J Syst Evol ›› 2022, Vol. 60 ›› Issue (6): 1229-1240.DOI: 10.1111/jse.12814

• Research Articles • Previous Articles     Next Articles

Phylogenomic and comparative analyses of Rheum (Polygonaceae, Polygonoideae)

Hua-Jie Zhang1,2†, Xu Zhang1,2,3†, Jacob B. Landis4,5, Yan-Xia Sun1,2, Jiao Sun1,2,3, Tian-Hui Kuang6, Li-Juan Li1,2,3, Bashir B. Tiamiyu1,2,3, Tao Deng6, Hang Sun6*, and Heng-Chang Wang1,2*   

  1. 1 CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
    2 Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
    3 University of Chinese Academy of Sciences, Beijing 100049, China
    4 School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY 14850, USA
    5 BTI Computational Biology Center, Boyce Thompson Institute, Ithaca, NY 14853, USA
    6 Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China

    These authors contributed equally to this study.
    * Authors for correspondence. Hang Sun. E‐mail: hsun@mail.kib.ac.cn; Heng‐Chang Wang. E‐mail: hcwang@wbgcas.cn
  • Received:2021-09-07 Accepted:2021-11-04 Online:2021-11-06 Published:2022-11-01


Species of Rheum have high medicinal value, with the center of diversity in the Qinghai–Tibet Plateau (QTP) and adjacent regions. However, phylogenetic relationships of Rheum are still unclear due to fragment markers providing insufficient informative loci. Here, we sequenced and annotated plastomes of nine Rheum species, and compared the genome structure among the novel nine species along with three published species. Comparative analyses revealed that plastomes of Rheum share a relatively conserved structure. Five highly divergent regions (accD, ccsA, matK, ndhF, and ndhH) can be used as valuable molecular markers for further species delimitation and population genetic studies. Twenty-two accessions representing 17 species were used for phylogenetic analysis, which generated a robust phylogenetic tree and revealed two major clades within Rheum. Phylogenetic results showed that glasshouse structures and cushions of Rheum are results of parallel evolution during adaptation to similar environments. Inconsistent tree topology between concatenated and coalescent methods was detected, implying that incomplete lineage sorting and hybridization may have occurred in the evolutionary history of Rheum. Divergence time estimation based on two fossil calibrations and three secondary calibrations revealed a Miocene to middle Oligocene origin of Rheum. Our study provides valuable genomic resources for the medicinally important genus Rheum, while gaining helpful insights into its systematics and evolution.

Key words: incomplete lineage sorting and hybridization, molecular marker, phylogenomic, plastomes, Rheum