Salvia miltiorrhiza 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. miltiorrhiza, 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. In addition, we identified 19 polycistronic transcription units and 136 putative antisense and intergenic noncoding RNA (ncRNA) genes. Comparison of the abundance of protein-coding transcripts (cRNA) with and without overlapping antisense ncRNAs (asRNA) suggest that the presence of asRNA is associated with increased cRNA abundance (p<0.05). using the smrt portal software (v1.3.2), 2687 potential dna modification sites and two motifs were predicted. include a tata box-like motif (cpgdmm1, "tatannnatna"), an unknown (cpgdmm2 "wnyantgaw"). specifically, 35 of 97 cpgdmm1 (36.1%) 91 369 cpgdmm2 (24.7%) found to be significantly modified (p<0.01). analysis genes downstream revealed increased abundance ncrna that are less than 400 bp away from cpgdmm1motif taking together, present study complex interplay among modifications, crna expression in chloroplast genome.
Journal: PloS one
DOI: 10.1371/journal.pone.0099314
Year: 2014