昆明杯冠藤与青羊参叶绿体基因组特征比较及系统发育分析

Characterization and phylogenetic analysis of chloroplast genome of Cynanchum wallichii and Cynanchum otophyllum

昆明杯冠藤和青羊参隶属于夹竹桃科鹅绒藤属,是重要的药用植物。本研究对昆明杯冠藤和青羊参叶绿体基因组进行测序、组装,并对两者叶绿体基因组的结构特征及其系统发育位置进行了分析。结果表明,昆明杯冠藤和青羊参叶绿体基因组均具有典型的四分体结构,注释到133个基因,两者总GC含量接近。密码子偏好性分析显示,昆明杯冠藤和青羊参叶绿体基因组中相对同义密码子使用度略有不同,但差异不大,且在密码子第3位有强烈的A或U偏好。在两者叶绿体基因组中分别检测到91个和103个简单重复序列,以A/T类型重复占比最大。核苷酸多态性分析显示,鹅绒藤属叶绿体基因组共有间区序列的核苷酸多态性值高于共有基因序列,基于共有间区序列的高变区设计了一对引物可对昆明杯冠藤和青羊参进行鉴别。系统发育分析表明,昆明杯冠藤和地梢瓜亲缘关系最近,青羊参、白首乌和隔山消在鹅绒藤属中形成稳定的单系分支,三者亲缘关系较近。对昆明杯冠藤和青羊参叶绿体基因组特征及其系统发育的比较分析将为两种植物的物种鉴定及鹅绒藤属植物的遗传多样性和系统进化研究奠定理论基础。

Cynanchum wallichii and Cynanchum otophyllum belong to the genus Cynanchum in the family Apocynaceae,and are important medicinal plants.In this study,we sequenced and assembled the chloroplast genomes of C.wallichii and C.otophyllum,and performed a phylogenetic analysis of the structural characteristics of their chloroplast genomes and their phylogenetic positions.The results showed that the chloroplast genomes of both C.wallichii and C.otophyllum had a typical tetrad structure,with 133 genes annotated,and the total GC contents of both were similar.Codon preference analysis showed that the relative synonymous codon usage in the chloroplast genomes of C.wallichii and C.otophyllum differed slightly,but the differences were not significant,and there was a strong A or U preference at the third codon position.In both chloroplast genomes,91 and 103 simple sequence repeats were detected respectively,and the largest proportion of A/T type repeats.Nucleotide polymorphism analysis showed that the nucleotide diversity of the intergenic sequences in the chloroplast genome of genus Cynanchum were generally higher than those of the common gene sequences.A pair of primers was designed based on the high variation region of the chloroplast genome to identify C.wallichii and C.otophyllum.The phylogenetic analysis showed that the C.wallichii and Cynanchum thesioides were the closest relatives,while the C.otophyllum,Cynanchum bungei and Cynanchum wilfordii formed a stable monophyletic clade within the genus Cynanchum,and the three species were closely related.The comparative analysis of the chloroplast genomic characteristics and phylogeny of C.wallichii and C.otophyllum will provide a theoretical basis for the species identification of the two plants and for the study of genetic diversity and phylogeny of the genus Cynanchum.