Biotechnology Bulletin ›› 2021, Vol. 37 ›› Issue (5): 38-47.doi: 10.13560/j.cnki.biotech.bull.1985.2020-1380

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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 Online:2021-05-26 Published:2021-06-11
  • Contact: WANG Hong-cheng E-mail:zhugg130@126.com;besthongcheng@163.com

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