辣椒脉斑驳病毒湖南分离物全基因组序列测定及分子特征

谭汝晴; 罗香文; 卜姗; 张宇; 张松柏; 张德咏; 刘勇

doi:10.19303/j.issn.1008-0384.2020.02.009

辣椒脉斑驳病毒湖南分离物全基因组序列测定及分子特征

doi: 10.19303/j.issn.1008-0384.2020.02.009

谭汝晴^1,,
罗香文²,
卜姗²,
张宇²,
张松柏^{1, 2},
张德咏^{1, 2},
刘勇^{1, 2, ,}

1.
湖南农业大学植物保护学院，湖南长沙 410120
2.
湖南省植物保护研究所，湖南长沙 410125

基金项目: 国家自然科学基金项目（31772133、31571981）；国家大宗蔬菜产业体系建设专项（CARS-23-D-02）；湖南省自然科学基金项目（2018JJ2234）

详细信息

作者简介:
谭汝晴（1994−），女，硕士研究生，主要从事植物病毒致病分子机制研究（E-mail：451704363@qq.com）

通讯作者:
刘勇（1966−），博士，研究员，主要从事蔬菜病害致害机制及绿色综合防控技术研究（E-mail：liuyong@hunaas.cn）

中图分类号: S 436.418.1+2
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出版历程
- 收稿日期: 2019-12-27
- 修回日期: 2020-03-04
- 刊出日期: 2020-02-01

Full Genomic Sequence and Molecular Characteristics of Hunan Isolate of Chilliveinal mottle Virus

TAN Ru-qing^1
,,
LUO Xiang-wen²,
BU Shan²,
ZHANG Yu²,
ZHANG Song-bai^{1, 2},
ZHANG De-yong^{1, 2},
LIU Yong^{1, 2
, ,}

1.
College of Plant Protection, Hunan Agricultural University, Changsha, Hunan　410120, China
2.
Hunan Plant Protection Research Institute, Changsha, Hunan　410125, China

摘要

摘要: 目的辣椒脉斑驳病毒（Chilli veinal mottle virus，ChiVMV）是东南亚茄科作物主产地主要病毒种类之一，严重危害辣椒等茄科作物的生产。测定ChiVMV的全基因组序列，分析其分子特征，可以明确该病毒的适应性进化以及对我国辣椒等茄科作物的潜在威胁提供科学基础。方法以湖南疑似感染ChiVMV辣椒为样本，采用small RNA高通量测序结合RT-PCR测定病毒全基因组序列，利用Mega、RDP及DnaSP等生物学软件分析其分子特征。结果 ChiVMV湖南分离物全长基因组序列为9 704 nt（不包含3'-A尾），与其他分离物的序列同源性为 84% ～ 94 %。系统发育分析表明，我国的ChiVMV聚类为一个亚簇，与其他国家和地区分离物不存在重组事件。基因的替换指数R=3.29，替换碱基类型主要是 C/T替换。结论碱基替换突变可能是ChiVMV湖南分离物适应性进化的主要因素。
- 辣椒脉斑驳病毒 /
- 全基因组序列 /
- 系统发育分析 /
- RNA突变和重组
Abstract: Objective Characteristics and full genomic sequence of Chilliveinal mottle virus (ChiVMV), one of the most recurring viral pathogens infecting chili pepper plants in South-East Asia were studied to decipher the evolution of the virus for improved estimation on its potential threat to Solanacae crops. Method The ChiVMV gene from Hunan isolate (ChiVMVhn) was sequenced using the small RNA high-throughput sequencing and RT-PCR. Molecular characteristics of the gene were analyzed by Mega, RDP, and DnaSP software. Result The gene of ChiVMVhn contained 9,704 nucleotides (excluding 3’-poly A) and shared 84%-94% identity with those from the other ChiVMVs. The phylogenetic analysis suggested that ChiVMVhn represented an evolutionary isolate distinctive from those reported previously elsewhere in the world. The nucleotide substitution in ChiVMVhn gene was R=3.29 and dominated by C/T. Conclusion RNA mutation, rather than recombination, in the genes was seen crucial in the evolution of ChiVMVhn. Further studies on varieties of ChiVMV would considerably aid the scientific understanding on the evolution and pathogenic potential of the virus.
- Chilliveinal mottle virus /
- genomic sequence /
- phylogenetic relationship /
- RNA mutation and recombinant

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图 1 基于ChiVMV全基因组序列的系统发育分析

注：引导值超过60%。使用CLUSTAL W程序（mega 5.0）生成树状图。

Figure 1. Phylogenetic tree constructed using full length sequences of genes from 10 ChiVMVs

Note：Bootstrap values exceeding 60% are shown. Dendrogram was generated using CLUSTAL W program (mega 5.0).

下载: 全尺寸图片幻灯片

图 2 基于ChiVMVCP基因序列的系统发育分析

注：使用CLUSTAL W程序（mega 5.0）生成树状图。

Figure 2. Phylogenetic tree constructed using CP genes sequences of ChiVMV isolates

Note: Dendrogram was generated using CLUSTAL W program (mega 5.0).

下载: 全尺寸图片幻灯片

图 3 基于ChiVMV全基因组序列的重组分析

Figure 3. Recombinant events based on full sequences of genes from ChiVMVs

下载: 全尺寸图片幻灯片

表 1 ChiVMV RT-PCR特异性引物

Table 1. Primers for amplifying genomic sequence of ChiVMV gene

引物编号 Primers	序列（5’-3’） Sequence (5’-3’)
CV1F	GTATTGCCTATGCTAAGGACA
CV1R	TCGCCACTATTGAATAGCTTG
CV2F	TCTTTATCTCAGCACACATCG
CV2R	TCGCCACTATTGAATAGCTTG
CV3F	CCCAAGCACATTGTTAAGGGA
CV8F	TAAAGTGCAATTCTTAATCGG
CV8R	AAGATAATGTAGTGCATAGCC
CV9F	CTGTCAAGTTATAAGAAGCCTA
CV9R	ACTAAACTCTTTAAGCCGTTG
CV12F	TCATTCCATCCTACAAGGGAC
CV12R	TCGGGCTAGTTCTAATAAGCAA

下载: 导出CSV

表 2 ChiVMV全基因组序列碱基替换指数

Table 2. Maximum composite likelihood estimation of nucleotide substitution pattern

碱基 Base	A	T	C	G
A	－	2.59	1.8	15.44
T	3.07	－	17.98	2.21
C	3.07	25.84	－	2.21
G	21.4	2.59	1.8	－

下载: 导出CSV

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