紫九牛叶绿体基因组密码子偏好性分析

郭 松<sup>1; 2</sup>; 梁湘兰<sup>1</sup>; 黄青青<sup>1</sup>; 卢 祥<sup>1; 2</sup>; 严其伟<sup>1; 2</sup>; 张 鹏<sup>1; 2</sup>; 覃逸明<sup> 1; 2*</sup>

引用本文:	郭松, 梁湘兰, 黄青青, 卢祥, 严其伟, 张鹏, 覃逸明.紫九牛叶绿体基因组密码子偏好性分析[J].广西植物,2022,42(8):1426-1432.[点击复制]
	GUO Song, LIANG Xianglan, HUANG Qingqing, LU Xiang, YAN Qiwei, ZHANG Peng, QIN Yiming.Codon usage bias in the chloroplast genome of Ventilago leiocarpa[J].Guihaia,2022,42(8):1426-1432.[点击复制]

【打印本页】【下载PDF全文】【查看/发表评论】【下载PDF阅读器】【关闭】

←前一篇|后一篇→

过刊浏览高级检索

本文已被：浏览 6260次下载 1741次	码上扫一扫！
分享到：微信更多字体:加大+\|默认\|缩小-
紫九牛叶绿体基因组密码子偏好性分析
郭松^1,2, 梁湘兰¹, 黄青青¹, 卢祥^1,2, 严其伟^1,2, 张鹏^1,2, 覃逸明^1,2*
1. 广西科技师范学院食品与生化工程学院, 广西来宾 546199;2. 广西科技师范学院特色瑶药资源研究与开发重点实验室, 广西来宾 546199

摘要:

为确定瑶药紫九牛叶绿体基因组密码子的使用模式及其成因,该研究以紫九牛叶绿体基因组50条蛋白质编码序列为研究对象,利用Codon W 1.4.2和在线软件CUSP和Chips分析其密码子偏好性。结果表明:(1)RSCU>1的密码子有29个,其中有28个以A/U结尾,说明叶绿体基因组的同义密码子中偏好以A/U结尾。(2)紫九牛叶绿体基因组密码子的GC含量GC₁(47.38%)>GC₂(39.81%)>GC₃(29.60%),ENC值大于45的有40个,说明紫九牛叶绿体基因组存在较弱的偏性。(3)中性绘图分析和ENC-plot分析说明了紫九牛叶绿体基因组密码子的偏好性既受到选择的作用,又受到突变因素的影响。(4)通过构建的高低基因表达库最终确定了15个最优密码子,分别为UUG、AUU、GUU、GUA、UCU、 CCU、ACU、ACA、GCU、CAA、AAC、GAA、UGU、CGU和GGU。该研究为紫九牛叶绿体基因组的确定以及遗传多样性分析提供了依据。

关键词: 紫九牛, 叶绿体基因组, 密码子, 偏好性分析, 最优密码子

DOI：10.11931/guihaia.gxzw202012011

分类号:Q75

文章编号:1000-3142(2022)08-1426-07

基金项目:广西科技师范学院高层次人才启动经费(GXKS2020GKY009); 广西科技师范学院特色瑶药资源研究与开发校级重点实验室经费(KJ5CSH000005)[Supported by Start-Up Fund for High-Level Talents of Guangxi Science & Technology Normal University(GXKS2020GKY009); Fund of Key Laboratory for Research and Development of Characteristic Yao Medicine Resources of Guangxi Science & Technology Normal University(KJ5CSH000005)]。

Codon usage bias in the chloroplast genome of Ventilago leiocarpa

GUO Song^1,2, LIANG Xianglan¹, HUANG Qingqing¹, LU Xiang^1,2, YAN Qiwei^1,2, ZHANG Peng^1,2, QIN Yiming^1,2*

1. College of Food and Biochemical Engineering, Guangxi Science &2.Technology Normal University, Laibin 546119, Guangxi, China;3.2. Key Laboratory for Research and Development of Characteristic Yao Medicine Resources, Guangxi Science &4.Technology Normal University, Laibin 546119, Guangxi, China 1. College of Food and Biochemical Engineering, Guangxi Science & Technology Normal University, Laibin 546119, Guangxi, China; 2. Key Laboratory for Research and Development of Characteristic Yao Medicine Resources, Guangxi Science & Technology Normal University, Laibin 546119, Guangxi, China

Abstract:

To determine the codon usage pattern of chloroplast genome of Ventilago leiocarpa, a total of 50 selected protein-coding sequences were analyzed using Codon W 1.4.2 and online softwares of CUSP and Chips. The results were as follows:(1)There were 29 codons with RSCU > 1, and 28 of them ended with A/U, indicating that synonymous codons in chloroplast genome tend to end with A/U.(2)GC content of codon in chloroplast genome of V. leiocarpa was GC₁(47.38%)> GC₂(39.81%)> GC₃(29.60%), and there were 40 with ENC value greater than 45, which indicates that there is weak bias in chloroplast genome of V. leiocarpa.(3)Neutral mapping analysis and ENC-plot analysis demonstrated that the codon preference of chloroplast genome of V. leiocarpa was affected by both selection and mutation factors.(4)Through the constructed high and low gene expression libraries, 15 optimal codons were finally determined, which were UUG, AUU, GUU, GUA, UCU, CCU, ACU, ACA, GCU, CAA, AAC, GAA, UGU, CGU and GGU. The present study took some basis for the determination of chloroplast genome and genetic diversity analysis of V. leiocarpa.

Key words: Ventilago leiocarpa, chloroplast genome, codon, usage bias analysis, optimal codons