J Syst Evol ›› 2021, Vol. 59 ›› Issue (3): 504-514.DOI: 10.1111/jse.12556

• Research Articles • Previous Articles     Next Articles

Comparative phylogenetic analyses of Chinese Horsfieldia (Myristicaceae) using complete chloroplast genome sequences

Chao-Nan Cai1,2, Hui Ma1, Xiu-Qin Ci1,3, John G. Conran4, and Jie Li1,3*   

  1. 1 Plant Phylogenetics and Conservation Group, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China
    2 University of Chinese Academy of Sciences, Beijing 100049, China
    3 Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla 666303, China
    4 Australian Centre for Evolutionary Biology and Biodiversity (ACEBB), and Sprigg Geobiology Centre (SGC), School of Biological Sciences, The University of Adelaide, Adelaide 5005, South Australia, Australia
  • Received:2019-06-28 Accepted:2019-12-01 Online:2019-12-12 Published:2021-05-01

Abstract: The biologist's ruler for biodiversity is the species; accurate species identification is fundamental to the conservation of endangered species and in-depth biological scientific exploration. However, the delimitation and affinities of Horsfieldia in China has been controversial, owing in part to very low levels of molecular divergence within the family Myristicaceae. Because species boundaries and phylogenetic relationships within Horsfieldia are also unclear, 13 samples were collected across its distribution in China and their genomes were subjected to shotgun sequencing using Illumina platforms. A total of 40 487 994–84 801 416 pair-end clean reads were obtained and, after assembly, the complete chloroplast genome was recovered for all samples. Annotation analysis revealed a total of 112 genes, including 78 protein-coding genes, 30 transfer RNA, and 4 ribosomal RNA genes. Six variable loci (petN-psbM, trnH-psbA, ndhC-trnV, psbJ-psbL, ndhF, and rrn5-rrn23) were identified. Phylogenetic analyses strongly support the presence of four distinct species of Horsfieldia in China. In addition, samples that had been identified previously as Horsfieldia kingii (Hook. f.) Warb. were indistinguishable from those of H. prainii (King) Warb., suggesting that if H. kingii does occur in China, it was not collected in this study. Similarly, the chloroplast genome of one H. hainanensis Merr. sample from Guangxi province was identical to H. tetratepala C. Y. Wu, suggesting that the distribution range of H. hainanensis might be narrower than assumed previously. The phylogenetic relationships between the Chinese Horsfieldia species based on the whole chloroplast genomes was supported strongly, indicating the potential for using entire chloroplast genomes as super-barcodes for further resolution of the phylogeny of the genus Horsfieldia.

Key words: chloroplast genome, Horsfieldia, Myristicaceae, phylogenetics, species delimitation, super-barcodes