比较基因组学应用PPT课件
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比较基因组学应用,1,Jian-Hong Xu ALE Building A365jhxuzju.edu.cn 15958019105, 0571-88982406Research Interested: Molecular evolution of genes, gene families and genomes in plants Expression and regulation of seed storage proteins in plants Mobile Elements and their regulations Epigenetics and small RNAs,Laboratory of Plant Genomics and Genetic Breeding (http:/mypage.zju.edu.cn/jianhong_xu),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(Structural Genomics) 基因组的遗传制图、物理制图及DNA测序功能基因组学(Functional Genomics)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(Comparative Genomics)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(Comparative genomics)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,Three models of evolution,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,Hardison 2010,10,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 (teosinte branched 1): control region 58-69kb,12,Zhou et al., Cell Research 2011,Studeret al., Nature Genetics 2011,13,Fu and Dooner, PNAS 2002,Lai et al., PNAS 2005,Gene duplication model,14,Rice,Wheat,Maize,Gene finding (mis-annotation),15,Jiao et al. 2010,Miura et al. 2010,OsSPL14,16,Gene family,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,Seed Storage Protein,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,Distribution of Seed Storage Protein,19,Rice (Oryza sativa),Poaceae (Grass),Panicoideae,Andropogoneae,Maize (Zea mays) Sorghum (Sorghum bicolor),Paniceae,Foxtail Millet (Setaria italica),Pooideae,Brachypodieae,Brachypodium (Brachypodium distachyon),Triticeae,Wheat (Triticum aestivum),Ehrhartoideae,Oryzeae,Taxonomic Family,Subfamily,Tribe,Species,20,Rice (Oryza sativa),Panicoideae,Andropogoneae,Maize (Zea mays) Sorghum (Sorghum bicolor),Paniceae,Foxtail Millet (Setaria italica),Pooideae,Brachypodieae,Brachypodium (Brachypodium distachyon),Triticeae,Wheat (Triticum aestivum),Ehrhartoideae,Oryzeae,Poaceae (Grass),Taxonomic Family,Subfamily,Tribe,Species,21,Rice (Oryza sativa),Panicoideae,Andropogoneae,Maize (Zea mays) Sorghum (Sorghum bicolor),Paniceae,Foxtail Millet (Setaria italica),Pooideae,Brachypodieae,Brachypodium (Brachypodium distachyon),Triticeae,Wheat (Triticum aestivum),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-, -),Taxonomic Family,Subfamily,Tribe,Species,Gene Family Subfamily,22,Rice (Oryza sativa),Panicoideae,Andropogoneae,Maize (Zea mays) Sorghum (Sorghum bicolor),Paniceae,Foxtail Millet (Setaria italica),Pooideae,Brachypodieae,Brachypodium (Brachypodium distachyon),Triticeae,Wheat (Triticum aestivum),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-, -),Taxonomic Family,Subfamily,Tribe,Species,Gene Family Subfamily,Subgroup (Locus),z1, k1 - (A, B, C, D) z2, k2 (-, -, -),s1 - (C, D) s2 (-, -, -),Prolamins,Xu, Bennetzen & Messing 2011,23,Osborne TB 1914 McKinney LL 1958; Esen A 1986 SDS-PAGE mRNA clone: few sequences,Prolamin genes in maize (zeins)I,24,BAC library Screening Sequencing Gene cluster,Prolamin genes in maize (zeins)II,15,22,25,Whole genome sequencing (B73) Whole genome blast (利用序列的同源性)-zeins :41 -zeins :1 -zeins :3 -zeins :2,Prolamin genes in maize (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),Distribution of Prolamins in Panicoideae,29,z1D,2,7,z216,z227,50,4,z1C1 z1A1,6,z2,1,9,z218,z210,Zeins and karirins synteny map,染色体上的定位,30,Phylogenetic Analysis of Alpha Prolamin Genes in Foxtail Millet, Sorghum and Maize,MEGA5:Tamura K, Peterson D, Peterson N, Stecher G, Nei M, and Kumar S (2011) MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Molecular Biology and Evolution 28: 2731-2739.,31,Phylogenetic analysis of cytochrome P450 genes,Sequence alignment of orthologous regions of a1 prolamin genes in maize, sorghum, foxtail millet, brachypodium, rice,32,Model for deletion of the a-prolaminfounder gene D in Panicoideae,33,s1C,k1C,k1C,k1A,z1C,z1A,Sequence alignment of orthologous regions of C and A types of prolamin genes in maize, sorghum, foxtail millet and rice,34,11.9,21.3,32.0,11.9,30.0,21.0,Estimation prolamin gene evolution time,1.2410-8,1.3010-8,9.0,3.0,16.2,14.4,3.2,adh 6.510-9,35,Oligocene (渐新世) C4,Xu, Bennetzen & Messing 2011,Gene pedigree of a-prolamins in maize, sorghum, foxtail millet,36,Xu & Messing 2008,Gene expression of zeins and kafirins (based on sequences),37,z1A2-1 transcripts - 90% of total,Endosperm tissue culture (t.c.) doesnt seem to significantly affect the