The chloroplast genome of salvia: Genomic characterization and phylogenetic analysis

Fei Zhao, Bryan T. Drew, Ya Ping Chen, Guo Xiong Hu, Bo Li, Chun Lei Xiang

Research output: Contribution to journalArticlepeer-review

14 Scopus citations


Premise of research. Previous studies based on plastid fragments and/or nuclear ribosomal DNA have had limited success resolving relationships within the genus Salvia. This study evaluates the efficacy of complete plastome sequences for phylogenetic inference within Salvia, using the recently established Salvia subg. Glutinaria as a case study. We use these plastomes to identify hypervariable and simple sequence repeat (SSR) regions for future studies within Salvia. Methodology. In order to produce a phylogenetic backbone for Salvia, we sequenced and assembled complete plastomes for six species of Salvia. These plastomes were combined with 11 plastomes (10 species) of Salvia from GenBank for analyses. This sampling represented seven of the 10 subgenera of Salvia. Genome features of these plastomes were analyzed, and hypervariable regions, SSRs, and longer repeats were identified. Phylogenetic relationships of 16 Salvia species were investigated using maximum likelihood and Bayesian methods based on four different data sets. Pivotal results. All of the 17 Salvia plastomes displayed a typical quadripartite structure, and 114 different genes were identified in each accession. In addition, a total of 18 hypervariable regions and 626 SSRs were identified. The monophyly of Salvia and Salvia subg. Glutinaria was supported in our phylogenetic analyses. Conclusions. Complete plastome sequences are promising for phylogenetic reconstruction of Salvia and likely other clades within Lamiaceae. In addition, we identified 18 hypervariable regions that should be useful as plastid phylogenetic markers for phylogenetic inferences within the genus and potentially as bar code markers for identifying different species of Salvia. The extended analysis of SSRs will be helpful for future population genetics studies and in elucidating the genetic diversity of Salvia and its relatives.

Original languageEnglish (US)
Pages (from-to)812-830
Number of pages19
JournalInternational Journal of Plant Sciences
Issue number8
StatePublished - Oct 1 2020


  • Lamiaceae
  • Mentheae
  • Nepetoideae
  • Salviinae
  • Ycf1

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Plant Science


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