[1]包国媛,李文辛,杨鑫光,等.海甜菜线粒体和叶绿体基因组密码子使用偏好性分析[J].江苏农业学报,2023,(09):1804-1817.[doi:doi:10.3969/j.issn.1000-4440.2023.09.002]
　BAO Guo-yuan,LI Wen-xin,YANG Xin-guang,et al.Analysis of codon usage bias in mitochondrial and chloroplast genomes of Beta vulgaris subsp.[J].,2023,(09):1804-1817.[doi:doi:10.3969/j.issn.1000-4440.2023.09.002]
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海甜菜线粒体和叶绿体基因组密码子使用偏好性分析()
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江苏农业学报[ISSN:1006-6977/CN:61-1281/TN]

卷:
期数:
2023年09期
页码:
1804-1817
栏目:
遗传育种·生理生化
出版日期:
2023-12-31

文章信息/Info

Title:
Analysis of codon usage bias in mitochondrial and chloroplast genomes of Beta vulgaris subsp.
作者:
包国媛1; 李文辛1; 杨鑫光1; 王雅琼1; 2; 3; 4
(1.青海民族大学生态环境与资源学院,青海西宁810007；2.青海省特色经济植物高值化利用重点实验室,青海西宁810007；3.青海省生物技术与分析测试重点实验室,青海西宁810007；4.青藏高原资源化学与生态环境保护国家民委重点实验室,青海西宁810007)
Author(s):
BAO Guo-yuan1; LI Wen-xin1; YANG Xin-guang1; WANG Ya-qiong1; 2; 3; 4
(1.The College of Ecological Environment and Resources, Qinghai Minzu University, Xining 810007, China； 2.Qinghai Provincial Key Laboratory of High-value Utilization of Characteristic Economic Plants, Xining 810007, China;3.Qinghai Provincial Biotechnology and Analytical Testing Key Laboratory, Xining 810007, China;4.Key Laboratory of Resource Chemistry and Eco-environmental Protection in Qinghai-Tibet Plateau, State Ethnic Affairs Commission, Xining 810007, China)
关键词:
海甜菜; 线粒体基因组; 叶绿体基因组; 密码子; 使用偏好性
Keywords:
Beta vulgaris subsp.; mitochondrial genome; chloroplast genome; codon; usage bias
分类号:
S556.3
DOI:
doi:10.3969/j.issn.1000-4440.2023.09.002
文献标志码:
A
摘要:
为明确海甜菜线粒体和叶绿体基因组密码子使用偏好性及影响因素,以海甜菜线粒体基因组136条蛋白编码序列(CDS)和叶绿体基因组52条蛋白编码序列为数据源,利用Codon W 和CUSP软件,结合密码子使用的中性绘图分析、有效密码子数分析(ENC-plot)、偏倚性分析(PR2-plot),探究海甜菜线粒体和叶绿体基因组密码子使用的偏好性,并明确最优密码子。结果显示:海甜菜线粒体和叶绿体基因组中所有密码子的平均G+C碱基含量分别为43.42%和37.92%；密码子第3位碱基多为A或U。线粒体和叶绿体基因组有效密码子数(ENC)分别为36.44～61.00和35.00～52.01,平均值为52.23和46.10。自然选择是影响海甜菜线粒体和叶绿体基因组密码子使用偏好性的主要原因；GCU、AGG、GCU、CGA等27个密码子可视为最优密码子。本研究结果为海甜菜线粒体和叶绿体基因组的研究和遗传多样性分析提供了参考依据。
Abstract:
In order to clarify the codon usage bias and influencing factors of the mitochondrial and chloroplast genomes of Beta vulgaris subsp., 136 protein coding sequences (CDS) of the mitochondrial genome and 52 protein coding sequences of the chloroplast genome of Beta vulgaris subsp. were used as data source. Using Codon W and CUSP software, combined with the neutral mapping analysis of codon usage, effective number of codons (ENC-plot) and bias analysis (PR2-plot), the codon usage bias in mitochondrial and chloroplast genomes of Beta vulgaris subsp. was explored, and the optimal codon was determined. The results showed that the average G+C content of all codons in the mitochondrial and chloroplast genomes of Beta vulgaris subsp. was 43.42% and 37.92%, respectively. The third base of the codon was mostly A or U. The effective number of codons (ENC) of mitochondrial and chloroplast genomes was 36.44-61.00 and 35.00-52.01, respectively, with an average of 52.23 and 46.10. Natural selection was the main reason affecting the codon usage preference of mitochondrial and chloroplast genomes in Beta vulgaris subsp.. Twenty-seven codons, such as GCU, AGG, GCU and CGA, could be regarded as the optimal codons. The results of this study provide a reference for the study of mitochondrial and chloroplast genomes and genetic diversity analysis of Beta vulgaris subsp.

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备注/Memo

备注/Memo:
收稿日期:2023-03-29基金项目:青海民族大学研究生创新项目 (54M2022005)；青海民族大学研究生精品示范课程项目(JK-2023-08)；2023年中央科研创新平台建设项目——青海省林业草原生态系统功能维护及可持续开发利用科研创新团队(30160101141)；青海民族大学2023年大学生创新创业训练计划项目作者简介:包国媛(1997-),女,青海互助人,硕士研究生,研究方向为植物资源开发利用。(E-mail)1791564133@qq.com通讯作者:王雅琼,(Tel)18297178818;(E-mail)wangyaqiong727@163.com
更新日期/Last Update: 2024-01-15