长沙地区南瓜的小西葫芦黄花叶病毒检测及其分子进化分析
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摘要
对长沙地区160份南瓜疑似病毒病样品进行小西葫芦黄花叶病毒(Zucchini yellow mosaic virus,ZYMV)检测,检出率达46.9%。为进一步明确长沙地区ZYMV分离物的分类地位和分子进化特征,克隆获得了1个长沙地区ZYMV外壳蛋白基因,与Gen Bank已报道的ZYMV外壳蛋白基因比对,并进行基因重组、系统发生、遗传差异、选择压力、种群结构和基因漂流分析。结果显示:长沙地区ZYMV外壳蛋白基因没有发生明显的重组,突变与负选择作用是其进化的主要驱动力,种群结构相对稳定,但正处于扩张的趋势中;ZYMV不同分离物外壳蛋白基因形成3个有明显地理相关性的美洲、欧洲和亚洲种群,美洲和欧洲种群与亚洲种群之间基因交流不频繁,可能受到遗传漂变的影响,而欧洲种群与亚洲种群之间基因交流较频繁。
Zucchini yellow mosaic virus(ZYMV) was detected in 160 suspected pumpkin virus samples in Changsha area, and the detection rate was 46.9%. To further clarify the classification and molecular evolution of ZYMV Changsha isolates, the coat protein gene was cloned and compared with the ZYMV coat protein gene reported in Gen Bank. And these sequences were analyzed for genetic recombination, phylogenetic, genetic differences, selection pressure, population structure and gene drift analysis. The results showed that no significant recombination of ZYMV coat protein gene was found. Mutation and negative selection are the main driving forces of its evolution, the population structure is relatively stable but is in the trend of expansion. The different isolates of ZYMV coat protein gene form 3 geographically relevant populations: America population, Europe population and Asia population. There is no frequent gene exchange between America and Europe and Asia, and each group may be affected by genetic drift, and gene exchange between Europe and Asia is more frequent.
Zucchini yellow mosaic virus(ZYMV) was detected in 160 suspected pumpkin virus samples in Changsha area, and the detection rate was 46.9%. To further clarify the classification and molecular evolution of ZYMV Changsha isolates, the coat protein gene was cloned and compared with the ZYMV coat protein gene reported in Gen Bank. And these sequences were analyzed for genetic recombination, phylogenetic, genetic differences, selection pressure, population structure and gene drift analysis. The results showed that no significant recombination of ZYMV coat protein gene was found. Mutation and negative selection are the main driving forces of its evolution, the population structure is relatively stable but is in the trend of expansion. The different isolates of ZYMV coat protein gene form 3 geographically relevant populations: America population, Europe population and Asia population. There is no frequent gene exchange between America and Europe and Asia, and each group may be affected by genetic drift, and gene exchange between Europe and Asia is more frequent.
引文
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[30]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.
[31]FU Y X,LI W H.Statistical tests of neutrality of mutations[J].Genetics,1993,133(3):693–709.
[32]TAJIMA F.Statistical method for testing the neutral mutation hypothesis by DNA polymorphism[J].Genetics,1989,123(3):585–595.
[33]LIBRADO P,ROZAS J.Dna SP v5:a software for comprehensive analysis of DNA polymorphism data[J].Bioinformatics,2009,25(11):1451–1452.
[34]ROOSSINCK M J.Mechanisms of plant virus evolution[J].Annual Review of Phytopathology,1997,35:191–209.
[35]OGAWA T,NAKAGAWA A,HATAYA T,et al.The genetic structure of populations of Potato virus Y,in Japan;based on the analysis of 20 full genomic sequences[J].Journal of Phytopathology,2012,160(11/12):661–673.
[2]LECOQ H,PITRAT M,CLéMENT M.Identification etcaractersation d’un potyvirusprovoquant la maladie du rabougrissmentjuane du melon[J].Agronomie,1981,1(10):827–834.
[3]BATESON M F,HENDERSON J,CHALEEPROM W,et al.Papaya ringspotpoty virus:isolate variability and the origin of PRSV type P(Australis)[J].J General Virology,1994,75:3547–3553.
[4]ATREYA C D,RACCAH B,PIRONE T P.A point mutation in the coat protein abolishes aphid transmissibility of a poty–viurs[J].Virology,1990,178(1):161–165.
[5]AREYA P L,ATEYA C D,PIRONE T P,et al.Amino acid substitutions in the coat protein result in loss of insect trans missibility of a plant virus[J].Microbiology,1991,88(17):7887–7891.
[6]CHEZZI C,SCHOUB B D.Differentiation between vaccinerelated and wild–type polioviruses using a heteroduplex mobility assay[J].Virol Methods,1996,62(2):93–102.
