A comparative study of complete chloroplast genome for the genus salvia

Salvia is the largest genus of plants in the mint family (Labiatae). Its systematic classification, species identification and resource utilization have not been studied deeply. The chloroplast genome (CG) can reveal the taxonomic position of a species. Salvia yunnanensis, S. roborowskii and S. prattii have medicinal importance. Here, we decoded them using the Hiseq sequencing platform (Illumina) and bioinformatics methods, and compared them with the CGs of six other CGs of Salvia decoded previously. The size of these nine CGs varied from a maximum of 151,089 bp to a minimum of 153,995 bp, and their structures were typically quadripartite. Each CG shared 114 identical unique genes (44 photosynthesis-related genes, 25 transcription- and translation-related genes, 34 RNA genes, six genes of unknown function, and five other genes). The AT content was higher than the guanine-cytosine content, whether in the whole CG or in codon regions. Some simple sequence repeats, tandem repeats as well as forward, reverse, complement, and palindromic repeats were detected in nine CGs. Comparative CG analyses showed that the intergenic spacers of rps16 – trnQ, psbA – ycf3, ycf4 – cemA, trnV – ndhC, ndhD – ndhE and some genes ( ycf1, ndhF, rpoC2 ) had more variable sites. All nine Salvia species formed a robust monophyletic branch in our phylogenetic tree, and our study supports the notion that S. officinalis should be divided into a new subgenus. These data provide molecular support for the systematic classification, species identification, resource utilization and breeding of this genus in the future.