目的 为探究黄芩属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，为黄芩属药用植物遗传育种、资源保护等研究提供理论依据。方法 从美国国家生物技术信息中心（NCBI）数据库中下载了16种黄芩属药用植物的叶绿体基因组，使用Codon W 1.4.2及CUSP和SPSS 27等软件对16种黄芩属药用植物叶绿体基因的编码区（CDS）序列密码子偏好性进行分析。结果 16种黄芩属药用植物的叶绿体基因组编码区的同义密码子和最优密码子使用偏好性一致，都是以A/U结尾，高频密码子有UUA、AGA。PR2-plot、中性图和ENC-plot的结果显示16种黄芩属药用植物叶绿体基因组的密码子使用偏好性同时受到自然选择和内部碱基突变的影响，但自然选择是叶绿体基因组密码子偏好性形成的主导因素。结论 16种黄芩属药用植物的叶绿体基因组密码子偏好A/U结尾，与其他因素相比自然选择是其密码子偏好形成的主导因素。

Objective To explore the codon usage bias of chloroplast genomes of medicinal plants in the genus Scutellaria and its affecting factors, provide a theoretical basis for subsequent genetic breeding and resources protection studies of Scutellaria medicinal plants.MethodsThe chloroplast genomes of 16 Scutellaria medicinal plants were downloaded from the NCBI database, and the coding sequences (CDS) codon preferences of the chloroplast genes of the 16 Scutellaria medicinal plants were analyzed using Codon W 1.4.2 and the software CUSP and SPSS 27. Results The synonymous codons and optimal codons of chloroplast genome coding region of 16 Scutellaria medicinal plants in usage bias were consistent, all ending in A/U, and the high-frequency codons were UUA and AGA. The results of PR2-plot, neutral map, and ENC-plot showed that the codon usage bias in the chloroplast genomes of the 16 Scutellaria medicinal plants were affected by both natural selection and internal base mutations, but natural selection was the dominating factor in the formation of codon bias in the chloroplast genomes. Conclusion The chloroplast genomes of 16 Scutellaria medicinal plants have codon preferences for A/U endings, and natural selection is the dominant factor in the formation of their codon preferences compared with other factors.

R286.12

国家重点研发计划项目(2017YFC1701701);国家中医药管理局科技司"中药质量保障与创新发展项目"(2024002845);河北省省级科技计划资助(H2024423018,22326418D);河北省二期现代农业产业技术体系创新团队(HBCT2023080201,HBCT2023080205);河北中医药大学大学生创新项目(s202414432021,s202414432050);河北省中医药管理局科研计划项目(2023351)