36种黄精属植物叶绿体基因组密码子使用偏好性分析

doi:10.3969/j.issn.1009-7791.2025.05.002

亚热带植物科学 ›› 2025, Vol. 54 ›› Issue (5): 497-507.DOI: 10.3969/j.issn.1009-7791.2025.05.002

36种黄精属植物叶绿体基因组密码子使用偏好性分析

李红，周梦丽，王霞，郭蕾，王瑞红*

(浙江理工大学生命科学与医药学院，浙江杭州 310018)

收稿日期:2025-04-30 接受日期:2025-07-30 出版日期:2025-10-31 发布日期:2025-12-17
通讯作者: 王瑞红
基金资助:
国家自然科学基金(31600183)；浙江省基础公益研究计划(LGN22H280005)；浙江理工大学基本科研业务费(24042128-Y)；浙江省“尖兵”“领雁”研发攻关计划(2023C02017)

Codon Usage Bias in the Chloroplast Genomes of 36 Polygonatum Species

LI Hong, ZHOU Meng-li, WANG Xia, GUO Lei, WANG Rui-hong*

(College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, Zhejiang China)

Received:2025-04-30 Accepted:2025-07-30 Online:2025-10-31 Published:2025-12-17
Contact: WANG Rui-hong

摘要/Abstract

摘要： 为探究黄精属Polygonatum药用植物叶绿体基因组密码子的使用偏好性及其影响因素，利用CodonW 1.4.2、CUSP以及SPSS27等软件对36种黄精属植物叶绿体基因组蛋白质编码序列(CDS)进行密码子偏好性分析。结果表明，有效密码子数在48.32～48.57之间，密码子适应指数在0.166～0.168之间，说明黄精属植物叶绿体基因组密码子偏好性较弱；36个黄精属物种确定了5个共有的最优密码子，分别为UUU、CUU、ACA、CAA、GGA，都偏好以A/U结尾。36种黄精属植物的密码子偏好性主要受到自然选择的影响。研究结果为黄精属药用植物遗传育种、种质资源保护等研究提供理论依据。

关键词: 黄精属, 叶绿体基因组, 密码子偏好性, 最优密码子, 自然选择

Abstract: In order to explore the bias of the use of codons and and its influencing factors in the chloroplast genome of Polygonatum medicinal plants, CodonW 1.4.2, CUSP and SPSS27 were used to analyze the codon bias of 36 Polygonatum species. The results showed that the effective number of codons (ENC) ranges between 48.32 and 48.57, and the codon adaptation index (CAI) ranges between 0.166 and 0.168, indicating that the codon preference of the chloroplast genome of Polygonatum was weak. The 36 species of Polygonatum identified five common optimal codons, namely UUU, CUU, ACA, CAA and GGA, which all preferred to end with A/U nucleotides. The codon bias of 36 species of Polygonatum was mainly affected by natural selection. The results provide a theoretical basis for the genetic breeding and germplasm resources protection of Polygonatum medicinal plants.

Key words: Polygonatum, chloroplast genome, codon usage bias, optimal codon, natural selection

中图分类号:

Q943.2

李红, 周梦丽, 王霞, 郭蕾, 王瑞红. 36种黄精属植物叶绿体基因组密码子使用偏好性分析[J]. 亚热带植物科学, 2025, 54(5): 497-507.

LI Hong, ZHOU Meng-li, WANG Xia, GUO Lei, WANG Rui-hong. Codon Usage Bias in the Chloroplast Genomes of 36 Polygonatum Species[J]. Subtropical Plant Science, 2025, 54(5): 497-507.

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36种黄精属植物叶绿体基因组密码子使用偏好性分析

Codon Usage Bias in the Chloroplast Genomes of 36 Polygonatum Species

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