Biodiv Sci ›› 2021, Vol. 29 ›› Issue (5): 586-595.DOI: 10.17520/biods.2020263

• Original Papers: Original Papers • Previous Articles     Next Articles

Characterization of complete chloroplast genome in Firmiana kwangsiensis and F. danxiaensis with extremely small populations

Qifeng Lu1, Zhihuan Huang2, Wenhua Luo1,*()   

  1. 1 Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, Guangxi 541006
    2 School of Architecture, University of South China, Hengyang, Hunan 421001
  • Received:2020-06-30 Accepted:2020-09-10 Online:2021-05-20 Published:2021-02-01
  • Contact: Wenhua Luo

Abstract:

Aims: Firmiana kwangsiensis and F. danxiaensis are endemic plant species with narrow distribution and small population in southern China, which have important ecological and economic value. However, our knowledge of the chloroplast genome level of F. kwangsiensis and F. danxiaensis are still limited. Also, the phylogenetic relationships among the Firmiana genus remain unclear.
Methods: The genome skimming sequencing data of F. kwangsiensis and F. danxiaensis were obtained by using the high-throughput sequencing, and the complete chloroplast genomes were assembled and then the structures were analyzed by bioinformatics methods.
Results: The results revealed that complete chloroplast genomes of the F. kwangsiensis and F. danxiaensis show a typical quadripartite structure of 160,836 bp and161,253 bp in length, consisting of a large single copy region (89,700 bp and 90,142 bp) and a small single copy region (19,970 bp and20,067 bp) that were separated by a pair of inverted repeat regions (25,583 bp and 25,522 bp each). The annotation results showed that chloroplast genomes of both species contain 131 genes, including 86 protein-coding, 37 transfer RNA (tRNA), and eight ribosomal RNA (rRNA) genes. In F. kwangsiensis, 26 forward repeats, two reverse repeats, 21 palindromic repeats, 23 tandem repeats, and 98 simple sequence repeats were found, and 23 forward repeats, five reverse repeats, 21 palindromic repeats, 30 tandem repeats, and 107 simple sequence repeats were found in F. danxiaensis. Phylogenetic analyses revealed that five Firmiana species were clustered into two branches with strong supports. Firmiana kwangsiensis, F. pulcherrima and F. colorata formed a branch, and the F. kwangsiensis was a sister relationship to F. pulcherrima in this branch, the other branch was F. danxiaensis and F. major.
Conclusion: The structures, gene arrangement and repeat sequences in F. kwangsiensis and F. danxiaensis chloroplast genome were high similar. Phylogenetic analyses revealed that five Firmiana species were clustered into two clades, F. kwangsiensis was closely related to F. pulcherrima, and F. danxiaensis was closely related to F. major. In addition, the SSRs in this study will provides important genetic information for phylogenetic, evolution for Firmiana species.

Key words: Firmiana kwangsiensis, Firmiana danxiaensis, chloroplast genome, high-throughput sequencing, repeat sequence, phylogenetic analysis