The Complete Chloroplast Genome Sequence of the Medicinal Plant Salvia miltiorrhiza

Chuyuan Li,Juyan Liu,Xiaohui Pang,Haibin Xu,Hui Yao,Chao Sun,Yingjie Zhu,Jingyuan Song,Jiang Xu,Xian’en Li,Shilin Chen,Jun Qian,Huanhuan Gao,Keqiang Wu

doi:10.1371/journal.pone.0057607

Abstract

Salvia miltiorrhiza is an important medicinal plant with great economic and medicinal value. The complete chloroplast (cp) genome sequence of Salvia miltiorrhiza, the first sequenced member of the Lamiaceae family, is reported here. The genome is 151,328 bp in length and exhibits a typical quadripartite structure of the large (LSC, 82,695 bp) and small (SSC, 17,555 bp) single-copy regions, separated by a pair of inverted repeats (IRs, 25,539 bp). It contains 114 unique genes, including 80 protein-coding genes, 30 tRNAs and four rRNAs. The genome structure, gene order, GC content and codon usage are similar to the typical angiosperm cp genomes. Four forward, three inverted and seven tandem repeats were detected in the Salvia miltiorrhiza cp genome. Simple sequence repeat (SSR) analysis among the 30 asterid cp genomes revealed that most SSRs are AT-rich, which contribute to the overall AT richness of these cp genomes. Additionally, fewer SSRs are distributed in the protein-coding sequences compared to the non-coding regions, indicating an uneven distribution of SSRs within the cp genomes. Entire cp genome comparison of Salvia miltiorrhiza and three other Lamiales cp genomes showed a high degree of sequence similarity and a relatively high divergence of intergenic spacers. Sequence divergence analysis discovered the ten most divergent and ten most conserved genes as well as their length variation, which will be helpful for phylogenetic studies in asterids. Our analysis also supports that both regional and functional constraints affect gene sequence evolution. Further, phylogenetic analysis demonstrated a sister relationship between Salvia miltiorrhiza and Sesamum indicum. The complete cp genome sequence of Salvia miltiorrhiza reported in this paper will facilitate population, phylogenetic and cp genetic engineering studies of this medicinal plant.

Highlights

Chloroplasts, one of the main distinguishing characteristics of plant cells, are generally accepted to have originated from cyanobacteria through endosymbiosis [1,2]
Genome Assembly and Validation The annotated cp genome sequence of Arabidopsis thaliana was taken from TAIR
Homologs of these two genes were identified in the Salvia miltiorrhiza cp genome by searching 454 reads using the BLASTn algorithm [41]

Summary

Introduction

Chloroplasts, one of the main distinguishing characteristics of plant cells, are generally accepted to have originated from cyanobacteria through endosymbiosis [1,2]. In addition to their central function of photosynthesis, chloroplasts participate in the biosynthesis of starch, fatty acids, pigments and amino acids [3]. The majority of the cp genomes range from 120 to 160 kb in length [5] and exhibit highly conserved gene order and contents [2,6]. Large-scale genome rearrangement and gene loss have been identified in several angiosperm lineages [7,8]. Cp genome sequences are useful for phylogenetic [9], DNA barcoding [10], population [11] and transplastomic [12] studies

Methods

Results

Discussion

Conclusion