Chinese Bulletin of Botany ›› 2021, Vol. 56 ›› Issue (6): 699-714.DOI: 10.11983/CBB21100

• EXPERIMENTAL COMMUNICATIONS • Previous Articles     Next Articles

Revealing the New Whole-genome Duplication Event of Four Paphiopedilum Species Based on Transcriptome Data

Meng Wang1, Ting Wang1,2, Zengqiang Xia1,3, Tingzhang Li1, Xiaohua Jin4, Yuehong Yan1, Jianbing Chen1,*()   

  1. 1Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The Orchid Conservation & Research Center of Shenzhen, Shenzhen 518114, China
    2College of Biodiversity Conservation, Southwest Forestry University, Kunming 650224, China
    3Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
    4State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
  • Received:2021-06-22 Accepted:2021-11-24 Online:2021-11-01 Published:2021-11-24
  • Contact: Jianbing Chen

Abstract: Polyploidization or whole-genome duplication (WGD) is a major driving force in species diversification. Repeated WGD has been found in species-rich groups or families such as ferns, Asteraceae or Fabaceae. However, there is a paradox between the abundant species diversity of Orchidaceae and the rarely discovered WGD events. We hypothesized that it could be due to the early research strategy of a small sample size of species belonging to not closely related groups. Paphiopedilum has a rich variation on chromosome number and morphology. Here, we select it as the representative group of orchids, and use the synonymous substitution rate (Ks), phylogenomic and relative dating methods to detect whether WGD events have been occurred in P. armeniacum, P. concolor, P. hirsutissimum or P. malipoense based on the shared transcriptome data. The result shows that three WGDs are detected in all four species of Paphiopedilum, which occurred in 110.17-119.77 Mya (WGD1), 60.95-74.19 Mya (WGD2), and 38.19-45.85 Mya (WGD3), respectively. WGD3 is a newly detected whole-genome duplication event in orchids and speculated to occur after the differentiation of Cypripedioideae and its sister groups, but before the differentiation of Paphiopedilum and its sister groups. In addition, the retained duplicated genes of three WGDs are functionally related with the environmental stress response at that time. It is speculated that WGD has improved the adaptability of the ancestors of Paphiopedilum to extreme environmental changes.

Key words: polyploidization, Ochidaceae, Cypripedioideae, adaptive evolution, synonymous substitution rate