Plant Diversity ›› 2023, Vol. 45 ›› Issue (05): 523-534.DOI: 10.1016/j.pld.2023.03.012

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Plastid phylogenomics and species discrimination in the “Chinese” clade of Roscoea (Zingiberaceae)

Hai-Su Hua,b, Jiu-Yang Maob, Xue Wangb, Yu-Ze Liangb, Bei Jiangb,c, De-Quan Zhanga,b,c   

  1. a. School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621010, Sichuan, China;
    b. College of Pharmacy, Dali University, Dali 671000, Yunnan, China;
    c. Yunnan Key Laboratory of Screening and Research on Anti-pathogenic Plant Resources from Western Yunnan (Cultivation), Dali 671000, Yunnan, China
  • Received:2022-11-21 Revised:2023-03-15 Online:2023-09-25 Published:2023-11-04
  • Contact: De-Quan Zhang,
  • Supported by:
    This study was supported by National Natural Science Foundation of China (32060091 & 31660081), Reserve Talents Project for Young and Middle-Aged Academic and Technical Leaders of Yunnan Province (202105AC160063).

Abstract: Roscoea is an alpine or subalpine genus from the pan-tropical family Zingiberaceae, which consists of two disjunct groups in geography, namely the “Chinese” clade and the “Himalayan” clade. Despite extensive research on the genus, Roscoea species remain poorly defined and relationships between these species are not well resolved. In this study, we used plastid genomes of nine species and one variety to resolve phylogenetic relationships within the “Chinese” clade of Roscoea and as DNA super barcodes for species discrimination. We found that Roscoea plastid genomes ranged in length from 163,063 to 163,796 bp, and encoded 113 genes, including 79 protein-coding genes, 30 tRNA genes, four rRNA genes. In addition, expansion and contraction of the IR regions showed obvious infraspecific conservatism and interspecific differentiation. Plastid phylogenomics revealed that species belonging to the “Chinese” clade of Roscoea can be divided into four distinct subclades. Furthermore, our analysis supported the independence of R. cautleoides var. pubescens, the recovery of Roscoea pubescens Z.Y. Zhu, and a close relationship between R. humeana and R. cautloides. When we used the plastid genome as a super barcode, we found that it possessed strong discriminatory power (90%) with high support values. Intergenic regions provided similar resolution, which was much better than that of protein-coding regions, hypervariable regions, and DNA universal barcodes. However, plastid genomes could not completely resolve Roscoea phylogeny or definitively discriminate species. These limitations are likely related to the complex history of Roscoea speciation, poorly defined species within the genus, and the maternal inheritance of plastid genomes.

Key words: Medicinal plant, Chloroplast genome, Molecular phylogeny, DNA barcoding, DNA sequencing, Species identification