柴胡属植物叶绿体基因组密码子偏好性分析

doi:10.3969/j.issn.1009-7791.2025.06.001

亚热带植物科学 ›› 2025, Vol. 54 ›› Issue (6): 599-612.DOI: 10.3969/j.issn.1009-7791.2025.06.001

• 研究论文 • 下一篇

柴胡属植物叶绿体基因组密码子偏好性分析

崔繁昊，赵心竹，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:2025-09-02 接受日期:2025-10-31 出版日期:2025-12-31 发布日期:2025-12-31
通讯作者: 王瑞红
基金资助:
国家自然科学基金项目(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)

Analysis of Codon Usage Bias in Chloroplast Genomes of Bupleurum

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

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

Received:2025-09-02 Accepted:2025-10-31 Online:2025-12-31 Published:2025-12-31
Contact: WANG Rui-hong

摘要/Abstract

摘要： 为探究柴胡属植物叶绿体基因组的密码子偏好性，本研究分析了35种柴胡属植物叶绿体基因组的密码子使用模式。利用Codon W、CUSP、MEGA软件及生信云平台等工具分析密码子相关参数，通过ENC-plot、中性制图、PR2-plot、最优密码子筛选等方法，探究影响密码子偏好性的主要因素并确定最优密码子。结果表明，35种柴胡属植物密码子的第一(GC1)、第二(GC2)、第三(GC3)位碱基的GC含量呈现GC1＞GC2＞GC3的特征，总GC含量介于38.13%～38.32%之间，提示该属叶绿体基因组密码子偏向使用A/U碱基为结尾。所有物种的有效密码子数(‌ENC)均大于35，表明密码子偏好性较弱。而ENC-plot、中性绘图、PR2-plot分析表明，影响35种柴胡属叶绿体基因组密码子使用偏好性的主要因素为自然选择，突变对其影响较弱。通过分析RSCU值确定12个共同最优密码子，均呈现“NNA”“NNU”模式。研究结果为柴胡属基因组研究、遗传改良及资源利用奠定理论基础。

关键词: 柴胡属, 密码子偏好性, 自然选择, 叶绿体基因组

Abstract: To explore the codon usage bias in the chloroplast genomes of Bupleurum species, this study analyzed the codon usage patterns in the chloroplast genomes of 35 Bupleurum species. Codon-related parameters were analyzed using tools including softwares of Codon W, CUSP, MEGA, and the Bioinformatics Cloud Platform. The main factors affecting codon usage bias were explored via ENC-plot analysis, neutral mapping, PR2-plot analysis, and optimal codon screening, with the optimal codons identified simultaneously. The results showed that the GC content of the first (GC1), second (GC2), and third bases (GC3) codon positions in the chloroplast genomes of the 35 Bupleurum species followed the order GC1＞GC2＞GC3, with the total GC content ranging from 38.13% to 38.32%, suggesting a preference for A/U-ended codons. The effective number of codons (ENC) values of all species were greater than 35, indicating weak codon usage bias. Analysis using ENC-plot, neutral mapping, and PR2-plot revealed that natural selection was the primary factor influencing codon usage bias in the chloroplast genomes of 35 species of Bupleurum, whereas mutational pressure had a relatively minor impact. By analyzing the relative synonymous codon usage (RSCU) values, 12 common optimal codons were identified, all of which exhibited ending patterns of “NNA” and “NNU”. This study provided a theoretical basis for future genomic research, genetic improvement, and resource utilization of Bupleurum species.

Key words: Bupleurum; codon usage bias, natural selection, chloroplast genome

中图分类号:

Q943

崔繁昊, 赵心竹, 李红, 周梦丽, 王瑞红. 柴胡属植物叶绿体基因组密码子偏好性分析[J]. 亚热带植物科学, 2025, 54(6): 599-612.

CUI Fan-hao, ZHAO Xin-zhu, LI Hong, ZHOU Meng-li, WANG Rui-hong. Analysis of Codon Usage Bias in Chloroplast Genomes of Bupleurum[J]. Subtropical Plant Science, 2025, 54(6): 599-612.

参考文献

[1] Kuang H, Sun S, Yang B, Xia Y, Feng W. New megastigmen sesquiterpene and indole alkaloid glucosides from the aerial parts of Bupleurum chinense DC [J]. Fisioterapia, 2009, 80(1): 35–38.

[2] 常修奇, 刘玫, 程薪宇, 王宇婷, 魏雪莹, 王雪微. 中国伞形科柴胡属果实结构的系统学价值[J]. 草业学报, 2015, 24(10): 108–119.

[3] 黄涵签, 王潇晗, 付航, 王妍, 杨世海. 柴胡属药用植物资源研究进展[J]. 中草药, 2017, 48(14): 2989–2996.

[4] 张宏伟, 刘湘丹, 朱洁怡, 佘玮韬, 何佳蔚, 晁志. 四种西南高山地区柴胡属植物根的生药学研究[J]. 中药材, 2023, 46(11): 2703–2707.

