J Syst Evol

• Research Articles •    

Ancestral gene duplications in mosses characterized by integrated phylogenomic analyses

Bei Gao1,2,3 , Mo‐Xian Chen4 , Xiao‐Shuang Li1 , Yu‐Qing Liang1 , Dao‐Yuan Zhang1 , Andrew J. Wood5 , Melvin J. Oliver6* , and Jian‐Hua Zhang3,7*   

  1. 1 State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
    2 School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
    3 State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
    4 Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
    5 Department of Plant Biology, Southern Illinois University‐Carbondale, Carbondale, IL 62901‐6509, USA
    6 Division of Plant Sciences, Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211, USA
    7 Department of Biology, Faculty of Science, Hong Kong Baptist University, Hong Kong, China
  • Received:2020-03-30 Accepted:2020-09-06 Online:2020-09-10

Abstract:

Mosses (Bryophyta) are a key group occupying an important phylogenetic position in land plant (embryophyte) evolution. The class Bryopsida represents the most diversified lineage, containing more than 95% of modern mosses, whereas other classes are species‐poor. Two branches with large numbers of gene duplications were elucidated by phylogenomic analyses, one in the ancestry of all mosses and another before the separation of the Bryopsida, Polytrichopsida, and Tetraphidopsida. The analysis of the phylogenetic progression of duplicated paralogs retained on genomic syntenic regions in the Physcomitrella patens genome confirmed that the whole‐genome duplication events WGD1 and WGD2 were re‐recognized as the ψ event and the Funarioideae duplication event, respectively. The ψ polyploidy event was tightly associated with the early diversification of Bryopsida, in the ancestor of Bryidae, Dicranidae, Timmiidae, and Funariidae. Together, four branches with large numbers of gene duplications were unveiled in the evolutionary past of P. patens. Gene retention patterns following the four large‐scale duplications in different moss lineages were analyzed and discussed. Recurrent significant retention of stress‐related genes may have contributed to their adaption to distinct ecological environments and the evolutionary success of this early‐diverging land plant lineage.

Key words: gene duplication, moss, phylogenomic, Physcomitrella, polyploidy, WGD