Plant Diversity ›› 2021, Vol. 43 ›› Issue (01): 15-26.DOI: 10.1016/j.pld.2020.07.004

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Comparative plastomic analysis and insights into the phylogeny of Salvia (Lamiaceae)

Hong Wua,b, Peng-Fei Maa, Hong-Tao Lia, Guo-Xiong Huc, De-Zhu Lia   

  1. a Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China;
    b University of Chinese Academy of Sciences, Beijing, 100049, China;
    c College of Life Sciences, Guizhou University, Guiyang, Guizhou, 550025, China
  • Received:2020-02-05 Revised:2020-07-13 Online:2021-02-25 Published:2021-03-25
  • Contact: Hong Wu, Peng-Fei Ma, Hong-Tao Li, Guo-Xiong Hu, De-Zhu Li
  • Supported by:
    We are grateful to the Germplasm Bank of Wild Species at the Kunming Institute of Botany (KIB) and Molecular Biology Experiment Center, Germplasm Bank of Wild Species for facilitating this study. This research was supported by the Large-scale Scientific Facilities of the Chinese Academy of Sciences (Grant No: 2017eLSFGBOWSe02). We thank Dr. Chun-Lei Xiang for reviewing the first draft for us.

Abstract: Salvia is the largest genus of Lamiaceae, with almost 1000 species, and has been divided into 11 subgenera. Salvia subg. Glutinaria, native to East Asia, is particularly important because of its potential medicinal value. However, the interspecific relationships of this subgenus have not been resolved and the plastomes of Salvia have rarely been studied. In the current study, we compared plastid genome structure and organization of 19 species of Salvia (14 newly sequenced and 5 previously published). Our comparative analysis showed that all Salvia plastomes examined have a quadripartite structure typical of most angiosperms and contain an identical set of 114 unique genes (80 protein-coding genes, 4 rRNA genes, and 30 tRNA genes). The plastome structure of all Salvia species is highly conserved like other Lamiaceae plastomes. Gene content, gene order, and GC content were highly similar in these plastomes. The inverted repeats/single copy region (IR/SC) boundaries of Salvia are highly conserved, and IR contraction only occurred in two species (Salvia mekongensis and S. rosmarinus). In Salvia, sequence divergence was higher in non-coding regions than in coding regions. We found that using large single copy (LSC) and small single copy regions (SSC) with exclusion of the rapidly evolving sites produced the highest resolution in phylogenetic analysis of Salvia, suggesting that using suitable informative sites to build trees is more conducive in phylogenetic research. This study assembled a powerful matrix data set for studying the phylogeny of Salvia, resolving the interspecific relationship of Salvia subg. Glutinaria. The newly sequenced plastid genomes will also enrich the plastome database of Salvia, providing the scientific basis for the development and utilization of germplasm resources of this large and important genus.

Key words: Lamiaceae, Salvia subg. Glutinaria, Plastome, Phylogeny