甘蓝型油菜HMG基因家族的生物信息学分析
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摘要
为研究甘蓝型油菜HMG(high mobility group)基因家族的起源、进化和功能,利用生物信息学方法对甘蓝型油菜和其近缘物种HMG基因家族进行鉴定,并对其进化、基因结构、组织表达、直系旁系同源基因进行系统分析。在甘蓝型油菜中鉴定到45个HMG家族成员,并根据进化树和基因结构将其分成5组。染色体定位发现,19条染色体中有18条染色体有HMG基因,说明该家族基因分布较广泛。在甘蓝型油菜与甘蓝、白菜和拟南芥分别鉴定到45、47和26个直系同源基因对。在甘蓝型油菜中鉴定到28个旁系同源基因对,而在其它3个物种中则比较少,这可能与甘蓝型油菜的多次基因组加倍有关。对45个甘蓝型油菜BnHMG基因在根和叶中的表达模式进行分析,结果显示,大多数基因在根和叶中均有表达,且呈现出不同的表达模式。
HMG( high mobility group) gene family is related to transcription,replication,recombination and DNA repair. Bioinformatics and identification of HMG gene families from rapeseed( Brassica napus L.) and its allied species was focused in this study. Evolution,gene structure,expression and orthologous/paralogous genes were analysed on origin and function of B. napus HMG gene family. 45 HMG family members were identified in B. napus and were divided into 5 groups according to evolutionary tree and gene structure. Chromosome localization results showed that 18 chromosome among 19 had HMG genes,indicating wide distribution of this family. Respectively 45,47 and 26 orthologous genes were identified among B. napus and the other 3 species as B. oleracea,B. rapa and A.thaliana. 28 paralogous gene pairs were identified in B. napus,but were fewer in other 3 species,which could be related to the multiple genome duplication in B. napus. Expression of 45 Bn HMG genes in leaves and roots revealed different patterns.
HMG( high mobility group) gene family is related to transcription,replication,recombination and DNA repair. Bioinformatics and identification of HMG gene families from rapeseed( Brassica napus L.) and its allied species was focused in this study. Evolution,gene structure,expression and orthologous/paralogous genes were analysed on origin and function of B. napus HMG gene family. 45 HMG family members were identified in B. napus and were divided into 5 groups according to evolutionary tree and gene structure. Chromosome localization results showed that 18 chromosome among 19 had HMG genes,indicating wide distribution of this family. Respectively 45,47 and 26 orthologous genes were identified among B. napus and the other 3 species as B. oleracea,B. rapa and A.thaliana. 28 paralogous gene pairs were identified in B. napus,but were fewer in other 3 species,which could be related to the multiple genome duplication in B. napus. Expression of 45 Bn HMG genes in leaves and roots revealed different patterns.
引文
[1]牛林海.裂叶牵牛、玉米、黄瓜HMG基因的克隆与功能研究[D].泰安:山东农业大学,2002.
[2]江玲霞,李纪委,贺彧,等.Sox基因家族功能的研究进展[J].生物技术通报,2008(6):44-48.
[3]常重杰,杜启艳,邵红伟.Sox基因家族研究的新进展[J].遗传,2002,24(4):470-476.
[4]Gupta R,Webster C I,Walker A R,et al.Chromosomal location and expression of the single-copy gene encoding high-mobility-group protein HMG-I/Y in Arabidopsis thaliana[J].Plant Molecular Biology,1997,34(3):529.
[5]Feng C,Liu S,Jian W,et al.BRAD,the genetics and genomics database for Brassica plants[J].BMC Plant Biology,2011,11(1):136.
[6]Liu S,Liu Y,Yang X,et al.The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes[J].Nature Communications,2014,5(5):3 930.
[7]Chalhoub B,Denoeud F,Liu S,et al.Plant genetics.Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome[J].Science,2014,345(6199):950-953.
[8]Springer P,Martienssen R.TAIR database quick search[M].Cold Spring Harbor Arabidopsis Molecular Genetics Course,1996.
[9]Finn R D,Bateman A,Clements J,et al.Pfam:the protein families database[J].Nucleic Acids Research,2014,42(Database issue):222-230.
[10]Xu Q,Jr D R.Assignment of protein sequences to existing domain and family classification systems:Pfam and the PDB[J].Bioinformatics,2012,28(21):2 763-2 772.
[11]Edgar R C.MUSCLE:a multiple sequence alignment method with reduced time and space complexity[J].BMC Bioinformatics,2004,5(5):113.
[12]Chung B Y,Hardcastle T J,Jones J D,et al.The use of duplex-specific nuclease in ribosome profiling and a user-friendly software package for Ribo-seq data analysis[J].RNA,2015,21(10):1 731-1 745.
[13]Hu B,Jin J,Guo A Y,et al.GSDS 2.0:an upgraded gene feature visualization server[J].Bioinformatics,2015,31(8):1 296-1 297.
[14]Zhai Y,Tchieu J,Jr S M.A web-based Tree View(TV)program for the visualization of phylogenetic trees[J].Journal of Molecular Microbiology&Biotechnology,2002,4(1):69-70.
[15]Bailey T L,Johnson J,Grant C E,et al.The MEME Suite[J].Nucleic Acids Research,2015,43(Web Server issue):39-49.
[16]Li L,Stoeckert C J,Roos D S.Ortho MCL:Identification of ortholog groups for eukaryotic genomes[J].Genome Research,2003,13(9):2 178-2 189.
[17]Krzywinski M,Schein J,Birol I,et al.Circos:an information aesthetic for comparative genomics[J].Genome Research,2009,19(9):1 639-1 645.
