loading page

Phylogenetic significance of the characteristics of simple sequence repeats at the genus level based on the complete chloroplast genome sequences of Cyatheaceae
  • +3
  • Ming Zhu,
  • Peipei Feng,
  • Jingyao Ping,
  • Jinye Li,
  • Ying-juan Su,
  • Ting Wang
Ming Zhu
South China Agricultural University College of Life Sciences
Author Profile
Peipei Feng
South China Agricultural University
Author Profile
Jingyao Ping
South China Agricultural University
Author Profile
Jinye Li
South China Agricultural University
Author Profile
Ying-juan Su
Sun Yat-Sen University
Author Profile
Ting Wang
South China Agricultural University
Author Profile

Abstract

Recent taxonomic and molecular phylogenetic studies have shown that Gymnosphaera should be recognized as an independent taxonomic unit at the genus level under the family Cyatheaceae. In this study, the complete chloroplast genomes of the eight species of Cyatheaceae were sequenced, and their phylogenetic relationships were reconstructed using the maximum likelihood, Bayesian inference, maximum parsimony, and neighbor-joining methods, and the characteristics of their simple sequence repeats (SSRs) were compared and analyzed for the first time. The results showed that when Cyatheaceae was divided into three genera,the number, relative abundance, relative density, and GC content of all SSRs and of SSRs of certain unit lengths in the chloroplast genomes of the eight species of Cyatheaceae were genus specific in the whole chloroplast genomes and in their different regions (large single-copy, small single-copy, inverted repeat, intergenic spacer, intron, rRNA gene, and coding sequence regions). The SSRs overall and the single-nucleotide SSRs had significant differences in number, relative abundance, relative density, and GC content between the chloroplast genomes, their intergenic regions, and large single-copy regions. When Cyatheaceae was divided into two genera, only the difference in GC content was significant. Therefore, our results support the restoration of the hierarchical status of Gymnosphaera. This study provides an important basis for the identification of the phylogenetic relationship of Cyatheaceae plants.

Peer review status:IN REVISION

12 Mar 2021Submitted to Ecology and Evolution
12 Mar 2021Assigned to Editor
12 Mar 2021Submission Checks Completed
16 Mar 2021Reviewer(s) Assigned
06 Apr 2021Review(s) Completed, Editorial Evaluation Pending
11 May 2021Editorial Decision: Revise Minor