尖刀唇石斛和翅梗石斛叶绿体全基因组分析

Sequence analysis of complete chloroplast genome of Dendrobium heterocarpum and Dendrobium trigonopus

目的测定尖刀唇石斛Dendrobium heterocarpum和翅梗石斛D.trigonopus叶绿体基因组,分析其序列特征并鉴定石斛属Dendrobium植物物种间亲缘关系。方法利用Illumina Hisep 2500测序平台对尖刀唇石斛和翅梗石斛进行二代测序,经组装、注释后得到2条完整的叶绿体全基因组序列,采用生物信息学方法分析其序列结构及石斛属的系统发育关系。结果尖刀唇石斛的叶绿体全基因组总长为159786 bp,总GC含量为37.2%,共注释得到131个基因,包括88个蛋白编码基因、37个tRNA基因和6个rRNA基因;翅梗石斛的叶绿体全基因组总长为159652 bp,总GC含量为37.1%,共注释得到131个基因,包括88个蛋白编码基因、37个tRNA基因和6个rRNA基因。尖刀唇石斛和翅梗石斛分别检测到112和127个简单重复序列(SSR),二者编码亮氨酸的密码子数量最多,编码色氨酸的密码子数量最少。系统发育树显示,尖刀唇石斛、反瓣石斛D.ellipsophyllum、翅梗石斛、梳唇石斛D.strongylanthum和长距石斛D.longicornu聚为一支,翅梗石斛与梳唇石斛和长距石斛的亲缘关系十分相近,支持率达到100%。结论对石斛属2种植物的叶绿体基因组结构和系统发育关系进行了分析,该研究结果将为石斛属药用植物的准确鉴定、开发利用及其资源保护提供科学依据。

Objective To determine the chloroplast genomes of Dendrobium heterocarpum and Dendrobium trigonopus, analyze their sequence characteristics, and identify the relationship between Dendrobium species. Methods In this study, the next-generation sequencing of D. heterocarpum and D. trigonopus was performed on the Illumina Hisep 2 500 sequencing platform.Two complete chloroplast genome sequences were obtained after assemblying and annotationing,. Then, the two sequence structure and the phylogenetic relationship of Dendrobium were analysed by bioinformatics methods. Results The study found that the total length of the chloroplast genome of D. heterocarpum was 159 786 bp and the total GC content was 37.2%. The whole genes annotated were 131, including 88 protein-coding genes, 37 tRNA genes and six rRNA genes. Similarly, the total length of the chloroplast genome of D. trigonopus was 159 652 bp and the total GC content was 37.1%. A total of 131 genes were annotated,which including 88 protein-coding genes, 37 tRNA genes and six rRNA genes in all. There were 112 and 127 simple repeat sequences were detected from D. heterocarpum and D. trigonopus respectively, and they both had the largest number of codons encoding leucine and the least number of codons encoding tryptophan. The phylogenetic tree showed that D. heterocarpum, D.ellipsophyllum, D. trigonopus, D. strongylanthum and D. longicornu were clustered together into one family. D. trigonopus was very similar to D. strongylanthum and D. longicornu, and the support rate reached 100%. Conclusion The chloroplast genome structure and phylogenetic relationship of two species of Dendrobium were analysed. The results of this study will provide a scientific basis for the accurate identification, development and utilization of Dendrobium medicinal plants and resource protection.