[1]原晓龙,康洪梅,王毅*. 云南蓝果树叶绿体基因组密码子偏好性分析[J].西北林学院学报,2020,35(4):26-31.[doi:10.3969/j.issn.1001-7461.2020.04.05]
　YUAN Xiao-long,KANG Hong-mei,WANG Yi*. Codon Usage Bias Analysis of Chloroplast Genome in Nyssa yunnanensis[J].JOURNAL OF NORTHWEST FORESTRY UNIVERSITY,2020,35(4):26-31.[doi:10.3969/j.issn.1001-7461.2020.04.05]
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 云南蓝果树叶绿体基因组密码子偏好性分析()
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《西北林学院学报》[ISSN:1001-7461/CN:61-1202/S]

卷:
第35卷
期数:
2020年第4期
页码:
26-31
栏目:
出版日期:
2020-09-29

文章信息/Info

Title:
 Codon Usage Bias Analysis of Chloroplast Genome in Nyssa yunnanensis
文章编号:
1001-7461(2020)04-0026-06
作者:
 原晓龙; 康洪梅; 王毅*
 (云南省林业和草原科学院 云南省森林植物培育与开发利用重点实验室/国家林业和草原局 云南珍稀濒特森林植物保护和繁育重点实验室，云南 昆明 650201)
Author(s):
 YUAN Xiao-long; KANG Hong-mei; WANG Yi*
 (Yunnan Provincial Key Laboratory of Cultivation and Exploitation of Forest Plants/Conservation of Rare,Endangered&Endemic Forest Plants,Public Key Laboratory of the National Forestry and Grassland Administration,Yunnan Academy of Forestry and Grassland,Kunming 650201,Yunnan,China)
关键词:
 ; 云南蓝果树; 叶绿体基因组; 密码子偏好性; 选择; 最优密码子
Keywords:
Nyssa yunnanensis;  chloroplast genome;  codon usage bias;  selection;  optimal codon
分类号:
Q71
DOI:
10.3969/j.issn.1001-7461.2020.04.05
文献标志码:
A
摘要:
 以云南蓝果树叶绿体基因组为研究对象，采用Codon W 1.4.2等软件，通过分析云南蓝果树叶绿体基因组52个基因密码子的偏好性，探究影响密码子使用偏性形成的主要因素。结果表明：1) Codon W和CUSP软件分析显示密码子第3位碱基GC含量为28.40%，ENC值>45的基因有39个，说明密码子偏好以AT结尾，且存在较弱偏性。2)中性绘图分析显示，GC12与GC3的相关系数为0.161 2，相关性不显著，说明密码子第1、第2位与第3位碱基组成存在显著差异。3) ENC绘图结合ENC比值频率表显示，大部分基因距离标准曲线较远，说明密码子偏好性主要受选择的影响。4) PR2-plot分析显示密码子第3位碱基使用频率方面，T>A，G>C，说明密码子偏好性受多重因素影响。5) 确定UUG、UCA、GCU、AAU、GAU和GGA为最优密码子。综上所述，云南蓝果树叶绿体基因组密码子的使用主要受选择的影响，受其他如突变等因素的影响较弱。
Abstract:
 The chloroplast genome of Nyssa yunnanensis was taken as the research object,the codon usage bias of 52 genes from the chloroplast genome of N.yunnanensis was analyzed by the software Codon W 1.4.2,and the main factors affecting the formation of codon usage bias was explored.The results showed as follows 1) According to the analysis results of the software Codon W and CUSP,the GC content of the 3rd base composition of the codons was 28.40%,there were 39 genes when ENC value was greater than 45,therefore,these phenomena illustrated that the codons preferred to end with AT,and had a weaker bias.2) Neutrality analysis revealed the correlation coefficient of GC12 and GC3 was 0.161 2,these had no significant correlation,which declared that the 1st two base composition and the 3rd of the codons existed significant variation.3) The combination of ENC plot with ENC ration table indicated that most genes were far from the standard curve,which suggested that the codon usage bias was principally affected by selection pressure.4) PR2-plot analysis revealed that the 3rd codon base composition in the frequency of utilization,T>A and G>C,which stated the codon usage bias was affected by multi-factors.5) The optimal codons were determined as UUG,UCA,GCU,AAU,GAU and GGA.It was summarized that the codon usage bias of the genes from the chloroplast genome of N.yunnanensis was mainly affected by selection pressure,other factors,such as mutation presented little effect.

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备注/Memo

备注/Memo:
 收稿日期：2019-09-10修回日期：2019-12-18
基金项目：国家自然科学基金(31860177); 云南省应用基础研究计划(2016FD097)。
作者简介：原晓龙。研究方向：林木分子生物技术与分子生物学。E-mail:xiaolony@126.com
*通信作者：王毅,博士,副研究员。研究方向:分子生物学。E-mail:22825818@qq.com
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