Complex Interplay among DNA Modification, Noncoding RNA Expression and Protein-Coding RNA Expression in Salvia miltiorrhiza Chloroplast Genome
作者： Haimei Chen , Jianhui Zhang , George Yuan , Chang Liu
DOI: 10.1371/JOURNAL.PONE.0099314
关键词:
摘要: Salvia miltiorrhiza is one of the most widely used medicinal plants. As a first step to develop chloroplast-based genetic engineering method for over-production active components from S. miltiorrhiza, we have analyzed genome, transcriptome, and base modifications chloroplast. Total genomic DNA RNA were extracted fresh leaves then subjected strand-specific RNA-Seq Single-Molecule Real-Time (SMRT) sequencing analyses. Mapping reads genome assembly allowed us determine relative expression levels 80 protein-coding genes. In addition, identified 19 polycistronic transcription units 136 putative antisense intergenic noncoding (ncRNA) Comparison abundance transcripts (cRNA) with without overlapping ncRNAs (asRNA) suggest that presence asRNA associated increased cRNA (p<0.05). Using SMRT Portal software (v1.3.2), 2687 potential modification sites two motifs predicted. The include TATA box–like motif (CPGDMM1, “TATANNNATNA”), an unknown (CPGDMM2 “WNYANTGAW”). Specifically, 35 97 CPGDMM1 (36.1%) 91 369 CPGDMM2 (24.7%) found be significantly modified (p<0.01). Analysis genes downstream revealed ncRNA are less than 400 bp away CPGDMM1motif Taking together, present study complex interplay among modifications, in chloroplast genome.
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