Genomic evidence for rediploidization and adaptive evolution following the whole-genome triplication

Xiao Feng, Qipian Chen, Weihong Wu, Jiexin Wang, Guohong Li, Shaohua Xu, Shao Shao, Min Liu, Cairong Zhong, Chung-I Wu, Suhua Shi () and Ziwen He ()
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Xiao Feng: Sun Yat-sen University
Qipian Chen: Sun Yat-sen University
Weihong Wu: Sun Yat-sen University
Jiexin Wang: Sun Yat-sen University
Guohong Li: Sun Yat-sen University
Shaohua Xu: Sun Yat-sen University
Shao Shao: Sun Yat-sen University
Min Liu: Sun Yat-sen University
Cairong Zhong: Hainan Academy of Forestry (Hainan Academy of Mangrove)
Chung-I Wu: Sun Yat-sen University
Suhua Shi: Sun Yat-sen University
Ziwen He: Sun Yat-sen University

Nature Communications, 2024, vol. 15, issue 1, 1-15

Abstract: Abstract Whole-genome duplication (WGD), or polyploidy, events are widespread and significant in the evolutionary history of angiosperms. However, empirical evidence for rediploidization, the major process where polyploids give rise to diploid descendants, is still lacking at the genomic level. Here we present chromosome-scale genomes of the mangrove tree Sonneratia alba and the related inland plant Lagerstroemia speciosa. Their common ancestor has experienced a whole-genome triplication (WGT) approximately 64 million years ago coinciding with a period of dramatic global climate change. Sonneratia, adapting mangrove habitats, experienced extensive chromosome rearrangements post-WGT. We observe the WGT retentions display sequence and expression divergence, suggesting potential neo- and sub-functionalization. Strong selection acting on three-copy retentions indicates adaptive value in response to new environments. To elucidate the role of ploidy changes in genome evolution, we improve a model of the polyploidization–rediploidization process based on genomic evidence, contributing to the understanding of adaptive evolution during climate change.

Date: 2024
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DOI: 10.1038/s41467-024-46080-7

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