J Syst Evol ›› 2022, Vol. 60 ›› Issue (6): 1263-1280.DOI: 10.1111/jse.12802

• Research Articles • Previous Articles     Next Articles

Phylogenomic relationships and species identification of the olive genus Olea (Oleaceae)

Wen-Pan Dong1, Jia-Hui Sun2, Yan-Lei Liu3, Chao Xu3, Yi-Heng Wang2, Zhi-Li Suo3, Shi-Liang Zhou3, Zhi-Xiang Zhang1*, and Jun Wen4*   

  1. 1 Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
    2 State Key Laboratory Breeding Base of Dao‐di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
    3 State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, China
    4 Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013‐7012, USA

    *Authors for correspondence. Zhi‐Xiang Zhang. E‐mail: zxzhang@bjfu.edu.cn; Jun Wen. E‐mail: wenj@si.edu
  • Received:2021-04-03 Accepted:2021-05-27 Online:2021-06-17 Published:2022-11-01


The olive genus Olea includes c. 30–40 taxa in three subgenera (Olea, Tetrapilus, and Paniculatae) within the family Oleaceae. Historically, the Olea genus was classified into four groups that were overall well supported by reconstructed phylogenies, despite incomplete sampling of subgenus Tetrapilus and poor resolution within clades. These analyses also showed that the genus was not monophyletic. Reliable identification of Olea species is important for both their conservation and utilization of this economically important genus. In this study, we used phylogenomic data from genome skimming to resolve relationships within Olea and to identify molecular markers for species identification. We assembled the complete plastomes, and nrDNA of 26 individuals representing 13 species using next-generation sequencing and added 18 publicly available accessions of Olea. We also developed nuclear SNPs using the genome skimming data to infer the phylogenetic relationships of Olea. Large-scale phylogenomic analyses of 138 samples of tribe Oleeae supported the polyphyly of Olea, with Olea caudatilimba and Olea subgenus Tetrapilus not sharing their most recent common ancestor with the main Olea clade (subgenus Paniculatae and subgenus Olea). The interspecific phylogenetic resolution was poor owing to a possible rapid radiation. By comparing with the plastome data, we identified the markers ycf1b and psbE-petL as the best Olea-specific chloroplast DNA barcodes. Compared with universal barcodes, specific DNA barcodes and super-barcode exhibited higher discriminatory power. Our results demonstrated the power of phylogenomics to improve phylogenetic relationships of intricate groups and provided new insights into barcodes that allow for accurate identification of Olea species.

Key words: Olea, phylogenomics, specific DNA barcode, species identification, super‐barcode