The analysis of genomic genetic diversity of Cucurbit aphid-borne yellows virus

To study the molecular characteristics, genetic structure and evolutionary mechanism of Cucurbit aphid-borne yellows virus (CABYV),in order to clarify the epidemic pattern of the virus in the field and formulate long-term sustainable prevention and control strategies which is of great significance. 120 melon leaves suspected to be infected with CABYV were randomly collected from Aksu City, Xinjiang. RT-PCR was used to detect the virus. MEGA 7.0 was used to construct phylogenetic tree, DnaSPv5.10 was used to analyze the genetic diversity among different sequences, and RDP v.4.31 software was used to analyze the possiblerecombination events of CABYV sequence. As verified by RT-PCR, 38 samples were CABYV positive, and the detection ratewas 31.67%. A new CABYV-2 was isolated, sequenced and cloned from these positive samples. The length of the genome was 5497 bp, encoding six open reading frames. Compared with 23 CABYV strains which isolate from different countries in NCBI database, CABYV-2 had the highest homology with KR231942.1 and the lowest homology with JF939812.1. The results of evolutionary tree analysis showed that 24 isolates were divided into two branchesdue to different geographical factors, including CABYV-2 and KR2319421 come together and belong to branch 1. The results of genetic diversity and neutral test showed that CABYV was highly variable and population was expanding. The results of recombination analysis showed that there were two recombination events, EU636992.1 and KR231949.1, which exacerbated the variation of CABYV. CABYV was isolated from Aksu, Xinjiang and KR231942.1 from Korea had the closest genetic relationship and the farthest genetic relationship with isolates from European countries. There were great genetic differences between branch 1 and branch 2 isolates. The recombination of cabyv among different hosts intensifies the variation of CABYV recombination and negative selection may be important reasons affecting the genetic variation of CABYV.

为研究瓜蚜传黄化病毒（Cucurbit aphid-borne yellows virus, CABYV）的分子特征、遗传结构与进化机制，明确该病毒的田间流行规律并制定长期可持续防控策略具有重要意义。本研究从新疆阿克苏市随机采集120份疑似感染CABYV的甜瓜叶片，采用逆转录聚合酶链式反应（Reverse Transcription-Polymerase Chain Reaction, RT-PCR）开展病毒检测。利用MEGA 7.0软件构建系统发育树，采用DnaSP v5.10软件分析不同序列间的遗传多样性，通过RDP v4.31软件对CABYV序列的潜在重组事件进行分析。经RT-PCR检测验证，共获得38份CABYV阳性样本，检测率为31.67%。从上述阳性样本中分离、测序并克隆得到一株新的CABYV-2毒株，其基因组全长为5497 bp，编码6个开放阅读框。与NCBI数据库中来自不同国家的23株CABYV毒株相比，CABYV-2与KR231942.1的同源性最高，与JF939812.1的同源性最低。系统发育树分析结果显示，受地理因素影响，24株病毒分离物可划分为两个分支；其中CABYV-2与KR231942.1聚为一支，隶属于分支1。遗传多样性与中性检验结果表明，CABYV具有较高的变异性，其种群处于扩张状态。重组分析结果显示，EU636992.1与KR231949.1存在两次重组事件，加剧了CABYV的变异程度。本研究从新疆阿克苏地区分离得到的CABYV毒株与韩国来源的KR231942.1毒株亲缘关系最近，与欧洲国家来源的分离物亲缘关系最远；分支1与分支2的分离物间存在显著遗传差异。不同宿主间的CABYV重组现象加剧了病毒的变异，而负选择可能是影响CABYV遗传变异的重要因素之一。