60种百合属植物叶绿体基因组密码子使用偏好性及系统发育分析

Codon usage bias and phylogenetic analysis of chloroplast genomes of 60 Lilium species

摘要:

百合属植物作为单子叶植物的重要代表类群，具有丰富的遗传资源和重要的应用价值，研究其叶绿体基因组对揭示遗传进化机制具有重要意义。为深入解析百合属植物的分子遗传特征及进化规律，本研究对60种百合属植物(约占全球该属物种的49.58%)的叶绿体基因组进行了基因组特征和同义密码子使用偏好性分析，明确了百合科不同植物类群的系统进化关系。密码子使用偏好性分析结果显示，60种百合属植物叶绿体基因组平均GC含量为37.00%，第3位密码子GC含量(GC₃)为29.70%，表现出明显的AT偏好性。有效密码子数(effective number of codons, ENC)平均值位于47.76?48.57之间，表明密码子使用偏好性相对较弱。通过ENC-GC_3s (同义密码子第三位GC含量)分析和奇偶规则2 (parity rule 2, PR2)分析发现，百合属植物叶绿体基因组密码子偏好性受到突变压力和自然选择等多种因素的共同影响，其中自然选择压力起主导作用。简单重复序列分析(simple sequence repeats, SSR)鉴定出5 750个SSRs，主要分布于基因间隔区(intergenic spacer region, IGS)和内含子(intron)，单核苷酸重复(以A/T为主)所占比例最高(41.91%)，进一步解释了基因组中A/T富集的特征。共线性分析表明，百合科植物基因排列模式相似，反向重复序列(inverted repeat region, IR)边界仅表现出微小差异。基于158个百合科物种叶绿体基因组序列构建的系统发育分析表明，百合属物种聚为一个单系类群，与现有分类系统基本一致，阐明了该属内部的系统发育关系。本研究从分子水平上揭示了百合属植物叶绿体基因组的密码子使用特征，为百合属植物的系统进化、分子标记开发以及叶绿体基因工程提供了重要的理论依据和数据支撑，对百合属植物资源的保护与开发利用具有重要意义。

Abstract:

Lilium, an important monocot genus, demonstrates rich genetic resources and application value. Chloroplast genomics of Lilium is essential for elucidating the evolutionary mechanisms. To elucidate the molecular genetic characteristics and evolutionary patterns of Lilium species, we comprehensively analyzed the genomic characteristics and synonymous codon usage bias of 60 Lilium species (representing approximately 49.58% of the genus worldwide). The results revealed that the 60 Lilium chloroplast genomes exhibited the average GC content of 37.00%, with GC content at the third codon position (GC₃) averaging 29.70%, indicating pronounced bias for AT bases. The average effective number of codons (ENC) ranged from 47.76 to 48.57, suggesting weak codon usage bias. Through ENC-GC_3s analysis and PR2 analysis, we determined that codon usage bias in Lilium chloroplast genomes was influenced by mutation pressure and natural selection, with natural selection playing a predominant role. Simple sequence repeat (SSR) analysis identified 5 750 SSRs, which were mainly distributed in intergenic spacer (IGS) regions and intron regions. Mononucleotide repeats, with A/T repeats being dominant, accounted for the highest proportion (41.91%), further explaining the A/T enrichment characteristic in the genome. Collinearity analysis showed that the gene arrangement patterns of Liliaceae species were similar, with only slight differences in the inverted repeat boundaries. Phylogenetic analysis based on chloroplast genome sequences of 158 Liliaceae species revealed that Lilium species formed a monophyletic clade, which was generally consistent with the existing taxonomic system, elucidating the phylogenetic relationships within the genus. This study provides comprehensive insights into the codon usage characteristics of Lilium chloroplast genomes at the molecular level, offering a theoretical foundation and data support for phylogenetic studies, molecular marker development, and chloroplast genetic engineering in Lilium. These findings have significant implications for the conservation and utilization of Lilium genetic resources.