番茄褪绿病毒的进化动态与适应性进化特征  

The Evolutionary Dynamics and Adaptive Evolution of Tomato Chlorosis Virus

作　　者：邹林峰 涂丽琴 沈建国 杜振国[1] 蔡伟 季英华[2] 高芳銮[1] ZOU LinFeng;TU LiQin;SHEN JianGuo;DU ZhenGuo;CAI Wei;JI YingHua;GAO FangLuan(Fujian Key Laboratory of Plant Virology,Institute of Plant Virology,Fujian Agriculture and Forestry University,Fuzhou 350002;Institute of Plant Protection,Jiangsu Academy of Agricultural Sciences,Nanjing 210014;Technology Center of Fuzhou Customs District,Fuzhou 350001;Comprehensive Technical Service Center of Rongcheng Customs District,Fuqing 350300,Fujian)

机构地区：[1]福建农林大学植物病毒研究所福建省植物病毒学重点实验室,福州350002 [2]江苏省农业科学院植物保护研究所,南京210014 [3]福州海关技术中心,福州350001 [4]榕城海关综合技术服务中心,福建福清350300

出　　处：《中国农业科学》2020年第23期4791-4801,共11页Scientia Agricultura Sinica

基　　金：国家重点研发计划(2018YFD0201208);国家自然科学基金(31572074,31770168);福建省农业科技重大专项(2017NZ0003-1)。

摘　　要：【目的】番茄褪绿病毒(tomato chlorosis virus,ToCV)是长线形病毒科(Closteroviridae)毛形病毒属(Crinivirus)成员,现已成为我国番茄和其他蔬菜作物上最为常见的病毒之一。研究旨在查明ToCV的进化历史,尤其是该病毒何时何地传入我国,并阐明其适应性进化机制。【方法】根据ToCV外壳蛋白(coat protein,CP)基因两侧保守区设计1对特异性引物,对随机抽取的13个ToCV分离物进行扩增克隆,将测序获得的新序列与GenBank下载的含有采样时间和地理信息的序列合并得到103条ToCV CP基因序列,采用日期随机化检验(date-randomization test,DRT)检测数据集中的时间信号,并应用贝叶斯谱系动力学框架重建该病毒的进化动态。同时,应用系统发育与性状关联分析(phylogeny-trait association analysis)评估地理因素对ToCV适应性进化的影响。【结果】13个ToCV分离物均成功扩增出预期大小(约800 bp)的特异性片段,核苷酸序列与已报道的ToCV不同分离物CP基因序列一致性均在98%以上;基于聚类排列的日期随机化检验结果显示,通过实际采样时间和日期随机化的数据集分别推断获得的替代速率在95%置信区间之间没有存在重叠,表明本研究的数据集具有足够的时间信号,可以用于后续的贝叶斯分子定年(Bayesian molecular dating)分析。贝叶斯系统发育分析显示ToCV的最近共祖时间(the most recent common ancestor)为1920年(95%置信区间:1849-1976),该病毒约于2005年左右从美国引入中国。该病毒的CP基因替代速率约为1.12×10-3替代/位点/年(95%置信区间:6.08×10-4-1.73×10-3),与动物RNA病毒的相当,表明ToCV正处于快速进化之中。此外,系统发育分析与性状关联分析结果显示ToCV分离物与其来源地区的关联系数(association index)、简约分值(parsimony score)和最大单系分支(maximum monophyletic clade)统计检验均呈极显著水平(P<0.01),表明地理因素与ToCV适应性进化之间存【Objective】Tomato chlorosis virus(ToCV),a member of the genus Crinivirus in the family Closteroviridae,has emerged as one of the most prevalent viruses in tomato and other vegetable plants in China.The objectives of this study are to investigate the evolutionary history of ToCV,particularly when and where this virus was introduced into China,and to elucidate its adaptive evolutionary mechanism.【Method】A specific primer pair flanking the coat protein gene(CP)of ToCV was designed.The CP of 13 randomly selected ToCV isolates from China was sequenced after reverse transcription and amplification using this primer pair.In addition to the novel sequence data,all published CP sequences with known sampling dates and geographic locations were obtained to assemble a total data set consisting of 103 CP sequences.A date-randomization test(DRT)was performed to assess the temporal signal in the data set and Bayesian phylodynamic framework was used to reconstruct the temporal dynamics of ToCV.Simultaneously,phylogeny-trait association analysis was used to identify whether geographic factors are involved in the adaptive evolution of ToCV.【Result】A fragment with expected size(≈800 bp)was obtained from all the 13 ToCV-positive samples selected in this study.The CP of the 13 ToCV isolates shared more than 98%nucleotide identity with the reported sequences of other ToCV isolates.The 95%credibility intervals of rate estimate from the real sampling dates did not overlap with those from 10 replicate data sets with cluster permuted sampling date,indicating the presence of sufficient temporal signal in the sequence data allowing us to proceed with the Bayesian molecular dating analyses.Bayesian phylogenetic analyses showed that the estimated time of the most recent common ancestor of ToCV was 1920 CE(95%credibility interval 1849-1976)and the ToCV in China's Mainland was introduced from the USA at around 2005 CE.ToCV has been evolving at a rate of 1.12×10^-3 substitutions/site/year(95%credibility interval 6.08×10^-4-1.73×

关 键 词：番茄褪绿病毒 贝叶斯谱系动力学 替代速率 时间信号 适应性进化 

分 类 号：S436.412.11[农业科学—农业昆虫与害虫防治]