Salvia miltiorriza is one of the most widely used medicinal plants.As a first step to develop a chloroplast-based genetic engineering method for the over-production of active components from S.miltiorriza,we have analyzed the genome,transcriptome,and base modifications of the S.miltiorrhiza chloroplast.Total genomic DNA and RNA were extracted from fresh leaves and then subjected to strand-specific RNA-Seq and Single-Molecule Real-Time(SMRT)sequencing analyses.Mapping the RNA-Seq reads to the genome assembly allowed us to determine the relative expression levels of 80 protein-coding genes.