[1]袁瑗,黄赛花,王成坤,等.大豆花叶病毒密码子使用及其进化分析[J].大豆科学,2014,33(06):801-807.[doi:10.11861/j.issn.1000-9841.2014.06.0801]
　YUAN Yuan,HUANG Sai-hua,WANG Cheng-kun,et al.Analysis on Codon Usage and Evolution of Soybean Mosaic Virus[J].Soybean Science,2014,33(06):801-807.[doi:10.11861/j.issn.1000-9841.2014.06.0801]
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大豆花叶病毒密码子使用及其进化分析

《大豆科学》[ISSN:1000-9841/CN:23-1227/S] 卷: 第33卷 期数: 2014年06期 页码: 801-807 栏目: 出版日期: 2014-12-25
Title:
Analysis on Codon Usage and Evolution of Soybean Mosaic Virus
作者:
袁瑗; 黄赛花; 王成坤; 智海剑
南京农业大学 大豆研究所/国家大豆改良中心，作物遗传与种质创新国家重点实验室，江苏 南京 210095
Author(s):
YUAN Yuan; HUANG Sai-hua; WANG Cheng-kun; ZHI Hai-jian
Soybean Research Institute of Nanjing Agricultural University/National Center for Soybean Improvement，National Key Laboratory for Crop Genetics and Germplasm Enhancement，Nanjing 210095,China
关键词:
大豆花叶病毒; 密码子偏性; 多元分析; 进化
Keywords:
Soybean Mosaic Virus; Codon usage bias; Multivariate analysis; Evolution
分类号:
S565.1
DOI:
10.11861/j.issn.1000-9841.2014.06.0801
文献标志码:
A
摘要:
对57个来自不同地区的大豆花叶病毒（SMV)分离物的基因组序列进行密码子使用偏性与进化分析。结果显示，SMV基因组GC含量较低；GC3<50%，说明SMV偏好使用以A/T结尾的密码子；SMV基因组密码子3个位置的GC含量均相互呈极显著相关（P＜0.01)，说明密码子3个位置的碱基组成相关；ENC值为49.42～51.78，密码子偏性存在但并不显著；对应性分析结果表明，第1轴显示67.84%的差异，ENC、GC3、GC12之间的相关性均达极显著水平(P<0.01)，说明密码子的偏性与碱基突变相关；中性绘图及ENC绘图分析均表明密码子使用模式主要受碱基突变影响；密码子使用频率比较结果显示SMV存在19个最优密码子；RSCU的聚类分析证明SMV密码子偏性与病毒地理来源相关。
Abstract:
The codon usage and evolution of 57 SMV isolates from different countries were analyzed in this study.The results indicated that GC content of codons was lower than AT in SMV isolates.GC3 content was less than 50%.SMV preferred to use those codons ending with A or T.GC content at three positions of codons(GC1,GC2 and GC3)had a significant correlation with each other(P<0.01).ENC value was between 49.42 and 51.78,which meant that the codon bias existed while it was not significant.Corresponding analysis(COA)indicated that Axis 1 appeared 67.84% variation.There were significant correlation(P<0.01)among ENC,GC3 and GC12.Above results with the analysis of Neutralityplot and ENC plot revealed that codon bias was influenced mainly by mutation pressure.And the comparative analysis of RSCU discovered 19 optimized codons in SMV.Cluster analysis based upon RSCU proved that SMV codon bias was related with their geographical origin.

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备注/Memo

基金项目转基因生物新品种培育科技重大专项(2008ZX08004-004)；国家自然科学基金(31171574，31371646)；现代农业产业技术体系(CARS-004)。

第一作者简介：袁瑗（1989-），女，博士，主要从事抗大豆花叶病毒基因定位研究。E-mail:2013201006@njau.edu.cn。

更新日期/Last Update: 2014-12-25