生物技术通报 ›› 2021, Vol. 37 ›› Issue (5): 38-47.doi: 10.13560/j.cnki.biotech.bull.1985.2020-1380

• 研究报告 • 上一篇    下一篇

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

朱斌(), 甘晨晨, 王洪程()   

  1. 贵州师范大学生命科学学院,贵阳 550001
  • 收稿日期:2020-11-13 出版日期:2021-05-26 发布日期:2021-06-11
  • 作者简介:朱斌,男,博士,副教授,硕士生导师,研究方向:油菜远缘杂交及种质资源创新;E-mail: zhugg130@126.com
  • 基金资助:
    贵州省科学计划项目(QKHJC20201Y102)

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

ZHU Bin(), GAN Chen-chen, WANG Hong-cheng()   

  1. School of Life Sciences, Guizhou Normal University,Guiyang 550001
  • Received:2020-11-13 Published:2021-05-26 Online:2021-06-11

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。

关键词: 球花石斛, 叶绿体基因组, 高通量测序, 系谱分析

Abstract:

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 151 686 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.

Key words: Dendrobium thyrsiflorum, chloroplast genome, high-throughput sequencing, phylogenetic analysis