Integrated phylogenomic analyses reveal recurrent ancestral large-scale duplication events in mosses

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: bioRxiv
Publication Type: Pre-print Publication
Publication Acceptance Date: 4/10/2019
Publication Date: 4/10/2019
Citation: Gao, B., Chen, M., Li, X., Liang, Y., Zhang, D., Wood, A., Oliver, M.J., Zhang, J. 2019. Integrated phylogenomic analyses reveal recurrent ancestral large-scale duplication events in mosses. bioRxiv. Article 603191. https://doi.org/10.1101/603191.
DOI: https://doi.org/10.1101/603191

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 important phylogenetic position for understanding land plant (embryophyte) evolution. The class Bryopsida represents the most diversified lineage and contains more than 95% of the modern mosses, whereas the other classes are by nature species-poor. The phylogeny of mosses remains elusive at present. Recurrent whole genome duplications have shaped the evolution trajectory of angiosperms, but little is known about the genome evolutionary history in mosses. It remains to be answered if there existed a historical genome duplication event associated with the species radiation of class Bryopsida. Here, the high-confidence moss phylogeny was generated covering major moss lineages. Two episodes of ancient genomic duplication events were elucidated by phylogenomic analyses, one in the ancestry of all mosses and another before the separation of the Bryopsida, Polytrichopsida and Tetraphidopsida, with estimated ages of the gene duplications clustered around 329 and 182 million year ago, respectively. The third episode of polyploidy event (termed ') was tightly associated with the early diversification of Bryopsida with an estimated age of ~87 million years. By scrutinizing the phylogenetic timing of duplicated syntelogs in Physcomitrella patens, the WGD1 and WGD2 events were confidently re-recognized as the ' event and the Funarioideae duplication event (~65 mya), respectively. Together, our findings unveiled four episodes of polyploidy events in the evolutionary past of Physcomitrella patens.