Analysis of Codon Bias in Chloroplast Genome of Trigonella Foenum-graecum

doi:10.11733/j.issn.1007-0435.2024.02.007

Acta Agrestia Sinica ›› 2024, Vol. 32 ›› Issue (2): 409-418.DOI: 10.11733/j.issn.1007-0435.2024.02.007

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Analysis of Codon Bias in Chloroplast Genome of Trigonella Foenum-graecum

DU Ming-chuan¹, WANG Wei², BAO Hai-juan¹, GE Cuo¹, ZHANG Rui¹, WANG Jiu-li¹, LIU Jing¹

1. College of Ecological Environment and Resources, Qinghai Minzu University, Qinghai Provincial Key Laboratory of Highvalue Utilization of Characteristic Economic Plants, Kairui Graduate Workstation of Medicinal Plant Resources of Qinghai Minzu University, Xining, Qinghai Province 810000, China;
2 Qinghai University, Xining, Qinghai Province 810000, China

Received:2023-08-14 Revised:2023-12-08 Online:2024-02-15 Published:2024-03-06

葫芦巴叶绿体基因组密码子偏好性分析

杜明川¹, 王伟², 鲍海娟¹, 格措¹, 张蕊¹, 王久利¹, 刘晶¹

1. 青海民族大学生态环境与资源学院, 青海省特色经济植物高值化利用重点实验室, 青海民族大学药用植物资源学凯瑞研究生工作站, 青海西宁 810000;
2. 青海大学, 青海西宁 810000

通讯作者: 刘晶,E-mail:654138133@qq.com
作者简介:杜明川(1996-),女,穿青人,贵州六盘水人,硕士研究生,主要从事药用植物种质资源开发与利用研究,E-mail:1321575830@qq.com
基金资助:
国家重点研发计划课题（2022YFD1602304）资助

Abstract

Abstract: In order to explore the codon usage bias of chloroplast genome in Trigonella foenum-graecum,Codon W 1.4.2 and online software CUSP were used to analyze the codons of 50 protein coding sequences. The results showed that the base at the end of the chloroplast genome codon of Trigonella foenum-graecum was mainly A/U,and the GC content was only 26.25%. The ENC value ranged from 35.05 to 53.66,and there were 20 ENC values>45,indicating that the codon bias of most gene coding sequences of Trigonella foenum-graecum was strong. There were 30 codons with RSCU≥1,of which 16 end with U and 13 end with A.The results of neutral mapping analysis,ENC-plot analysis and PR2-plot bias analysis showed that the codon usage bias of the chloroplast genome of Trigonella foenum-graecum was affected by many factors such as mutation pressure,and the main factor was natural selection. Finally,21 codons such as GCU,AGA,CGU were selected as the optimal codons.

Key words: Fenugreek, Chloroplast genome, Codon bias, Selection, Optimal codons

摘要： 为探究葫芦巴（Trigonella foenum-graecum L.）叶绿体基因组密码子的使用偏好性，利用Codon W 1.4.2和在线软件CUSP对筛选到的50条蛋白质编码序列密码子进行分析。结果表明：葫芦巴叶绿体基因组密码子末位碱基以A/U为主，GC含量仅为26.25%。ENC取值范围为35.05～53.66，且ENC值>45的有20个，说明葫芦巴大部分基因编码序列的密码子偏性较强。RSCU≥1的密码子有30个，其中16个以U结尾、13个以A结尾。中性绘图分析、ENC-plot分析及PR2-plot偏倚分析结果发现，葫芦巴叶绿体基因组密码子使用偏好性受到突变压力等多种因素的影响，主要因素为自然选择。最终筛选出GCU，AGA，CGU等21个密码子为最优密码子。

关键词: 葫芦巴, 叶绿体基因组, 密码子偏好性, 选择, 最优密码子

CLC Number:

S681.9

DU Ming-chuan, WANG Wei, BAO Hai-juan, GE Cuo, ZHANG Rui, WANG Jiu-li, LIU Jing. Analysis of Codon Bias in Chloroplast Genome of Trigonella Foenum-graecum[J]. Acta Agrestia Sinica, 2024, 32(2): 409-418.

杜明川, 王伟, 鲍海娟, 格措, 张蕊, 王久利, 刘晶. 葫芦巴叶绿体基因组密码子偏好性分析[J]. 草地学报, 2024, 32(2): 409-418.

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Analysis of Codon Bias in Chloroplast Genome of Trigonella Foenum-graecum

葫芦巴叶绿体基因组密码子偏好性分析

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