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Revisiting ancient polyploidy in leptosporangiate ferns.

Authors
  • Chen, Hengchi1, 2
  • Fang, Yuhan3
  • Zwaenepoel, Arthur1, 2
  • Huang, Sanwen3
  • Van de Peer, Yves1, 2, 4, 5
  • Li, Zhen1, 2
  • 1 Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium. , (Belgium)
  • 2 VIB Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium. , (Belgium)
  • 3 Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, 518124, China. , (China)
  • 4 Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, 0028, South Africa. , (South Africa)
  • 5 College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China. , (China)
Type
Published Article
Journal
New Phytologist
Publisher
Wiley (Blackwell Publishing)
Publication Date
Feb 01, 2023
Volume
237
Issue
4
Pages
1405–1417
Identifiers
DOI: 10.1111/nph.18607
PMID: 36349406
Source
Medline
Keywords
Language
English
License
Unknown

Abstract

Ferns, and particularly homosporous ferns, have long been assumed to have experienced recurrent whole-genome duplication (WGD) events because of their substantially large genome sizes, surprisingly high chromosome numbers, and high degrees of polyploidy among many extant members. As the number of sequenced fern genomes is limited, recent studies have employed transcriptome data to find evidence for WGDs in ferns. However, they have reached conflicting results concerning the occurrence of ancient polyploidy, for instance, in the lineage of leptosporangiate ferns. Because identifying WGDs in a phylogenetic context is the foremost step in studying the contribution of ancient polyploidy to evolution, we here revisited earlier identified WGDs in leptosporangiate ferns, mainly the core leptosporangiate ferns, by building KS -age distributions and applying substitution rate corrections and by conducting statistical gene tree-species tree reconciliation analyses. Our integrative analyses not only identified four ancient WGDs in the sampled core leptosporangiate ferns but also identified false positives and false negatives for WGDs that recent studies have reported earlier. In conclusion, we underscore the significance of substitution rate corrections and uncertainties in gene tree-species tree reconciliations in calling WGD events and advance an exemplar workflow to overcome such often-overlooked issues. © 2022 The Authors. New Phytologist © 2022 New Phytologist Foundation.

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