基于全基因组编码区序列的烟草花叶病毒分子进化分析
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摘要
为揭示烟草花叶病毒分子进化特征,从GenBank中下载已报道的烟草花叶病毒全基因组编码区序列,进行重组、系统发育、遗传变异、种群结构和基因漂流等分析。结果表明:突变和负选择作用是驱动烟草花叶病毒进化的主要作用力,种群结构稳定,处于扩张趋势中,基因变异程度低,重组在烟草花叶病毒分子进化中作用不明显。烟草花叶病毒不同分离物形成3个有一定地理相关性的种群ChinaⅠ、ChinaⅡ和Europe。欧洲分离物核苷酸序列多样性比中国的差异大,Europe和ChinaⅠ种群可能受到遗传漂变影响,Europe与ChinaⅡ、ChinaⅠ与ChinaⅡ之间存在发生基因交流的渠道。
To reveal the molecular evolution of Tobacco mosaic virus(TMV),the complete genomic coding sequences of TMV from GenBank were subjected to molecular evolutionary analysis,including recombination,phylogeny,genetic variation,population structure,gene flow,etc.The results indicated that mutation and negative selection were the main driving forces for TMV evolution,rather than recombination.The TMV populations had stable structure,but were expanding,and the gene mutation was low.Three geographically correlative species of TMV named ChinaⅠ,ChinaⅡand Europe were found.The Europe isolates exhibited greater nucleotide diversity than the China ones;Europe and ChinaⅠpopulations could be influenced by genetic drift,and there were gene exchange channels between Europe and ChinaⅡ and between ChinaⅠand ChinaⅡ.
To reveal the molecular evolution of Tobacco mosaic virus(TMV),the complete genomic coding sequences of TMV from GenBank were subjected to molecular evolutionary analysis,including recombination,phylogeny,genetic variation,population structure,gene flow,etc.The results indicated that mutation and negative selection were the main driving forces for TMV evolution,rather than recombination.The TMV populations had stable structure,but were expanding,and the gene mutation was low.Three geographically correlative species of TMV named ChinaⅠ,ChinaⅡand Europe were found.The Europe isolates exhibited greater nucleotide diversity than the China ones;Europe and ChinaⅠpopulations could be influenced by genetic drift,and there were gene exchange channels between Europe and ChinaⅡ and between ChinaⅠand ChinaⅡ.
引文
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[27]Yin Xiao,Zheng Fangqiang,Tang Wei,et al.Genetic structure of Rice black-streaked dwarf virus populations in China[J].Archives of Virology,2013,158(12):2505-2515.
[28]Fu Y X,Li W H.Statistical tests of neutrality of mutations[J].Genetics,1993,133(3):693-709.
[29]Tajima F.Statistical method for testing the neutral mutation hypothesis by DNA polymorphism[J].Genetics,1989,123(3):585-595.
[30]Librado P,Rozas J.DnaSP v 5:a software for comprehensive analysis of DNA polymorphism data[J].Bioinformatics,2009,25(11):1451-1452.
[31]Roossinck,M J.Mechanisms of plant virus evolution[J].Annual Review of Phytopathology,1997,35:191-209.
[32]Cuevas J M,Delaunay A,Rupar M,et al.Molecular evolution and phylogeography of Potato virus Y based on the CP gene[J].Journal of General Virology,2012,93:2496-2501.
[33]Ogawa T,Nakagawa A,Hataya T,et al.The genetic structure of populations of Potato virus Y,in Japan;based on the analysis of 20full genomic sequences[J].Journal of Phytopathology,2012,160(11/12):661-673.
[34]宋丽云.我国烟草TMV和CMV种群结构遗传分析[D].北京:中国农业科学院,2012.
[35]谢扬军.烟草普通花叶病毒株系分化研究[D].北京:中国农业科学院,2009.
[2]洪健,李德葆,周雪平.植物病毒分类图谱[M].北京:科学出版社,2001:189-193.
[3]邵碧英,吴祖建,林奇英,等.烟草花叶病毒及其弱毒株基因组的cDNA克隆和序列分析[J].植物病理学报,2003,33(4):296-301.
[4]Korbelin J,Willingmann P,Adam G,et al.The complete sequence of Tobacco mosaic virus isolate Ohio V reveals a high accumulation of silent mutations in all open reading frames[J].Archives of Virology,2012,157(2):387-396.
[5]Pe珘na E J,Ferriol I,Sambade A,et al.Experimental virus evolution reveals a role of plant microtubule dynamics and TORTIFOLIA1/SPIRAL2in RNA trafficking[J].PLoS ONE,2014,9(8):e105364-e105364.
[6]Fillmer K,Adkins S,Pongam P,et al.Complete genome sequence of Tomato mosaic virus isolated from jasmine in the United States[J].Genome Announcements,2015,3(4):e00706-e00715.
[7]王劲波,王凤龙,钱玉梅,等.山东烟区主要病毒的株系鉴定[J].中国烟草学报,1998,4(1):24-32.
