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.

The quest to resolve recent radiations: Plastid phylogenomics of extinct and endangered Hawaiian endemic mints (Lamiaceae)

“…The sequence demonstrates the typical quadripartite structure of other angiosperms, with a large single copy (LSC) region of 81,364 bp and a small single copy (SSC) region of 17,499 bp, separated by a pair of inverted repeats (IRa and IRb) of 25,436 bp. The length and structure of the sequence is similar to other plastid genome sequences of members in the order Lamiales (Lukas and Novak, 2013;Mariotti et al, 2010;Qian et al, 2013) (Fig. 3, see also Fig.…”

“…The Hawaiian mint genome did not demonstrate any rearrangements or inversions, which have been found in Jasmin nudiflorum, Schwalbea americana, and a few other species (Welch et al, 2016) (Lee et al, 2007;Wicke et al, 2013). The lengths of the mint chloroplast genomes, including lengths of the inverted repeat and small single copy region, were similar to other species in this family, such as Origanum vulgare and Salvia miltiorrhiza (Lukas and Novak, 2013;Qian et al, 2013), with most of the differences in length being due to short indels within the long single copy region.…”

“…To assemble the chloroplast genomes for the Stachys species, we first assembled the sequence for Stachys chamissonis, as this represents the species that is most closely related to the Hawaiian mints in phylogenies constructed from short chloroplast sequences (Lindqvist and Albert, 2002;Roy et al, 2013). We conducted five separate YASRA runs, using recently available chloroplast genome sequences as references: S. haliakalae, Olea europaea, Sesamum indicum (NC_016433) (Yi et al, 2012), Origanum vulgare (JX880022) (Lukas and Novak, 2013), and Salvia miltiorrhiza (NC_020431) (Qian et al, 2013). The contigs from the runs with each reference were aligned and an interim consensus sequence called.…”

The complete chloroplast genome sequence and phylogenetic analysis of Chuanminshen (Chuanminshenviolaceum Sheh et Shan)

“…Compared with other cp genome sequences, Chuanminshen cp genome was smaller than Panax ginseng 156,318 bp (Kim and Lee 2004), Nicotiana tabacum 155,943 bp (Shinozaki et al 1986), and much longer than Salvia miltiorrhiza Bge151328 bp (Qian et al 2013), a model plant of Chinese herbal medicine (Zhang et al 2015). Statistical analysis showed that Chuanminshen is the sixth largest cp genome in size and has the highest GC content among the 15 chloroplast genome sequences (including Chuanminshen) of Apiaceae plant family.…”

The Complete Chloroplast Genome Sequences of<em> Fritillaria ussuriensis</em> Maxim. and <em>Fritillaria cirrhosa</em> D. Don, and Comparative Analysis with Other<em> Fritillaria</em> Species

“…Chloroplasts play an important role in photosynthesis and carbon fixation as well as in the biosynthesis of starch, fatty acids, and amino acids [6]. The cp genome ranges from 120 to 180 kb in higher plants and has a quadripartite structure consisting of a large single copy (LSC) and small single copy (SSC) region and two copies of a larger inverted repeat (IR) [7].…”