Acta Agrestia Sinica

Acta Agrestia Sinica ›› 2024, Vol. 32 ›› Issue (8): 2374-2385.DOI: 10.11733/j.issn.1007-0435.2024.08.005

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Codon Usage Bias Analysis of the Chloroplast Genome of Isatis Indigotica

YU Zhi-wei1,2, CHEN Yuan1, GUO Feng-xia1, DONG Peng-bin1, WANG Hong-yan1   

  1. 1. College of Agronomy, College of Life Science and Technology, Gansu Agricultural University, State Key Laboratory of Aridland Crop Science, Lanzhou, Gansu Province 730070, China;
    2. Lanzhou Agro-technical Research and Popularization Center, Lanzhou, Gansu Province 730030, China
  • Received:2023-12-28 Revised:2024-02-05 Published:2024-09-07

菘蓝叶绿体基因组密码子使用偏好性分析

余志伟1,2, 陈垣1, 郭凤霞1, 董鹏斌1, 王红燕1   

  1. 1. 甘肃农业大学农学院/生命科学技术学院/干旱生境作物学国家重点实验室, 甘肃 兰州 730070;
    2. 兰州市农业科技研究推广中心, 甘肃 兰州 730030
  • 通讯作者: 陈垣,E-mail:chenyuan@gsau.edu.cn
  • 作者简介:余志伟(1994-),男,汉族,甘肃定西人,硕士研究生,主要从事药用植物资源与利用研究,E-mail:785564234@qq.com
  • 基金资助:
    道地中药材优势特色产业集群良种繁育(2022GSCYJQ07-33);连花清瘟胶囊FDA注册原料药材板蓝根标准化基地建设(YLQT201605010);教育部精准扶贫项目(XZ20190236);中药材新品种选育及基地建设(7010722087);甘肃省农业农村厅-甘肃省中药材产业体系首席专家项目(GARS-ZYC-1)资助

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Abstract: To investigate the codon usage bias and its influencing factors in the chloroplast genome of Isatis indigotica Fort.,this study analyzed the codon usage patterns of 52 protein-coding sequences using Codon W 1.4.2 software and CUSP online software. The results revealed that the total GC content of codons in the chloroplast genome of I. indigotica was 37.59%,with GC1 > GC2 > GC3,all being less than 50%. This indicated a low GC content for the third base of codons,suggesting a preference for A or U base. Furthermore,the analysis of codon usage indices such as ENC,CAI,CBI and FOP showed ranges of 35.92 to 55.32,0.10 to 0.31,-0.24 to 0.20 and 0.24 to 0.54 respectively,pointing towards a relatively weak codon usage bias. Through various techniques such as neutral plot analysis,PR2-plot analysis,ENC-plot analysis,and correspondence analysis,we identified that selection pressure and mutation influenced the codon usage bias in I. indigotica chloroplast genome. However,natural selection emerged as the main factor affecting it. Additionally,optimal codon analysis identified a total of fourteen optimal codons with a preference for ending with A or U base. In conclusion,our findings can provide a theoretical foundation for valuable insights into phylogenetic evolution,environmental adaptability,and germplasm enhancement of I. indigotica.

Key words: Isatis indigotica, Chloroplast genome, Selection, Codon usage bias, Optimal codon

摘要： 为探究菘蓝(Isatis indigotica Fort.)叶绿体基因组密码子使用偏好性及其影响因素，本研究使用Codon W 1.4.2软件和在线软件CUSP对筛选到的52个蛋白质编码序列进行密码子使用模式分析。结果表明：菘蓝叶绿体基因组密码子总GC含量(Total GC content of codon,GCall)为37.59%，密码子第1位碱基GC含量(GC content of the first base of codon,GC1)＞密码子第2位碱基GC含量(GC content of the second base of codon,GC2)＞密码子第3位碱基GC含量(GC content of the third base of codon,GC3)，且均小于50%，说明密码子第3位碱基拥有较低的GC含量且密码子偏好使用A或U。有效密码子数(Effective number of codon,ENC)值为35.92~55.32，密码子适应指数(Codon adaptation index,CAI)值为0.10~0.31，密码子偏好指数(Codon bias index,CBI)值为-0.24~0.20，最优密码子使用频率(Frequency of optimal codons,FOP)值为0.24~0.54，说明密码子使用偏好性较弱；通过中性绘图分析、PR2-plot分析、ENC-plot分析和对应性分析，发现菘蓝叶绿体基因组密码子使用偏好性受选择压力和突变等因素的共同影响，主要因素为自然选择。最优密码子分析共筛选出14个最优密码子，且均以A或U结尾。以上研究可为菘蓝的系统进化、环境适应性和种质改良提供理论基础。

关键词: 菘蓝, 叶绿体基因组, 选择, 密码子使用偏好性, 最优密码子

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