J Syst Evol

• Research Articles •    

Phylotranscriptomics reveals extensive gene duplication in the subtribe Gentianinae (Gentianaceae)

Chun‐Lin Chen1† , Lei Zhang1† , Jia‐Liang Li1 , Xing‐Xing Mao1 , Lu‐Shui Zhang1 , Quan‐Jun Hu1 , Jian‐Quan Liu1,2* , and Zhen‐Xiang Xi1 *   

  1. 1 Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of Education and State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu 610065, China
    2 State Key Laboratory of Grassland Agro‐Ecosystems, College of Life Sciences, Lanzhou University, Lanzhou 730000, China
  • Received:2019-07-28 Accepted:2020-06-17 Online:2020-06-23

Abstract:

Gene duplication plays an important role in plants for diversification and adaptation to new habitats. In this study, we aim to reconstruct the genome‐scale phylogeny and identify large‐scale gene duplication events for the subtribe Gentianinae (Gentianaceae), which is a great symbol of the alpine plants in the Qinghai–Tibet Plateau. We sequenced and assembled 70 transcriptomes from 67 species, representing all six recognized genera in the subtribe Gentianinae plus the closely related outgroups. Using phylogenomic approaches, the backbone relationships of Gentianinae were almost fully resolved with high bootstrap support. Although instances of conflicts were observed between nuclear and plastid phylogenies, six major clades of Gentianinae were consistently recovered in both phylogenies. In addition, we revealed a high occurrence of duplicated genes in our transcriptome assemblies. Using several gene tree reconciliation methods, we collectively identified 10 nodes in the species tree with large concentrations of duplicated genes. Further analysis indicated that many of these duplicated genes likely arose from hybrid polyploidy, which might also account for some of the topological incongruences between nuclear and plastid phylogenies in Gentianinae.

Key words: gene duplication, Gentianinae, hybridization, phylogeny, transcriptome