[7]郑光宇,董涛.在新疆发生的小西葫芦黄化花叶病毒的研究初报[J].植物病理学报,1991,21(1):72.
[8]DIANA L,DALIA W,VINOD S,et al.A high level of transgenic viral small RNA is associated with broad potyvirus resistance in cucurbits[J].Molecular Plant–Microbe Interactions,2011,24(24):1220–1238.
[9]WEI Ting,MICHAEL N P,DIETNAR B,et al.Development of a short oligonucleotide microarray for the detection and identification of multiple potyviruses[J].Journal of Virological Methods,2009,162(1/2):109–118.
[10]LUO H,WYLIE S J,JONES M G K.Identification of plant viruses using one–dimensional gel electrophoresis and peptide mass fingerprints[J].Journal of Virological Methods,2010,165(2):297–301.
[11]COUTTS B A,KEHOE M A,WEBSTER C G,et al.Zucchini yellow mosaic virus:biological properties,detection procedures and comparison of coat protein gene sequences[J].Arch Virol,2011,156(12):2119–2131.
[12]NEHA S,SATYA V B,ANJU S,et al.Comparative genomic and proteomic phylogenetic analysis of Indian isolate of partial coat protein gene sequence of zucchini yellow mosaic virus(ZYMV)using data mining[J].Proteomics Bioinform,2012,5(9):196–203.
[13]AZARFR A,IZADPANAH K,AFSHANFARA,et al.Purification and the complete genome sequence of Zucchini Yellow Mosaic Virus Fars isolate[J].Iran Journal of Plant Pathology,2012,48(3):403–409.
[14]CHEN Y K,HONG Y H.First report of Begonia chloroticringspot caused by Zucchini yellow mosaic virusin Taiwan[J].Plant Disease,2008,92(8):1247.
[15]GU Q S,FAN Z F,ROGGERO P,et al.Cloning and sequence analysis of the coat protein gene of Zucchini yellow mosaic virus from China[J].Acta Phytopatholo-gica Sinica,2003,33(6):498–502.
[16]LIN S S,WU H W,JAN F J,et al.Modifications of the helper component–protease of Zucchini yellow mosaic for generation of attenuated mutants for cross protection against severe infection[J].Phytopathology,2007,97(3):287–296.
[17]BANANEJ K,KESHAVARZ T,VAHDAT A.Biological and molecular variability of Zucchini yellow mosaic virusin Iran[J].Phytopatho,2008,156(11/12):654–659.
[18]赵芹,谢大森,何晓明,等.广东地区冬瓜感染的小西葫芦黄花叶病毒检测及其外壳蛋白基因多样性分析[J].园艺学报,2016,43(1):151–160.
[19]ALZOHAIRY A M.Bio Edit:an important software for molecular biology[J].Gerf Bulletin of Biosciences,2011,2(1):60–61.
[20]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.
[21]GOFFARD N,WEILLER G.Path Express:a web–based tool to identify relevant pathways in gene expression data[J].Nucleic Acids Research,2007,35(Web Server issue):176–181.
[22]MARTIN D P.RDP4:Detection and analysis of recombination patterns in virus genomes[J].Virus Evolution,2015,1(1):vev003.
[23]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.
[24]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.
[25]POSADA D.j Model Test:phylogenetic model averaging[J].Molecular Biology and Evolution,2008,25(7):1253–1256.
[26]FU Y X.Statistical tests of neutrality of mutations against population growth,hitchhiking and background selection[J].Genetics,1997,147(2):915–925.
[27]HUDSON R R.A new statistic for detecting genetic differentiation[J].Genetics,2000,155(4):2011–2014.
[28]PAMILO P,BIANCHI N O.Evolution of the Zfx and Zfygenes:rates and interdependence between the genes[J].Molecular Biology and Evolution,1993,10(2):271–281.
[29]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.
[30]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.
[31]FU Y X,LI W H.Statistical tests of neutrality of mutations[J].Genetics,1993,133(3):693–709.
[32]TAJIMA F.Statistical method for testing the neutral mutation hypothesis by DNA polymorphism[J].Genetics,1989,123(3):585–595.
[33]LIBRADO P,ROZAS J.Dna SP v5:a software for comprehensive analysis of DNA polymorphism data[J].Bioinformatics,2009,25(11):1451–1452.
[34]ROOSSINCK M J.Mechanisms of plant virus evolution[J].Annual Review of Phytopathology,1997,35:191–209.
[35]OGAWA T,NAKAGAWA A,HATAYA T,et al.The genetic structure of populations of Potato virus Y,in Japan;based on the analysis of 20 full genomic sequences[J].Journal of Phytopathology,2012,160(11/12):661–673.