21种贝母属植物叶绿体基因组密码子使用偏好分析

doi:10.3969/j.issn.1009-7791.2026.02.001

亚热带植物科学 ›› 2026, Vol. 55 ›› Issue (2): 131-143.DOI: 10.3969/j.issn.1009-7791.2026.02.001

• 研究论文 • 下一篇

21种贝母属植物叶绿体基因组密码子使用偏好分析

赵心竹，崔繁昊，李红，周梦丽，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:2025-11-10 接受日期:2025-12-25 出版日期:2026-04-30 发布日期:2026-04-30
通讯作者: 王瑞红
基金资助:
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)；国家自然科学基金(31600183)

Analysis of Codon Usage Bias in the Chloroplast Genomes of 21 Fritillaria Species

ZHAO Xin-zhu, CUI Fan-hao, LI Hong, ZHOU Meng-li, WANG Rui-hong^*

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

Received:2025-11-10 Accepted:2025-12-25 Online:2026-04-30 Published:2026-04-30
Contact: WANG Rui-hong

摘要/Abstract

摘要： 为分析贝母属植物叶绿体基因组密码子使用偏好性，探究其密码子使用模式及影响因素，运用CodonW1.4.4和CUSP在线软件计算贝母属21个物种的叶绿体基因组密码子相关参数，并绘制相应的统计图。结果表明，贝母属叶绿体基因组具备A/U偏好性，与双子叶植物共性一致。中性绘图斜率(0.45～0.52)表明自然选择与突变压力共同作用，ENC-plot中超过50%基因点位于标准曲线下方，且PR2-plot显示第三位碱基T＞A、G＞C的失衡，共同支持自然选择为主导因素。RSCU热图聚类显示，近缘物种具有高度相似的密码子使用模式；筛选出10个共有最优密码子，全部以A/U结尾，与A/U偏好性高度一致。该研究结果为深入理解贝母属叶绿体基因组的进化机制、分子系统发育重建提供科学依据。

关键词: 贝母属, 叶绿体基因组, 密码子偏好性, 最优密码子, 自然选择

Abstract: To analyze the codon usage bias in the chloroplast genomes of Fritillaria species, and to investigate their codon usage patterns and influencing factors, we employed CodonW1.4.4 and the online tool CUSP to calculate relevant codon parameters from the chloroplast genomes of 21 Fritillaria species. Corresponding statistical plots were generated. The results revealed a strong A/U bias in the chloroplast genomes of Fritillaria, consistent with patterns commonly observed in dicotyledonous plants. The slope of the neutral plot (ranging from 0.45 to 0.52) indicated that both natural selection and mutation pressure contributed to codon usage. In the ENC-plot, more than 50% of the genes fell below the standard curve, and the PR2-plot demonstrated an imbalance in the third nucleotide position (T＞A, G＞C), collectively supporting natural selection as the dominant factor. Cluster analysis based on the RSCU heatmap showed that closely related species shared highly similar codon usage patterns. Ten common optimal codons were identified, all ending with A or U, which is highly consistent with the A/U bias. These findings provide important scientific insights for understanding the evolutionary mechanisms of chloroplast genomes in Fritillaria, reconstructing molecular phylogenies.

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

中图分类号:

Q943

赵心竹, 崔繁昊, 李红, 周梦丽, 王瑞红. 21种贝母属植物叶绿体基因组密码子使用偏好分析[J]. 亚热带植物科学, 2026, 55(2): 131-143.

ZHAO Xin-zhu, CUI Fan-hao, LI Hong, ZHOU Meng-li, WANG Rui-hong. Analysis of Codon Usage Bias in the Chloroplast Genomes of 21 Fritillaria Species[J]. Subtropical Plant Science, 2026, 55(2): 131-143.

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21种贝母属植物叶绿体基因组密码子使用偏好分析

Analysis of Codon Usage Bias in the Chloroplast Genomes of 21 Fritillaria Species

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