@article{7837ecf697ac449c9f1da4647401308e,
title = "Ancestral gene duplications in mosses characterized by integrated phylogenomic analyses",
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.",
keywords = "gene duplication, moss, phylogenomic, Physcomitrella, polyploidy, WGD",
author = "Bei Gao and Chen, {Mo Xian} and Li, {Xiao Shuang} and Liang, {Yu Qing} and Zhang, {Dao Yuan} and Wood, {Andrew J.} and Oliver, {Melvin J.} and Jianhua Zhang",
note = "Funding Information: This study was supported by the NSFC‐Xinjiang Key Project (Grant No. U1703233 to DZ) and National Science Foundation (Collaborative Research: Dimensions: Grant No. 1638972 to MJO). The School of Life Sciences of The Chinese University of Hong Kong provided the computational resources for this project. BG conceived the study, performed the bioinformatic analyses, and wrote the manuscript. MC, DZ, XL, YL, and AJW contributed to the result discussion. MJO and JZ contributed to the data interpretation and critically revised and improved the manuscript. All authors read and approved the manuscript. Funding Information: This study was supported by the NSFC-Xinjiang Key Project (Grant No. U1703233 to DZ) and National Science Foundation (Collaborative Research: Dimensions: Grant No. 1638972 to MJO). The School of Life Sciences of The Chinese University of Hong Kong provided the computational resources for this project. BG conceived the study, performed the bioinformatic analyses, and wrote the manuscript. MC, DZ, XL, YL, and AJW contributed to the result discussion. MJO and JZ contributed to the data interpretation and critically revised and improved the manuscript. All authors read and approved the manuscript. Publisher Copyright: {\textcopyright} 2020 The Authors. Journal of Systematics and Evolution published by John Wiley & Sons Australia, Ltd on behalf of Institute of Botany, Chinese Academy of Sciences",
year = "2022",
month = jan,
doi = "10.1111/jse.12683",
language = "English",
volume = "60",
pages = "144--159",
journal = "Journal of Systematics and Evolution",
issn = "1674-4918",
publisher = "Wiley-Blackwell",
number = "1",
}