杜兰落花生球蛋白基因家族的生物信息学分析
|
摘要
为了解球蛋白基因家族在杜兰落花生(Arachis duranensis)种子中的特征,利用生物信息学方法对杜兰落花生球蛋白基因进行全基因组鉴定及表达模式分析。结果表明,杜兰落花生含有9个球蛋白基因,家族成员间理化特性总体差异不大,亲缘关系相近的蛋白具有相似的保守基序组成。根据物种间的球蛋白系统进化树,球蛋白进化关系符合物种之间的亲缘关系。杜兰落花生球蛋白在进化过程中较为保守,受纯化选择主导,但在部分进化枝上存在正选择位点。栽培种花生转录组数据分析表明,15个花生球蛋白基因在花生种子中检测到表达,其中4个表达量远超其它成员,在花生荚果成熟后期表达量仍较高。
To get insight into globulin genes in Arachis duranensis,genome-wide identification and expression analysis of AdARA gene family were investigated using bioinformatics methods.Results showed that A.duranensis contained 9 globulin genes,physicochemical among the family members were not significant.Motif compose of the closely related proteins were similar.Phylogenetic of globulins revealed that evolutionary relationship of globulins accorded with genetic relationship between species.AdARA proteins were conservative in evolution process and under negative selection,but positively selected sites were identified at a clade.By analyzing RNA-seq transcriptome data of cultivar peanut,it showed that 15 arachin genes were expressed in seed,the expression of 4 arachin genes greatly exceeded the others,the expression level of 4 arachin genes were also high at Pattee stage 10.
To get insight into globulin genes in Arachis duranensis,genome-wide identification and expression analysis of AdARA gene family were investigated using bioinformatics methods.Results showed that A.duranensis contained 9 globulin genes,physicochemical among the family members were not significant.Motif compose of the closely related proteins were similar.Phylogenetic of globulins revealed that evolutionary relationship of globulins accorded with genetic relationship between species.AdARA proteins were conservative in evolution process and under negative selection,but positively selected sites were identified at a clade.By analyzing RNA-seq transcriptome data of cultivar peanut,it showed that 15 arachin genes were expressed in seed,the expression of 4 arachin genes greatly exceeded the others,the expression level of 4 arachin genes were also high at Pattee stage 10.
引文
[1] Thompson M J,Eisenberg D. Transproteomic evidence of a loop-deletion mechanism for enhancing protein thermostability[J]. J Mol Biol,1999,290(2):595-604.
[2] Shewry P R,Halford N G. Cereal seed storage proteins:structures,properties and role in grain utilization[J]. J Exp Bot,2002,53(370):947-958.
[3] Fujiwara T,Nambara E,Yamagishi K,et al. The Arabidopsis book[M]//Meyerowitz E M. Rockville:American Society of Plant Biologists,2002:1-12.
[4] Nielsen N C,Dickinson C D,Cho T J,et al. Characterization of the glycinin gene family in soybean[J]. Plant Cell,1989,1(3):313-328.
[5] Momma K,Hashimoto W,Ozawa S,et al. Quality and safety evaluation of genetically engineered rice with soybean glycinin:analyses of the grain composition and digestibility of glycinin in transgenic rice[J]. Biosci Biotechnol Biochem,1999,63(2):314-318.
[6]全先庆,杨辉霞,单雷,等.花生球蛋白基因克隆及其表达分析[J].安徽农业科学,2006,34(21):5483-5 484,5490.
[7]黄上志,傅家瑞.花生种子的发育与贮藏蛋白质的合成和积累[J].植物生理学报,1992,18(2):142-150.
[8] Yan Y S,Lin X D,Zhang Y S,et al. Isolation of peanut genes encoding arachins and conglutins by expressed sequence tags[J]. Plant Sci,2005,169(2):439-445.
[9]杜寅,王强,刘红芝,等.不同品种花生蛋白主要组分及其亚基相对含量分析[J].食品科学,2013,34(9):42-46.
[10]李春. 11S球蛋白和淀粉合成关键基因家族在单、双子叶植物间的比较分子进化研究[D].南京:南京农业大学,2011.
[11] Kawakatsu T,Yamamoto M P,Hirose S,et al. Characterization of a new rice glutelin gene Glu D-1 expressed in the starchy endosperm[J]. J Exp Bot,2008,59(15):4233-4245.
[12] Beilinson V,Chen Z,Shoemaker R,et al. Genomic organization of glycinin genes in soybean[J]. Theor Appl Genet,2002,104(6):1132-1140.
