 Bra3 glutenin gliadin S rich S poor HMW zein kafirin d b Poaceae Grass setarin d b TaxonomicFamily Subfamily Tribe Species GeneFamilySubfamily Subgroup Locus z1 k1 A B C D z2 k2 s1 C D s2 Prolamins Xu Bennetzen Messing2011 23 OsborneTB1914McKinneyLL1958 EsenA1986SDS PAGEmRNAclone fewsequences Prolamingenesinmaize zeins I 24 BAClibraryScreeningSequencingGenecluster Prolamingenesinmaize zeins II 15 22 25 Wholegenomesequencing B73 Wholegenomeblast 利用序列的同源性 zeins 41 zeins 1 zeins 3 zeins 2 Prolamingenesinmaize zeins III 26 ATGGCAGCCAAAATATTTTGCTTCCTTATGCTCCTTGGTCTTTCTGCAAGTGCTGCTACCGCAACCATTTTCCCACAATGCTCACAAGCTCCTATAGCTTCCTTTCTTCCCCCATACCTCTCACCAGCGGTGTCTTCAGTATGTGAAAACCCAATTCTTCAACCCTACAGGATCCAACAGGCAATCGCAGCAGGCATCTTACCTTTATCACCCTTGTTCCTCCAACAACCGTCAGCCCTATTACAGCAGTTACCTTTGGTGCATTTGTTGGCACAAAACATCAAGGCACAACAACTACAACAACTTGTGCTAGGAAACCTTGCTGCCTACTCTCAGCAACAGCAGTTTCTTCCATTCAACCAACTGGCTGCATTGAACTCTGCTGCTTATTTGCAACAACAACTACCATTCAGTCAGCTAGCTGCTGCCTACCCCCAGCAATTTCTTCCATTCAACCAACTGGCAGCATTGAACTCTGCTGCTTATTTACAACAGCAACAGCTACCACCATTCAGCCAGCTAGCTGATGTGAGCCCTGTTGCCTTCTTGACACAACAACAGTTGTTGCCGTTCTACCTGCACGCTGCGCCTAACGCTGGCACCCTCTTACAACTGCAACAATTGCTGCCATTCAACCAACTTGCTTTGACAAACCCAACAACGTTCTACCAACAACCCATCATTGGCGGTGCCCTCTTTTAG http blast maizegdb org home php a BLAST UI 27 Blast结果 28 zeins 41 zeins 1 zeins 3 zeins 2 19kD22kD 10kDa18kDa 16kD27kD50kD 15kD Zeins B73 z1A1 z1A2 9 3 z1B 9 z1D 5 z1C1 z1C2 14 1 kafirins 23 kafirins 1 kafirins 2 kafirins 1 1 k1A 2 k1C 20 k1D 1 Kafirins Btx623 setarins 15 setarins 1 setarins 3 setarins 6 s1C 9 s1D 6 Setarins Yugu1 DistributionofProlaminsinPanicoideae 29 z1D 2 7 z2 16 z2 27 50 4 z1C1z1A1 6 z2 1 9 z2 18 z2 10 Zeinsandkaririnssyntenymap 染色体上的定位 30 PhylogeneticAnalysisofAlphaProlaminGenesinFoxtailMillet SorghumandMaize MEGA5 TamuraK PetersonD PetersonN StecherG NeiM andKumarS 2011 MEGA5 MolecularEvolutionaryGeneticsAnalysisusingMaximumLikelihood EvolutionaryDistance andMaximumParsimonyMethods MolecularBiologyandEvolution28 2731 2739 31 PhylogeneticanalysisofcytochromeP450genes Sequencealignmentoforthologousregionsofa1prolamingenesinmaize sorghum foxtailmillet brachypodium rice 32 Modelfordeletionofthea prolaminfoundergeneDinPanicoideae 33 s1C k1C k1C k1A z1C z1A SequencealignmentoforthologousregionsofCandAtypesofprolamingenesinmaize sorghum foxtailmilletandrice 34 11 9 21 3 32 0 11 9 30 0 21 0 Estimationprolamingeneevolutiontime 1 24 10 8 1 30 10 8 9 0 3 0 16 2 14 4 3 2 adh6 5 10 9 35 Oligocene 渐新世 C4 Xu Bennetzen Messing2011 Genepedigreeofa prolaminsinmaize sorghum foxtailmillet 36 Xu Messing2008 Geneexpressionofzeinsandkafirins basedonsequences 37 z1A2 1transcripts 90 oftotal Endospermtissueculture t c doesn tseemtosignificantlyaffecttheexpressionprofileattheseloci Miclaus Xu Messing2011 