目的 探究百合属Lilium药用植物叶绿体基因组密码子使用偏性及影响因素，为百合属药用植物育种提供理论参考。方法 使用CodonW1.4.2、CUSP、SPSS等软件分析9种百合属药用植物的密码子偏好性。结果 9种百合属植物密码子不同位点的GC含量均小于0.5，且GC1＞GC2＞GC3；其有效密码子数值均大于45。共筛选到21个最优密码子，其中有20个以A/U碱基结尾。PR2-plot分析、ENC-plot分析和中性绘图分析显示，百合属叶绿体基因组密码子偏好性主要受自然选择影响，同时也受突变因素影响。叶绿体蛋白编码序列的系统发育树和相对同义密码子使用度值的聚类分析结果，均支持渥丹Lilium concolor从钟花组独立归并到卷瓣组。结论 9种百合属植物叶绿体基因组密码子偏好性较弱，自然选择是影响密码子偏好性形成的主要因素，渥丹归入卷瓣组更合理。

Objective To explore the codon usage preferences and influencing factors of chloroplast (cp) genes in medicinal plants of the genus Lilium L. and provide a theoretical reference for breeding medicinal plants in Lilium. Methods CodonW1.4.2, CUSP, and SPSS software were employed to analyze the codon preferences of nine medicinal plants in Lilium. Results All of the GC content of different codon positions in nine Lilium species was less than 50%, with GC1＞GC2＞GC3. The effective number of codons (ENc) in the cp genomes of Lilium species is all more significant than 45. A total of 21 optimal codons were identified. Among them, 20 concluded with A/U bases. The PR2 plot analysis, ENC plot analysis, and neutral plot analysis demonstrated that the codon usage bias in the cp genomes of Lilium species is primarily influenced by natural selection and mutational factors. Furthermore, the phylogenetic tree of cp protein-coding sequences and the cluster analysis of relative synonymous codon usage (RSCU) values supported that Lilium concolor should be separated from the Sect. Lophophorum and merged into the Sect. Sinomartagon. Conclusion The codon preferences in the cp genomes of nine plants within the Lilium exhibit a relatively weak bias. Natural selection is the main factor affecting codon preference and placing L. concolor in the Sect. Sinomartagon is a more plausible classification.

R282.12

云南省生物医药重大专项（202002AA100007）；云南省兴滇英才支持计划（YNWR-QNBJ-2020251）