[5] Li J, Li H, Zhi J, Shen C, Yang X, Xu J. Codon usage of expansin genes in Populus trichocarpa [J]. Current Bioinformatics, 2017, 12(5): 452–461.

[6] Novoa E M, Pavon-Eternod M, Pan T, de Pouplana L R. A role for tRNA modifications in genome structure and codon usage [J]. Cell, 2012, 149(1): 202–213.

[7] Rao Y, Wu G, Wang Z, Chai X, Nie Q, Zhang X. Mutation bias is the driving force of codon usage in the Gallus gallus genome [J]. DNA research, 2011, 18(6): 499–512.

[8] Kong W Q, Yang J H. The complete chloroplast genome sequence of Morus cathayana and Morus multicaulis, and comparative analysis within genus Morus L [J]. Peer J, 2017, 5: e3037.

[9] Suzuki H, Morton B R. Codon adaptation of plastid genes [J]. PLoS One, 2016, 11(5): e0154306.

[10] 周承哲, 朱晨, 李小桢, 傅海峰, 赖钟雄, 郭玉琼. 茶树密码子使用偏性分析方法及其研究进展[J]. 分子植物育种, 2020, 18(5): 1480–1488.

[11] 陈柯伊, 李朝娜, 成敏敏, 赵扬辉, 周明兵, 杨海芸. 不同叶色矢竹叶绿体结构和光系统特性差异[J]. 植物学报, 2018, 53(4): 509–518.

[12] 张悦. 红豆杉科叶绿体基因组结构多样化研究[D]. 北京: 北京林业大学硕士学位论文, 2019.

[13] 陆奇丰, 骆文华, 黄至欢. 两种梧桐叶绿体基因组密码子使用偏性分析[J]. 广西植物, 2020, 40(2): 173–183.

[14] Deng Y, Luo Y, He Y, Qin X, Li C, Deng X. Complete chloroplast genome of Michelia shiluensis and a comparative analysis with four Magnoliaceae species [J]. Forests, 2020, 11(3): 267.

[15] Jiang L, Li M, Zhao F, Chu S, Zha L, Xu T, Peng H, Zhang W. Molecular identification and taxonomic implication of herbal species in genus Corydalis (Papaveraceae) [J]. Molecules, 2018, 23(6): 1393.

[16] Yang C, Ma Y, Cheng B, Zhou L, Yu C, Luo L, Pan H, Zhang Q. Molecular evidence for hybrid origin and phenotypic variation of Rosa section Chinenses [J]. Genes, 2020, 11(9): 996.

[17] Wright F. The ‘effective number of codons’ used in a gene [J]. Gene, 1990, 87(1): 23–29.

[18] Gajbhiye S, Patra P K, Yadav M K. New insights into the factors affecting synonymous codon usage in human infecting Plasmodium species [J]. Acta tropica, 2017, 176: 29–33.

[19] 何刀山, 阳小强, 秦雅林, 何海燕, 谢维, 罗治国, 李鹏. ‘湘辣14号’叶绿体基因组密码子偏好性分析[J]. 中国果菜, 2025, 45(1): 47–54,79.

[20] 冉然, 张晓明, 宛涛, 伊卫东. 密码子偏好性的相关研究及方法分析[J]. 草原与草业, 2022, 34(3): 5–10.

[21] 杨国锋, 苏昆龙, 赵怡然, 宋智斌, 孙娟. 蒺藜苜蓿叶绿体密码子偏好性分析[J]. 草业学报, 2015, 24(12): 171–179.

[22] Sueoka N. Directional mutation pressure and neutral molecular evolution [J]. Proceedings of the National Academy of Sciences, 1988, 85(8): 2653–2657.

[23] 朱恒星, 戴前莉, 魏卓, 卢敏, 黄飞逸, 陈本文. 17种楠属植物叶绿体基因组密码子偏好性分析[J]. 南方农业学报, 2024, 55(12): 3646–3655.

[24] 代江鹏, 蔡一鸣, 刘巧珍, 高晓霞, 朱爽. 甘草属7种植物叶绿体基因组密码子使用偏好性分析[J]. 中草药, 2023, 54(9): 2907–2916.

[25] 原晓龙, 李云琴, 张劲峰, 王毅. 降香黄檀叶绿体基因组密码子偏好性分析[J]. 广西植物, 2021, 41(4): 622–630.

[26] Zhang P, Xu W, Lu X, Wang, L. Analysis of codon usage bias of chloroplast genomes in Gynostemma species [J]. Physiology and Molecular Biology of Plants, 2021, 27(12): 2727–2737.

[27] Xiao M, Hu X, Li Y, Liu Q, Shen S, Jiang T, Zhang L, Zhou Y, Li Y, Luo X, Bai L, Yan W. Comparative analysis of codon usage patterns in the chloroplast genomes of nine forage legumes [J]. Physiology and Molecular Biology of Plants, 2024, 30(2): 153–166.

[28] 秦斗文, 徐庭亮, 闫京艳, 巨秀婷. 柔毛郁金香叶绿体基因组密码子偏好性分析[J]. 江苏农业科学, 2023, 51(22): 41–47.