[13] Bertioli D J,Cannon S B,Froenicke L,et al. The genome sequences of Arachis duranensis and arachis ipaensis,the diploid ancestors of cultivated peanut[J]. Nat Genet,2016,48(4):438-446.
[14] Li C,Zhang Y M. Molecular evolution of glycinin andβ-conglycinin gene families in soybean(Glycine max L.Merr.)[J]. Heredity,2011,106(4):633-641.
[15] Edgar R C. MUSCLE:multiple sequence alignment with high accuracy and high throughput[J]. Nucleic Acids Res,2004,32(5):1792-1797.
[16] Kumar S,Stecher G,Tamura K. MEGA7:molecular evolutionary genetics analysis version 7. 0 for bigger datasets[J]. Mol Biol Evol,2016,33(7):1870-1874.
[17]郭安源,朱其慧,陈新,等. GSDS:基因结构显示系统[J].遗传,2007,29(8):1 023-1 026.
[18] Bailey T L,Boden M,Buske F A,et al. MEME SUITE:tools for motif discovery and searching[J]. Nucleic Acids Res,2009,37(Web Server):202-208.
[19] Yang Z. PAML 4:phylogenetic analysis by maximum likelihood[J]. Mol Biol Evol,2007,24(8):1586-1591.
[20] Suyama M,Torrents D,Bork P. PAL2NAL:robust conversion of protein sequence alignments into the corresponding Codon alignments[J]. Nucleic Acids Res,2006,34(Web Server):609-612.
[21] Clevenger J,Chu Y,Scheffler B,et al. A developmental transcriptome map for allotetraploid Arachis hypogaea[J]. Front Plant Sci,2016,7:1446.
[22] Kim D,Langmead B,Salzberg S L. HISAT:a fast spliced aligner with low memory requirements[J]. Nat Methods,2015,12(4):357-360.
[23] Pertea M,Pertea G M,Antonescu C M,et al. String Tie enables improved reconstruction of a transcriptome from RNA-seq reads[J]. Nat Biotechnol,2015,33(3):290-295.
[24] Saeed A I,Bhagabati N K,Braisted J C,et al.[9]TM4Microarray Software Suite[M]//Methods in Enzymology. Elsevier,2006:134-193.
[25] Pattee H E,Johns E B,Singleton J A,et al. Composition changes of peanut fruit parts during maturation1[J]. Peanut Sci,1974,1(2):57-62.
[26] Ikai A. Thermostability and aliphatic index of globular proteins[J]. J Biochem,1980,88(6):1895-1898.
[27] Blanc G,Barakat A,Guyot R,et al. Extensive duplication and reshuffling in the Arabidopsis genome[J]. Plant Cell,2000,12(7):1093.
[28] Chen X P,Li H J,Pandey M K,et al. Draft genome of the peanut A-genome progenitor(Arachis duranensis)provides insights into geocarpy,oil biosynthesis,and allergens[J]. Proc Natl Acad Sci USA,2016,113(24):6785-6790.
[29]雷忠萍,贺道华,海江波,等.雷蒙德氏棉扩展蛋白基因家族的鉴定和特征分析[J].华北农学报,2016,31(6):44-55.
[30] Gao L Z. Very low gene duplication rate in the yeast genome[J]. Science,2004,306(5700):1367-1370.
[31] Byrne K P. The Yeast Gene Order Browser:Combining curated homology and syntenic context reveals gene fate in polyploid species[J]. Genome Res,2005,15(10):1456-1461.
[2] Shewry P R,Halford N G. Cereal seed storage proteins:structures,properties and role in grain utilization[J]. J Exp Bot,2002,53(370):947-958.
[3] Fujiwara T,Nambara E,Yamagishi K,et al. The Arabidopsis book[M]//Meyerowitz E M. Rockville:American Society of Plant Biologists,2002:1-12.
[4] Nielsen N C,Dickinson C D,Cho T J,et al. Characterization of the glycinin gene family in soybean[J]. Plant Cell,1989,1(3):313-328.
[5] Momma K,Hashimoto W,Ozawa S,et al. Quality and safety evaluation of genetically engineered rice with soybean glycinin:analyses of the grain composition and digestibility of glycinin in transgenic rice[J]. Biosci Biotechnol Biochem,1999,63(2):314-318.
[6]全先庆,杨辉霞,单雷,等.花生球蛋白基因克隆及其表达分析[J].安徽农业科学,2006,34(21):5483-5 484,5490.
