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Engineering >> 2019, Volume 5, Issue 5 doi: 10.1016/j.eng.2019.01.017

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

a College of Pharmacy, Shandong University of Traditional Chinese Medicine (TCM), Jinan 250355, China
b Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
c State Key Laboratory of Innovative Natural Medicine and TCM Injections, Jiangxi Qingfeng Pharmaceutical Co. Ltd., Ganzhou 341000, China
d Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
e School of Biological Science, The University of Queensland, Brisbane, QLD 4072, Australia
f College of Pharmacy, Dali University, Dali 671000, China
g Institute of Medicinal Plants, Yunnan Academy of Agricultural Sciences, Kunming 650205, China

Received: 2018-07-23 Revised: 2018-11-27 Accepted: 2019-01-07 Available online: 2019-08-16

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Abstract

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. is a large genus of Labiatae that includes important medicinal plants. In this herbgenomics study, the complete chloroplast (cp) genomes of two Salvia (S.) 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 direct 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 singlenucleotide 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.

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