[8]雷彩燕,王振跃,张振臣,等.烟草花叶病毒株系研究进展[J].河南农业科学,2005(12):14-16.
[9]Goelet P,Lomonossoff G P,Butler P J G,et al.Nucleotide sequence of Tobacco mosaic virus RNA[J].Proceedings of the National Academy of Sciences,USA,1982,79:5818-5822.
[10]Regenmortel M H V V,Fauquet C M,Bishop D H L,et al.Virus taxonomy:classification and nomenclature of viruses:seventh report of the International Committee on Taxonomy of Viruses[M].San Diego:Academic Press,2000.
[11]贾琳,姚玉婷,肖明.猪瘟病毒编码区基因选择压力及重组分析[J].科学通报,2013,58(34):3570-3578.
[12]张新珩,刘远佳,吴波良,等.广东省鸡传染性贫血病毒编码区基因的克隆与分子进化分析[J].中国兽医学报,2014,34(3):402-405.
[13]丁铭,方琦,张丽珍,等.云南五个不同地区烟草花叶病毒外壳蛋白基因的序列比较[J].中国病毒学,2004,19(1):76-78.
[14]秦西云,卢训,方琦,等.云南烟草中烟草花叶病毒株系比较与分析[J].中国烟草学报,2013,19(6):106-113.
[15]刘金亮,王凤婷,魏毅,等.烟草花叶病毒南瓜分离物CP基因的克隆、序列分析及其原核表达[J].华北农学报,2010,25(5):6-10.
[16]Alzohairy A M.BioEdit:An important software for molecular biology[J].Gerf Bulletin of Biosciences,2011,2(1):60-61.
[17]Larkin M A,Blackshields G,Brown N P,et al.Clustal W and Clustal X version 2.0[J].Bioinformatics,2007,23(21):2947-2948.
[18]Goffard N,Weiller G.PathExpress:a web-based tool to identify relevant pathways in gene expression data[J].Nucleic Acids Research,2007,35(S2):176-181.
[19]Martin D P.RDP4:Detection and analysis of recombination patterns in virus genomes[J].Virus Evolution,2015,1(1):vev003.
[20]Tamura K,Peterson D,Peterson N,et al.MEGA5:molecular evolutionary genetics analysis using maximum likelihood,evolutionary distance,and maximum parsimony methods[J].Molecular Biology and Evolution,2011,28(10):2731-2739.
[21]Tomitaka Y,Ohshima K.A phylogeographical study of the Turnip mosaic virus population in East Asia reveals an‘emergent’lineage in Japan[J].Molecular Ecology,2006,15(14):4437-4457.
[22]Posada D.jModelTest:phylogenetic model averaging[J].Molecular Biology and Evolution,2008,25(7):1253-1256.
[23]Fu Y X.Statistical tests of neutrality of mutations against population growth,hitchhiking and background selection[J].Genetics,1997,147(2):915-925.
[24]Hudson R R.A new statistic for detecting genetic differentiation[J].Genetics,2000,155(4):2011-2014.
[25]Pamilo P,Bianchi N O.Evolution of the Zfx and Zfy genes:rates and interdependence between the genes[J].Molecular Biology and Evolution,1993,10(2):271-281.
[26]Nguyen,H D,Tran,H T N,Ohshima K.Genetic variation of the Turnip mosaic virus population of Vietnam:a case study of founder,regional and local influences[J].Virus Research,2013,171(1):138-149.
[27]Yin Xiao,Zheng Fangqiang,Tang Wei,et al.Genetic structure of Rice black-streaked dwarf virus populations in China[J].Archives of Virology,2013,158(12):2505-2515.
[28]Fu Y X,Li W H.Statistical tests of neutrality of mutations[J].Genetics,1993,133(3):693-709.
[29]Tajima F.Statistical method for testing the neutral mutation hypothesis by DNA polymorphism[J].Genetics,1989,123(3):585-595.
[30]Librado P,Rozas J.DnaSP v 5:a software for comprehensive analysis of DNA polymorphism data[J].Bioinformatics,2009,25(11):1451-1452.
[31]Roossinck,M J.Mechanisms of plant virus evolution[J].Annual Review of Phytopathology,1997,35:191-209.
[32]Cuevas J M,Delaunay A,Rupar M,et al.Molecular evolution and phylogeography of Potato virus Y based on the CP gene[J].Journal of General Virology,2012,93:2496-2501.
[33]Ogawa T,Nakagawa A,Hataya T,et al.The genetic structure of populations of Potato virus Y,in Japan;based on the analysis of 20full genomic sequences[J].Journal of Phytopathology,2012,160(11/12):661-673.
[34]宋丽云.我国烟草TMV和CMV种群结构遗传分析[D].北京:中国农业科学院,2012.
[35]谢扬军.烟草普通花叶病毒株系分化研究[D].北京:中国农业科学院,2009.