[7]黄上志,傅家瑞.花生种子的发育与贮藏蛋白质的合成和积累[J].植物生理学报,1992,18(2):142-150.
[8] Yan Y S,Lin X D,Zhang Y S,et al. Isolation of peanut genes encoding arachins and conglutins by expressed sequence tags[J]. Plant Sci,2005,169(2):439-445.
[9]杜寅,王强,刘红芝,等.不同品种花生蛋白主要组分及其亚基相对含量分析[J].食品科学,2013,34(9):42-46.
[10]李春. 11S球蛋白和淀粉合成关键基因家族在单、双子叶植物间的比较分子进化研究[D].南京:南京农业大学,2011.
[11] Kawakatsu T,Yamamoto M P,Hirose S,et al. Characterization of a new rice glutelin gene Glu D-1 expressed in the starchy endosperm[J]. J Exp Bot,2008,59(15):4233-4245.
[12] Beilinson V,Chen Z,Shoemaker R,et al. Genomic organization of glycinin genes in soybean[J]. Theor Appl Genet,2002,104(6):1132-1140.
[13] Bertioli D J,Cannon S B,Froenicke L,et al. The genome sequences of Arachis duranensis and arachis ipaensis,the diploid ancestors of cultivated peanut[J]. Nat Genet,2016,48(4):438-446.
[14] Li C,Zhang Y M. Molecular evolution of glycinin andβ-conglycinin gene families in soybean(Glycine max L.Merr.)[J]. Heredity,2011,106(4):633-641.
[15] Edgar R C. MUSCLE:multiple sequence alignment with high accuracy and high throughput[J]. Nucleic Acids Res,2004,32(5):1792-1797.
[16] Kumar S,Stecher G,Tamura K. MEGA7:molecular evolutionary genetics analysis version 7. 0 for bigger datasets[J]. Mol Biol Evol,2016,33(7):1870-1874.
[17]郭安源,朱其慧,陈新,等. GSDS:基因结构显示系统[J].遗传,2007,29(8):1 023-1 026.
[18] Bailey T L,Boden M,Buske F A,et al. MEME SUITE:tools for motif discovery and searching[J]. Nucleic Acids Res,2009,37(Web Server):202-208.
[19] Yang Z. PAML 4:phylogenetic analysis by maximum likelihood[J]. Mol Biol Evol,2007,24(8):1586-1591.
[20] Suyama M,Torrents D,Bork P. PAL2NAL:robust conversion of protein sequence alignments into the corresponding Codon alignments[J]. Nucleic Acids Res,2006,34(Web Server):609-612.
[21] Clevenger J,Chu Y,Scheffler B,et al. A developmental transcriptome map for allotetraploid Arachis hypogaea[J]. Front Plant Sci,2016,7:1446.
[22] Kim D,Langmead B,Salzberg S L. HISAT:a fast spliced aligner with low memory requirements[J]. Nat Methods,2015,12(4):357-360.
[23] Pertea M,Pertea G M,Antonescu C M,et al. String Tie enables improved reconstruction of a transcriptome from RNA-seq reads[J]. Nat Biotechnol,2015,33(3):290-295.
[24] Saeed A I,Bhagabati N K,Braisted J C,et al.[9]TM4Microarray Software Suite[M]//Methods in Enzymology. Elsevier,2006:134-193.
[25] Pattee H E,Johns E B,Singleton J A,et al. Composition changes of peanut fruit parts during maturation1[J]. Peanut Sci,1974,1(2):57-62.
[26] Ikai A. Thermostability and aliphatic index of globular proteins[J]. J Biochem,1980,88(6):1895-1898.
[27] Blanc G,Barakat A,Guyot R,et al. Extensive duplication and reshuffling in the Arabidopsis genome[J]. Plant Cell,2000,12(7):1093.
[28] Chen X P,Li H J,Pandey M K,et al. Draft genome of the peanut A-genome progenitor(Arachis duranensis)provides insights into geocarpy,oil biosynthesis,and allergens[J]. Proc Natl Acad Sci USA,2016,113(24):6785-6790.
[29]雷忠萍,贺道华,海江波,等.雷蒙德氏棉扩展蛋白基因家族的鉴定和特征分析[J].华北农学报,2016,31(6):44-55.
[30] Gao L Z. Very low gene duplication rate in the yeast genome[J]. Science,2004,306(5700):1367-1370.
[31] Byrne K P. The Yeast Gene Order Browser:Combining curated homology and syntenic context reveals gene fate in polyploid species[J]. Genome Res,2005,15(10):1456-1461.