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The Complete Chloroplast Genome Sequence of the Medicinal Plant Salvia miltiorrhiza
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 quadripar...
Autores principales: | , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Public Library of Science
2013
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3584094/ https://www.ncbi.nlm.nih.gov/pubmed/23460883 http://dx.doi.org/10.1371/journal.pone.0057607 |
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author | Qian, Jun Song, Jingyuan Gao, Huanhuan Zhu, Yingjie Xu, Jiang Pang, Xiaohui Yao, Hui Sun, Chao Li, Xian’en Li, Chuyuan Liu, Juyan Xu, Haibin Chen, Shilin |
author_facet | Qian, Jun Song, Jingyuan Gao, Huanhuan Zhu, Yingjie Xu, Jiang Pang, Xiaohui Yao, Hui Sun, Chao Li, Xian’en Li, Chuyuan Liu, Juyan Xu, Haibin Chen, Shilin |
author_sort | Qian, Jun |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-3584094 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-35840942013-03-04 The Complete Chloroplast Genome Sequence of the Medicinal Plant Salvia miltiorrhiza Qian, Jun Song, Jingyuan Gao, Huanhuan Zhu, Yingjie Xu, Jiang Pang, Xiaohui Yao, Hui Sun, Chao Li, Xian’en Li, Chuyuan Liu, Juyan Xu, Haibin Chen, Shilin PLoS One Research Article 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. Public Library of Science 2013-02-27 /pmc/articles/PMC3584094/ /pubmed/23460883 http://dx.doi.org/10.1371/journal.pone.0057607 Text en © 2013 Qian et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Qian, Jun Song, Jingyuan Gao, Huanhuan Zhu, Yingjie Xu, Jiang Pang, Xiaohui Yao, Hui Sun, Chao Li, Xian’en Li, Chuyuan Liu, Juyan Xu, Haibin Chen, Shilin The Complete Chloroplast Genome Sequence of the Medicinal Plant Salvia miltiorrhiza |
title | The Complete Chloroplast Genome Sequence of the Medicinal Plant Salvia miltiorrhiza
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title_full | The Complete Chloroplast Genome Sequence of the Medicinal Plant Salvia miltiorrhiza
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title_fullStr | The Complete Chloroplast Genome Sequence of the Medicinal Plant Salvia miltiorrhiza
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title_full_unstemmed | The Complete Chloroplast Genome Sequence of the Medicinal Plant Salvia miltiorrhiza
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title_short | The Complete Chloroplast Genome Sequence of the Medicinal Plant Salvia miltiorrhiza
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title_sort | complete chloroplast genome sequence of the medicinal plant salvia miltiorrhiza |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3584094/ https://www.ncbi.nlm.nih.gov/pubmed/23460883 http://dx.doi.org/10.1371/journal.pone.0057607 |
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