[18]Song X M,Huang Z N,Duan W K,et al.Genomewide analysis of the b HLH transcription factor family in Chinese cabbage(Brassica rapa ssp.pekinensis)[J].Molecular Genetics and Genomics,2014,289(1):77-91.
[19]Song X M,Liu T K,Duan W K,et al.Genome-wide analysis of the GRAS gene family in Chinese cabbage(Brassica rapa ssp.pekinensis)[J].Genomics,2014,103(1):135-146.
[20]Song X,Liu G,Duan W,et al.Genome-wide identification,classification and expression analysis of the heat shock transcription factor family in Chinese cabbage[J].Molecular Genetics and Genomics,2014,289(4):541-551.
[21]Song X,Duan W,Huang Z,et al.Comprehensive analysis of the flowering genes in Chinese cabbage and examination of evolutionary pattern of CO-like genes in plant kingdom[J].Scientific Reports,2015,5:14 631.
[22]Song X,Wang J,Ma X,et al.Origination,expansion,evolutionary trajectory,and expression bias of AP2/ERF superfamily in Brassica napus[J].Frontiers in Plant Science,2016,7(307):1 186.
[23]Song X,Li Y,Hou X.Genome-wide analysis of the AP2/ERF transcription factor superfamily in Chinese cabbage(Brassica rapa ssp.pekinensis)[J].BMC Genomics,2013,14:573.
[2]江玲霞,李纪委,贺彧,等.Sox基因家族功能的研究进展[J].生物技术通报,2008(6):44-48.
[3]常重杰,杜启艳,邵红伟.Sox基因家族研究的新进展[J].遗传,2002,24(4):470-476.
[4]Gupta R,Webster C I,Walker A R,et al.Chromosomal location and expression of the single-copy gene encoding high-mobility-group protein HMG-I/Y in Arabidopsis thaliana[J].Plant Molecular Biology,1997,34(3):529.
[5]Feng C,Liu S,Jian W,et al.BRAD,the genetics and genomics database for Brassica plants[J].BMC Plant Biology,2011,11(1):136.
[6]Liu S,Liu Y,Yang X,et al.The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes[J].Nature Communications,2014,5(5):3 930.
[7]Chalhoub B,Denoeud F,Liu S,et al.Plant genetics.Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome[J].Science,2014,345(6199):950-953.
[8]Springer P,Martienssen R.TAIR database quick search[M].Cold Spring Harbor Arabidopsis Molecular Genetics Course,1996.
[9]Finn R D,Bateman A,Clements J,et al.Pfam:the protein families database[J].Nucleic Acids Research,2014,42(Database issue):222-230.
[10]Xu Q,Jr D R.Assignment of protein sequences to existing domain and family classification systems:Pfam and the PDB[J].Bioinformatics,2012,28(21):2 763-2 772.
[11]Edgar R C.MUSCLE:a multiple sequence alignment method with reduced time and space complexity[J].BMC Bioinformatics,2004,5(5):113.
[12]Chung B Y,Hardcastle T J,Jones J D,et al.The use of duplex-specific nuclease in ribosome profiling and a user-friendly software package for Ribo-seq data analysis[J].RNA,2015,21(10):1 731-1 745.
[13]Hu B,Jin J,Guo A Y,et al.GSDS 2.0:an upgraded gene feature visualization server[J].Bioinformatics,2015,31(8):1 296-1 297.
[14]Zhai Y,Tchieu J,Jr S M.A web-based Tree View(TV)program for the visualization of phylogenetic trees[J].Journal of Molecular Microbiology&Biotechnology,2002,4(1):69-70.
[15]Bailey T L,Johnson J,Grant C E,et al.The MEME Suite[J].Nucleic Acids Research,2015,43(Web Server issue):39-49.
[16]Li L,Stoeckert C J,Roos D S.Ortho MCL:Identification of ortholog groups for eukaryotic genomes[J].Genome Research,2003,13(9):2 178-2 189.
[17]Krzywinski M,Schein J,Birol I,et al.Circos:an information aesthetic for comparative genomics[J].Genome Research,2009,19(9):1 639-1 645.
[18]Song X M,Huang Z N,Duan W K,et al.Genomewide analysis of the b HLH transcription factor family in Chinese cabbage(Brassica rapa ssp.pekinensis)[J].Molecular Genetics and Genomics,2014,289(1):77-91.
[19]Song X M,Liu T K,Duan W K,et al.Genome-wide analysis of the GRAS gene family in Chinese cabbage(Brassica rapa ssp.pekinensis)[J].Genomics,2014,103(1):135-146.
[20]Song X,Liu G,Duan W,et al.Genome-wide identification,classification and expression analysis of the heat shock transcription factor family in Chinese cabbage[J].Molecular Genetics and Genomics,2014,289(4):541-551.
[21]Song X,Duan W,Huang Z,et al.Comprehensive analysis of the flowering genes in Chinese cabbage and examination of evolutionary pattern of CO-like genes in plant kingdom[J].Scientific Reports,2015,5:14 631.
[22]Song X,Wang J,Ma X,et al.Origination,expansion,evolutionary trajectory,and expression bias of AP2/ERF superfamily in Brassica napus[J].Frontiers in Plant Science,2016,7(307):1 186.
[23]Song X,Li Y,Hou X.Genome-wide analysis of the AP2/ERF transcription factor superfamily in Chinese cabbage(Brassica rapa ssp.pekinensis)[J].BMC Genomics,2013,14:573.