Plant Diversity ›› 2019, Vol. 41 ›› Issue (04): 213-219.DOI: 10.1016/j.pld.2019.05.003

• Articles •     Next Articles

Phylogenomic analyses reveal intractable evolutionary history of a temperate bamboo genus (Poaceae: Bambusoideae)

Cen Guoa,b, Zhen-Hua Guoa, De-Zhu Lia   

  1. a Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China;
    b Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
  • Received:2019-03-12 Revised:2019-05-24 Online:2019-08-25 Published:2019-09-17
  • Contact: Zhen-Hua Guo,E-mail;De-Zhu Li,E-mail
  • Supported by:
    This work was supported by the National Natural Science Foundation of China (Grant No. 31470322 and 31430011). We thank Dr. Xia-Ying Ye for providing ddRAD-seq data of Fargesia nitida. We are grateful to Prof. Jun-Bo Yang, Dr. Guo-Qian Yang, Ms. Jing Yang and Mr. Ji-Xiong Yang at CAS Kunming Institute of Botany's Germplasm Bank of Wild Species, for providing experimental supports. We also thank the support from the UCAS Joint PhD Training Program.

Abstract: Shibataea is a genus of temperate bamboos (Poaceae:Bambusoideae) endemic to China, but little is known about its phylogenetic position and interspecific relationships. To elucidate the phylogenetic relationship of the bamboo genus Shibataea, we performed genome-scale phylogenetic analysis of all seven species and one variety of the genus using double digest restriction-site associated DNA sequencing (ddRAD-seq) and whole plastid genomes generated using genome skimming. Our phylogenomic analyses based on ddRAD-seq and plastome data congruently recovered Shibataea as monophyletic. The nuclear data resolved S. hispida as the earliest diverged species, followed by S. chinensis, while the rest of Shibataea can be further divided into two clades. However, the plastid and nuclear topologies conflict significantly. By comparing the results of network analysis and topologies reconstructed from different datasets, we identify S. kumasasa as the most admixed species, which may be caused by incomplete lineage sorting (ILS) or interspecific gene flow with four sympatric species. This study highlights the power of ddRAD and plastome data in resolving complex relationships in the intractable bamboo genus.

Key words: Shibataea, ddRAD-seq, Genome skimming, Phylogeny, Incongruence