石斛属叶绿体基因组密码子使用偏性及系统发育分析

Analysis of Codon Usage Bias and Phylogenetic in the Chloroplast Genome of Dendrobium

石斛(Dendrobium)是集药用与观赏价值于一体的珍贵中药材,为促进药用植物叶绿体基因工程的发展,本研究利用CodonW、SPSSAU、CUSP以及MEGA 7.0等软件对石斛属叶绿体基因组密码子使用模式以及系统发育关系进行了分析。分析结果显示:31种石斛叶绿体基因组编码序列GC含量为37.90%~38.70%,密码子第三位碱基GC3含量范围为26.10%~30.0%,说明密码子第三位碱基富含A和U;有效密码子数ENC值为48.89~51.92,说明石斛属叶绿体基因组密码子偏好性较弱;对不同组的6种石斛进行绘图分析,表明石斛属植物叶绿体基因组密码子使用偏好性主要受选择压力影响;以ENC值和RSCU值为参考标准,筛选出的22个最优密码子中有17个以C/U结尾。系统发育分析显示石斛属31个物种可聚为3大类,且鼓槌石斛、竹枝石斛与同属的其他物种存在较远的亲缘关系。本研究旨在为石斛属植物分类鉴定、基因组密码子优化及系统发育的相关研究提供依据。

Dendrobium is a precious Chinese herbal with both medicinal and ornamental values, to promote the development of chloroplast genetic engineering in medicinal plants, characteristics of codon usage and phylogenetic analysis in chloroplast genomes of Dendrobium was studied by CodonW, SPSSAU, CUSP and MEGA 7.0. The results show that the GC content of 31 species chloroplast protein-coding sequence is 37.90% ~38.70%, and the GC3 content of codon ranged from 26.10% to 30.0%, indicating 3rd position was rich in A and U. The average range of effective number codon was from 48.89 to 51.92, which suggest a weak codon preference among these species. The plot analysis indicating the codon bias in the chloroplast genome was mainly affected by selection pressure. Based on ENC and RSCU values, 17 codons were end with C/U among 22 identified optimal codons.Phylogenetic analysis showed that 31 species of Dendrobium could be divided into three categories, what’s more,Dendrobium chrysotoxum and Dendrobium salaccense revealed further relationships with other species of Dendrobium. The study aims to provide a basis for the taxonomic identification, genomic codon optimization and phylogeny of Dendrobium.