The Chloroplast Genome ofSalvia: Genomic Characterization and Phylogenetic Analysis

Premise of research. Previous studies based on plastid fragments and/or nuclear ribosomal DNA have had limited success resolving relationships within the genusSalvia. This study evaluates the efficacy of complete plastome sequences for phylogenetic inference withinSalvia, using the recently establishedSalviasubg.Glutinariaas a case study. We use these plastomes to identify hypervariable and simple sequence repeat (SSR) regions for future studies withinSalvia. Methodology. In order to produce a phylogenetic backbone forSalvia, we sequenced and assembled complete plastomes for six species ofSalvia. These plastomes were combined with 11 plastomes (10 species) ofSalviafrom GenBank for analyses. This sampling represented seven of the 10 subgenera ofSalvia. Genome features of these plastomes were analyzed, and hypervariable regions, SSRs, and longer repeats were identified. Phylogenetic relationships of 16Salviaspecies were investigated using maximum likelihood and Bayesian methods based on four different data sets. Pivotal results. All of the 17Salviaplastomes 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 ofSalviaandSalviasubg.Glutinariawas supported in our phylogenetic analyses. Conclusions. Complete plastome sequences are promising for phylogenetic reconstruction ofSalviaand 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 ofSalvia. The extended analysis of SSRs will be helpful for future population genetics studies and in elucidating the genetic diversity ofSalviaand its relatives.