A Comparative Analysis of the Chloroplast Genomes of Four Salvia Medicinal Plants

被引：52

作者：

Liang, Conglian ^{[1
,2
,3
]}

Wang, Lei ^{[1
,2
,4
]}

Lei, Juan ^{[5
]}

Duan, Baozhong ^{[6
]}

Ma, Weisi ^{[7
]}

Xiao, Shuiming ^{[2
]}

Qi, Haijun ^{[3
]}

Wang, Zhen ^{[3
]}

Liu, Yaoqi ^{[7
]}

Shen, Xiaofeng ^{[2
]}

Guo, Shuai ^{[2
]}

Hu, Haoyu ^{[2
]}

Xu, Jiang ^{[2
]}

Chen, Shilin ^{[2
]}

机构：

[1] Shandong Univ Tradit Chinese Med TCM, Coll Pharm, Jinan 250355, Shandong, Peoples R China

[2] China Acad Chinese Med Sci, Inst Chinese Materia Med, Beijing 100700, Peoples R China

[3] Jiangxi Qingfeng Pharmaceut Co Ltd, State Key Lab Innovat Nat Med & TCM Inject, Ganzhou 341000, Peoples R China

[4] Capital Med Univ, Beijing Childrens Hosp, Natl Ctr Childrens Hlth, Beijing 100045, Peoples R China

[5] Univ Queensland, Sch Biol Sci, Brisbane, Qld 4072, Australia

[6] Dali Univ, Coll Pharm, Dali 671000, Peoples R China

[7] Yunnan Acad Agr Sci, Inst Med Plants, Kunming 650205, Yunnan, Peoples R China

来源：

ENGINEERING | 2019年 / 5卷 / 05期

关键词：

Salvia; Chloroplast genome; Comparative analysis; PRZEWALSKII EXTRACT; INVERTED REPEAT; PLASTID GENOME; SEQUENCE; TRANSFORMATION; MILTIORRHIZA; SUBSTITUTION; ORGANIZATION; GENERATION; PROTEINS;

D O I：

10.1016/j.eng.2019.01.017

中图分类号：

T [工业技术];

学科分类号：

08 ;

摘要：

Herbgenomics is an emerging field of traditional Chinese medicine (TCM) research and development. By combining TCM research with genomics, herbgenomics can help to establish the scientific validity of TCM and bring it into wider usage within the field of medicine. Salvia Linn. (S. Linn.) is a large genus of Labiatae that includes important medicinal plants. In this herbgenomics study, the complete chloroplast (cp) genomes of two Salvia spp.-namely, S. przewalskii and S. bulleyana, which are used as a surrogate for S. miltiorrhiza-were sequenced and compared with those of two other reported Salvia spp.-namely, S. miltiorrhiza and S. japonica. The genome organization, gene number, type, and repeat sequences were compared. The annotation results showed that both Salvia plants contain 114 unique genes, including 80 protein-coding, 30 transfer RNA (tRNA), and four ribosomal RNA (rRNA) genes. Repeat sequence analysis revealed 21 forward and 22 palindromic sequences in both Salvia cp genomes, and 17 and 21 tandem repeats in S. przewalskii and S. bulleyana, respectively. A synteny comparison of the Salvia spp. cp genomes showed a high degree of sequence similarity in the coding regions and a relatively high divergence of the intergenic spacers. Pairwise alignment and single-nucleotide polymorphism (SNP) analyses found some candidate fragments to identify Salvia spp., such as the intergenic region of the trnV-ndhC, trnQ-rps16, atpI-atpH, psbA-ycf3, ycf1, rpoC2, ndhF, matK, rpoB, rpoA, and accD genes. All of the results-including the repeat sequences and SNP sites, the inverted repeat (IR) region border, and the phylogenetic analysis-showed that S. przewalskii and S. bulleyana are extremely similar from a genetic standpoint. The cp genome sequences of the two Salvia spp. reported here will pave the way for breeding, species identification, phylogenetic evolution, and cp genetic engineering studies of Salvia medicinal plants. (C) 2019 THE AUTHORS. Published by Elsevier LTD on behalf of Chinese Academy of Engineering and Higher Education Press Limited Company.

引用

页码：907 / 915

页数：9

共 79 条

[1] BASIC LOCAL ALIGNMENT SEARCH TOOL [J].

ALTSCHUL, SF ;

GISH, W ;

MILLER, W ;

MYERS, EW ;

LIPMAN, DJ .

JOURNAL OF MOLECULAR BIOLOGY, 1990, 215 (03) :403-410

[2]

[Anonymous], 2015, PHARMACOPOEIA PEOPLE

[3]

[Anonymous], PROC R SOC LONDON SE

[4] Chloroplast genomes of Arabidopsis halleri ssp gemmifera and Arabidopsis lyrata ssp petraea: Structures and comparative analysis [J].

Asaf, Sajjad ;

Khan, Abdul Latif ;

Khan, Muhammad Aaqil ;

Waqas, Muhammad ;

Kang, Sang-Mo ;

Yun, Byung-Wook ;

Lee, In-Jung .

SCIENTIFIC REPORTS, 2017, 7

[5]

Awano T, 2009, P NATL ACAD SCI USA, V106, P2794, DOI [10.1073/pnas.0812297106, 10.1073/pnas.0905845106]

[6] Tandem repeats finder: a program to analyze DNA sequences [J].

Benson, G .

NUCLEIC ACIDS RESEARCH, 1999, 27 (02) :573-580

[7] Scaffolding pre-assembled contigs using SSPACE [J].

Boetzer, Marten ;

Henkel, Christiaan V. ;

Jansen, Hans J. ;

Butler, Derek ;

Pirovano, Walter .

BIOINFORMATICS, 2011, 27 (04) :578-579

[8] Trimmomatic: a flexible trimmer for Illumina sequence data [J].

Bolger, Anthony M. ;

Lohse, Marc ;

Usadel, Bjoern .

BIOINFORMATICS, 2014, 30 (15) :2114-2120

[9] Chloroplasts extend stromules independently and in response to internal redox signals [J].

Brunkard, Jacob O. ;

Runkel, Anne M. ;

Zambryski, Patricia C. .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2015, 112 (32) :10044-10049

[10] Systematic investigation of insertional and deletional RNA-DNA differences in the human transcriptome [J].

Chen, Cai ;

Bundschuh, Ralf .

BMC GENOMICS, 2012, 13

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