title: The complete chloroplast genome sequence of the medicinal plant Salvia miltiorrhiza.
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.
authors: The National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
authors: Jun
authors: J
authors: Qian
authors: Jingyuan
authors: J
authors: Song
authors: Huanhuan
authors: H
authors: Gao
authors: Yingjie
authors: Y
authors: Zhu
authors: Jiang
authors: J
authors: Xu
authors: Xiaohui
authors: X
authors: Pang
authors: Hui
authors: H
authors: Yao
authors: Chao
authors: C
authors: Sun
authors: Xian'en
authors: X
authors: Li
authors: Chuyuan
authors: C
authors: Li
authors: Juyan
authors: J
authors: Liu
authors: Haibin
authors: H
authors: Xu
authors: Shilin
authors: S
authors: Chen
mesh_terms: D000926:Anticodon / Q000235:genetics; D001483:Base Sequence; D002874:Chromosome Mapping; D003062:Codon / Q000235:genetics; D005091:Exons / Q000235:genetics; D017343:Genes, Plant / Q000235:genetics; D014644:Genetic Variation; D054628:Genome, Chloroplast / Q000235:genetics*; D007438:Introns / Q000235:genetics; D019686:Lamiaceae / Q000235:genetics; D018895:Microsatellite Repeats / Q000235:genetics; D008969:Molecular Sequence Data; D016366:Open Reading Frames / Q000235:genetics; D010802:Phylogeny; D010946:Plants, Medicinal / Q000235:genetics*; D015203:Reproducibility of Results; D027561:Salvia miltiorrhiza / Q000235:genetics*
chemical_list: D000926:Anticodon; D003062:Codon