[29] Li G, Zhang L, Xue P. Codon usage pattern and genetic diversity in chloroplast genomes of Panicum species [J]. Gene, 2021, 802: 145866.

[30] Chen J, Ma W, Hu X, Zhou, K. Synonymous codon usage bias in the chloroplast genomes of 13 oil-tea Camellia samples from south China [J]. Forests, 2023, 14(4): 794.

[31] 毛立彦, 黄秋伟, 龙凌云, 檀小辉, 谢红辉, 唐毓玮, 丁丽琼. 7种睡莲属植物叶绿体基因组密码子偏好性分析[J]. 西北林学院学报, 2022, 37(2): 98–107.

[32] Li Y, Hu X, Xiao M, Huang J, Lou Y, Hu F, Fu X, Li Y, He H, Cheng J. An analysis of codon utilization patterns in the chloroplast genomes of three species of Coffea [J]. BMC genomic data, 2023, 24(1): 42.

[33] Sablok G, Nayak K C, Vazquez F, Tatarinova T V. Synonymous codon usage, GC3, and evolutionary patterns across plastomes of three pooid model species: emerging grass genome models for monocots [J]. Molecular Biotechnology, 2011, 49(2): 116–128.

[34] 罗火林, 张亚楠, 罗丽萍, 熊冬金, 杨柏云. 兰科植物FT基因的密码子偏性分析[J]. 分子植物育种, 2016, 14(1): 51–58.

[35] 王芳, 周盛茂, 赵雪利. 葫芦茶叶绿体基因组密码子偏好性分析[J]. 西南林业大学学报(自然科学), 2025, 45(1): 34–43.

[36] 李显煌, 杨生超, 辛雅萱, 屈亚亚, 杨琳懿, 冯发玉, 范伟, 辛培尧. 灯盏花叶绿体基因组密码子偏好性分析[J]. 云南农业大学学报(自然科学), 2021, 36(3): 384–392.

[37] Geng X, Huang N, Zhu Y, Qin L, Hui L. Codon usage bias analysis of the chloroplast genome of cassava [J]. South African Journal of Botany, 2022, 151: 970–975.

[38] Gao M, Huo X, Lu L, Liu M, Zhang G. Analysis of codon usage patterns in Bupleurum falcatum chloroplast genome [J]. Chinese Herbal Medicines, 2023, 15(2): 284–290.

[39] 王平, 赵琴, 严少普, 赵心蝶, 李雪, 郝丽, 贺艺, 李可涵, 李怀珠. 柴胡属5种植物叶绿体基因组密码子偏好性分析[J]. 分子植物育种, 2025, 1-13. https://www.cnki.com.cn/Article/ CJFDTotal-FZZW20231012005.htm

[40] 康路, 谢登峰, 何兴金. 胡萝卜Daucus carota var. sativa密码子偏好性及属内质体基因组核苷酸多样性分析[J]. 分子植物育种, 2020, 18(7): 2077–2086.

[41] 余潇, 赵振宁, 邓莉兰. 两型豆属叶绿体基因组特征及密码子偏好性分析[J]. 西北农业学报, 2024, 33(3): 435–451.

[42] Zhou M, Long W, Li X. Analysis of synonymous codon usage in chloroplast genome of Populus alba [J]. Journal of Forestry Research, 2008, 19(4): 293–297.

[43] Parvathy S T, Udayasuriyan V, Bhadana V. Codon usage bias [J]. Molecular Biology Reports, 2022, 49(1): 539–565.

[44] Pluhar W. AT2-AT3-Profiling: a new look at synonymous codon usage [J]. Journal of Theoretical Biology, 2006, 243(3): 308–321.

[45] Kim H, Chang C S. Genetic variation in geographically peripheral populations of Bupleurum euphorbioides (Apiaceae) with comparison to a widespread congener, B. longiradiatum [J]. Integrative Biosciences, 2005, 9(1): 27–35.

编辑推荐

Metrics

闽ICP备11008787号-5　

柴胡属植物叶绿体基因组密码子偏好性分析

Analysis of Codon Usage Bias in Chloroplast Genomes of Bupleurum

PDF

可视化

摘要/Abstract

引用本文

使用本文

参考文献

相关文章 4

编辑推荐

Metrics

[1]	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.
[2]	张翊凡, 颜茵, 陈育明, 黄思铭, 李明河. 龙石斛叶绿体基因组特征及系统发育分析[J]. 亚热带植物科学, 2025, 54(4): 378-386.
[3]	黄定旭, 马怀富, 梁盛, 何琴琴, 张廷跃, 孔令雄, 刘邦友, 康凯莉, 彭涛. 沼寒藓叶绿体基因组结构特征及其与近缘物种比较[J]. 亚热带植物科学, 2025, 54(2): 121-131.
[4]	陈章雪，陈彬，田敏，黄瑛琳，张淼，陈炳华. 福建新记录种缘生穴子蕨及其叶绿体基因组分析[J]. 亚热带植物科学, 2024, 53(4): 363-368.