expression profile at these loci.,Miclaus, Xu & Messing 2011,Expression profile at the z1A loci,38,Silent,Miclaus, Xu & Messing 2011,Expression profile at the z1B and z1D loci,39,%,Zein copy,Miclaus, Xu & Messing 2011,Song et al. 2001,Expression profile at the z1C locus,40,Kawakatsu & Takaiwa 2010,TG(T/C/A)AAAG TGA(G/C)TCA,Trans- and Cis-elements for cereal SSP gene regulation,41,Alignment of O2 and OHP regions in rice, sorghum, maize,42,Alignment of PBF regions in sorghum, maize,43,PBF (Prolamin binding factor),Opaque2-like (bZIP),Xu & Messing 2008,Prolamin promoter regions in rice, wheat, sorghum, maize,44,Higher methylation of the 19- vs. 22-kDa (z1C) promotersOnly CHH context for z1B,%,Miclaus, Xu & Messing 2011,Methylation pattern in the 500bp promoter sequence,45,z1A,z1B,z1C,Miclaus, Xu & Messing 2011,TCCACGTAGA,46,z1B1,z1B4,z1B6,DNA methylation pattern in the promoters of z1B gene loci,47,DNA methylation pattern in the promoters and gene bodies of z1B gene loci,48,http:/pfam.sanger.ac.uk/ http:/pfam.janelia.org/,49,http:/planttfdb.cbi.pku.edu.cn/,50,多序列联配 Multiple Sequence Alignment (MSA) ClustalW: http:/www.ebi.ac.uk/Tools/msa/clustalw2/ Muscle:http:/www.drive5.com/muscle/ MAFFT:http:/mafft.cbrc.jp/alignment/software/ T-coffee:http:/www.tcoffee.org/Projects/tcoffee/,51,系统进化树构建 MEGA :http:/www.megasoftware.net PAUP:http:/paup.csit.fsu.edu PHYLIP :http:/evolution.genetics.washington.edu/phylip.html PHYML :http:/atgc.lirmm.fr/phyml PAML :http:/abacus.gene.ucl.ac.uk/software/paml.html MrBayes :http:/mrbayes.sourceforge.net/ RAxML :http:/www.exelixis-lab.org/,52,http:/weblogo.berkeley.edu/,ClustalW: online, local (download software),http:/megasoftware.net/,53,Genome Level,Sequencing technology Whole genome sequencing Bioinformatics,Data resources and analysis workspaces for comparative genomics,54,Gale & Devos 1998,Comparative genomics of grass genomes,DNA,55,Yu et al. 2002. A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science, 296, 79-92 (93-11)Goff et al. 2002. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science, 296, 92-100 (Nipponbare)International Rice Genome Sequencing Project 2005 The map-based sequence of the rice genome. Nature 436, 793-800 (Nipponbare),Complete genome sequencing in grasses I,56,Paterson et al. 2009. The sorghum bicolor genome and the diversification of grasses. Nature, 457, 551-556 (Btx623)Schnable et al. 2009. The B73 maize genome: complexity, diversity, and dynamics. Science, 326, 1112-1115 (B73)International Brachypodium Initiative. 2010. Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature, 463, 763-768 (Bd21),Complete genome sequencing in grasses II,57,Bennetzen et al. 2012. Reference genome sequence of the model plant Setaria. Nature Biotechnology, 30, 555-561(Yugu1)Zhang et al. 2012. Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential. Nature Biotechnology, 30, 549-554 (Zhang gu),Complete genome sequencing in grasses III,58,Brenchley et al. 2012. Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature, 491, 705-710The International Barley Genome Sequencing Consortium. 2012. A physical, genetic and functional sequence assembly of the barley genome. Nature, 491, 711-716,Complete genome sequencing in grasses IV,59,60,Maize,Sorghum,Foxtail millet,Wheat,Brachypodium,Rice,10,10,9,7,5,12,2300,730,515,6000,272,389,32540, xxxxx,34496, 27640,38801, 24-29,000,xxxxx, xxxxx,xxxxx, 25532,37544, 28236,50-70 my,Species,Chromosome number,Genome size (Mb),Gene model,61,62,63,64,65,66,RG* refers to Reference Genome aNumber of orthologous genes bNumber of collinear blocks cPercentage of genome coverage dNumber of paralogous genes eNumber of duplicated blocks fAsterisks for the wheat and barley genomes highlight the highly saturated gene-based genetic maps used in the analysis,67,68,Ancestral grass karyotype (AGK) reconstruction,69,Model for grass chromosome evolution and shuffling,70,RNA,71,osa-miR444c (5p/3p),Dynamic arm expression of osa-miR444c in different libraries,72,Heatmap of arm swtiching of Osa-miRNAs in different tissues and abiotic stresses,Different tissues,Different abiotic stresses,73,Tissue-specific and overlap of pre-miRNA harboring arm switching under abiotic stresses,34.6% 98/283,37.7% 121/321,22.4% 38/170,24.4% 49/201,74,灰飞虱小RNA高通量测序(混合样品),75,76,Stem-loop RT-PCR和测序验证,77,miRNA家族在不同动物中的保守性,78,miRNA靶标基因的GO分析,79,表 RNA-seq检测到与肺癌相关的基因变化类型,80,谢谢!,81,- 配套讲稿:
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