球花石斛(Dendrobium thyrsiflorum)叶绿体基因组特征及亲缘关系解析  

Characteristics of the Complete Chloroplast Genome of Dendrobium thyrsiflorum and Its Phylogenetic Relationship Analysis

作　　者：朱斌 甘晨晨 王洪程 ZHU Bin;GAN Chen-chen;WANG Hong-cheng(School of Life Sciences,Guizhou Normal University,Guiyang 550001)

机构地区：[1]贵州师范大学生命科学学院,贵阳550001

出　　处：《生物技术通报》2021年第5期38-47,共10页Biotechnology Bulletin

基　　金：贵州省科学计划项目(QKHJC(2020)1Y102)。

摘　　要：球花石斛(Dendrobium thyrsiflorum)主要分布在我国云南地区,是非常重要的传统中药材及观赏花卉。本研究整合二代、三代测序数据,从头组装了球花石斛的完整叶绿体基因组。球花石斛叶绿体基因组全长151 686 bp,为典型的四分结构,包含106个unigenes,其中编码基因71个,tRNA 31个,rRNA 4个。球花石斛叶绿体基因组检测到58个SSR(simple sequence repeat)位点,以单碱基重复A/T类型为主。密码子偏好性分析显示,亮氨酸为使用频率最高的氨基酸(10.15%),具有偏好性的密码子有31个,且绝大多数偏好性密码子以A/U结尾。通过共有编码基因序列(coding sequence,CDs)对27种石斛进行系统进化分析,将所选石斛分为9大类群,其中球花石斛与霍山石斛亲缘关系密切。本研究结果阐明了球花石斛的叶绿体基因组特征,为其资源筛选、鉴定,遗传多样性分析提供分子依据。Dendrobium thyrsiflorum,which is widely distributed in Yunnan province,is an important garden flower and used as a traditional Chinese medicine.In the present study,we de novo assembled the complete chloroplast(CP)genome of D.thyrsiflorum through the integration of the PacBio long and Illumina short reads.The CP genome exhibited a typical quadripartite cycle of 151686 bp containing 106 unigenes,and they were 71 encoding genes,31 tRNA genes and 4 rRNA genes.Additionally,58 SSR(simple sequence repeat)loci dominantly occupied by the type of A/T were detected in the CP genome.Codon bias analysis showed that the leucine was preferentially used at 10.15%frequency,there were 31 biased codons and the majority of the biased codons were ended with A/U.Phylogenetic analysis using 27 CP genomes of the Dendrobium based on the common coding sequence,we classified these Dendrobium species into 9 groups,and D.thyrsiflorum presented the closest relationship with D.huoshanense.This study comprehensively deciphered the characteristics of D.thyrsiflorum genome,which may provide molecular information for future resources selection and identification,and genetic diversity analysis.

关 键 词：球花石斛 叶绿体基因组 高通量测序 系谱分析 

分 类 号：S567.239[农业科学—中草药栽培]