基于CP基因的中国云南省烟草TMV群体遗传多样性分析

Population genetic diversity analysis of tobacco mosaic virus on tobacco in Yunnan based on the CP gene sequences

为探明云南烟草上烟草花叶病毒(tobacco mosaic virus,TMV)的群体遗传多样性特征,本研究使用TMV外壳蛋白(coat protein,CP)基因的特异性引物对采自云南各烟区的疑似烟草花叶病样品进行检测,通过克隆测序获得138个TMV CP基因序列,对其进行了一致性比对,及系统发育、错配分布、遗传变异、群体多样性等分析。变异分析显示,138条CP基因序列共有变异位点数122个,占总位点数的25.42%,变异类型只有核苷酸替换,核酸多样性为0.018,单倍型多样性为0.970;一致性比对结果显示,138条序列的核苷酸和氨基酸序列一致性均为96%~100%;重组分析未检测到重组信号;对来自云南烟草,NCBI上其他地区烟草及云南地区其他寄主的TMV分离物的CP基因进行系统发育分析,结果显示,所有TMV分离物在进化上可分为4个组,本试验获得的分离物分布在1、2、3组,其中只有来源昭通地区的分离物倾向于聚成簇,表明云南烟草TMV分离物的适应性进化受地理适应性所驱动,与寄主适应性基本无关;错配分布分析显示,云南烟草TMV群体呈多峰分布,表明该群体近期未经历群体扩张事件;群体间遗传分化分析结果表明,除昭通和曲靖烟草TMV群体与其他TMV群体之间很容易发生遗传漂变促使群体发生遗传分化外,其余大部分TMV群体之间的基因流都可以抵制遗传漂变。本研究首次报道了云南各烟区TMV分离物群体遗传变异情况,研究结果可为TMV的抗病育种和制定更为有效的防治策略提供重要参考。

This study investigated the population genetic diversity of tobacco mosaic virus(TMV)on tobacco in Yunnan province.Specific primers targeting the TMV coat protein(CP)gene were used to detect suspected samples with mosaic symptoms from various tobacco-growing regions in Yunnan.A total of 138 TMV CP gene sequences were obtained through cloning,sequencing,and BLAST with NCBI database.These sequences were then analyzed for consistency,systematic development,mismatch distribution,genetic variation,and population diversity.Variation analysis showed that TMV CP gene contained 122 mutation sites,accounting for 25.42%out of the total mutation sites.The nucleotide substitution was the only type of mutation,with a nucleic acid diversity of 0.018 and a haplotype diversity of 0.970.Consistency comparison results revealed that the identities of nucleotide and amino acid sequences of the 138 TMV CP gene were 96%to 100%.Recombination analysis did not detect any recombination signals.A phylogenetic analysis was conducted on the CP genes of TMV isolates from Yunnan tobacco,tobacco from other regions on NCBI,and other hosts in Yunnan.The results showed that all TMV isolates could be divided into four groups in evolution.All 138 isolates obtained in this experiment were distributed in group 1,2,and 3,with only the isolates from Zhaotong region tending to cluster,indicating that the adaptive evolution of TMV isolates from Yunnan tobacco was driven by geographical adaptability and basically independent on host adaptability.Mismatch distribution analysis indicated that TMV populations from Yunnan tobacco exhibit multimodal distribution,suggesting that they have not undergone any group expansion events recently.The genetic differentiation analysis between populations indicate that it is easy for genetic drift to occur between tobacco TMV populations in Zhaotong and Qujing and other TMV populations,leading to genetic differentiation in the populations,However,the genetic drift may be resisted by gene flow among other TMV populations.This study is the first report on the genetic variation of TMV populations in various tobacco-growing regions of Yunnan.The findings provide important references for disease resistance breeding and the development of more effective control strategies against TMV.