Expressionprofileatthez1Aloci 38 Silent Miclaus Xu Messing2011 Expressionprofileatthez1Bandz1Dloci 39 Zeincopy Miclaus Xu Messing2011 Songetal 2001 Expressionprofileatthez1Clocus 40 Kawakatsu Takaiwa2010 TG T C A AAAGTGA G C TCA Trans andCis elementsforcerealSSPgeneregulation 41 AlignmentofO2andOHPregionsinrice sorghum maize 42 AlignmentofPBFregionsinsorghum maize 43 PBF Prolaminbindingfactor Opaque2 like bZIP Xu Messing2008 Prolaminpromoterregionsinrice wheat sorghum maize 44 Highermethylationofthe19 vs 22 kDa z1C promotersOnlyCHHcontextforz1B Miclaus Xu Messing2011 Methylationpatterninthe500bppromotersequence 45 z1A z1B z1C Miclaus Xu Messing2011 TCCACGTAGA 46 z1B1 z1B4 z1B6 DNAmethylationpatterninthepromotersofz1Bgeneloci 47 DNAmethylationpatterninthepromotersandgenebodiesofz1Bgeneloci 48 http pfam sanger ac uk http pfam janelia org 49 50 多序列联配MultipleSequenceAlignment MSA ClustalW http www ebi ac uk Tools msa clustalw2 Muscle 51 系统进化树构建MEGA PAUP http paup csit fsu eduPHYLIP http evolution genetics washington edu phylip htmlPHYML http atgc lirmm fr phymlPAML http abacus gene ucl ac uk software paml htmlMrBayes 52 http weblogo berkeley edu ClustalW online local downloadsoftware 53 GenomeLevel SequencingtechnologyWholegenomesequencingBioinformatics Dataresourcesandanalysisworkspacesforcomparativegenomics 54 Gale Devos1998 Comparativegenomicsofgrassgenomes DNA 55 Yuetal 2002 Adraftsequenceofthericegenome OryzasativaL ssp indica Science 296 79 92 93 11 Goffetal 2002 Adraftsequenceofthericegenome OryzasativaL ssp japonica Science 296 92 100 Nipponbare InternationalRiceGenomeSequencingProject2005Themap basedsequenceofthericegenome Nature436 793 800 Nipponbare CompletegenomesequencingingrassesI 56 Patersonetal 2009 Thesorghumbicolorgenomeandthediversificationofgrasses Nature 457 551 556 Btx623 Schnableetal 2009 TheB73maizegenome complexity diversity anddynamics Science 326 1112 1115 B73 InternationalBrachypodiumInitiative 2010 GenomesequencingandanalysisofthemodelgrassBrachypodiumdistachyon Nature 463 763 768 Bd21 CompletegenomesequencingingrassesII 57 Bennetzenetal 2012 ReferencegenomesequenceofthemodelplantSetaria NatureBiotechnology 30 555 561 Yugu1 Zhangetal 2012 Genomesequenceoffoxtailmillet Setariaitalica providesinsightsintograssevolutionandbiofuelpotential NatureBiotechnology 30 549 554 Zhanggu CompletegenomesequencingingrassesIII 58 Brenchleyetal 2012 Analysisofthebreadwheatgenomeusingwhole genomeshotgunsequencing Nature 491 705 710TheInternationalBarleyGenomeSequencingConsortium 2012 Aphysical geneticandfunctionalsequenceassemblyofthebarleygenome Nature 491 711 716 CompletegenomesequencingingrassesIV 59 60 Maize Sorghum Foxtailmillet Wheat Brachypodium Rice 10 10 9 7 5 12 2300 730 515 6000 272 389 32540 xxxxx 34496 27640 38801 24 29