The Chloroplast and Mitochondrial Genomes of Salvia miltiorrhiza

Abstract

Salvia miltiorrhiza is one of the most widely used medicinal plants. Here, we discuss research progresses made on its chloroplast and mitochondrial genomes. In these studies, strand-specific RNA-Seq and single-molecule real-time (SMRT) sequencing analyses were conducted. Then, the RNA-Seq reads were mapped to the genome assembly to determine the relative expression levels of genes, DNA modifications and RNA editing events. For the chloroplast, the expression levels of all 80 protein-coding genes and 136 putative antisense and intergenic noncoding RNA (ncRNA) genes were detected. A total of 2687 putative modification sites were identified. Further analysis identified two DNA modification motifs: “TATANNNATNA” and “WNYANTGAW”. For the mitochondrial genome, the assembled genome has been validated extensively. A pipeline was developed to predict the RNA editing events using REDItools. A total of 1123 editing sites were identified, including 225 “C” to “U” sites in the protein-coding regions. The nucleotides on both strands at 115 of the 225 sites had undergone RNA editing, which were called symmetrical RNA editing (SRE). Taken together, a complex interplay among DNA transcriptome, modifications in S. miltiorrhiza plastome has been reported. In addition, symmetrical RNA editing events have been identified in its mitochondrial genome.