Ancestral gene duplications in mosses characterized by integrated phylogenomic analyses

Authors: GAO, BEI - The Chinese University Of Hong Kong (CUHK); CHEN, MOXIAN - The Chinese University Of Hong Kong (CUHK); LI, XIAOSHUANG - The Chinese University Of Hong Kong (CUHK); LIANG, YUQING - The Chinese University Of Hong Kong (CUHK); ZHANG, DAOYUAN - Chinese Academy Of Sciences; WOOD, ANDREW - Southern Illinois University; Oliver, Melvin; ZHANG, JIANHUA - The Chinese University Of Hong Kong (CUHK)

Submitted to: Journal of Systematics and Evolution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/6/2020
Publication Date: 1/1/2022
Citation: Gao, B., Chen, M., Li, X., Liang, Y., Zhang, D., Wood, A., Oliver, M.J., Zhang, J. 2022. Ancestral gene duplications in mosses characterized by integrated phylogenomic analyses. Journal of Systematics and Evolution. 60(1): 144-159. https://doi.org/10.1111/jse.12683.
DOI: https://doi.org/10.1111/jse.12683

Interpretive Summary: In order to fully understand how plants have adapted to different environments and large-scale events in order to direct efforts for crop improvement it is important to determine how plant genomes have evolved over time. Of particular interest are the whole genome duplication events that resulted in large "bursts" of species diversity at specific times in the earth's history. These events are thought to play a role in adaptation to changing environments. We used a transcriptome data (sequence data derived from RNA of expressed genes) in plants to follow the early evolution of plant genomes in an ancient lineage of mosses. We observed large-scale duplications within moss genomes that occurred during the time when large numbers of species evolved in one member of this group (the Bryopsida). We provided robust evidence for the ancient whole genome duplication in the common ancestor of the mosses . This research helps to inform our efforts to understand how early plants adapted to new and challenging environments and informs our efforts to adapt crop plants to changing environments.

Technical 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 ' event and the Funarioideae duplication event, respectively. The ' 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.