Experimental and simulation studies have supported the adaptive potential of polyploidy, especially in the face of dramatic and fluctuating environmental conditions 37, 38, 39. Despite the challenges that have emerged since the WGD, such as stable chromosome segregation, detrimental ecological interactions with diploid progenitors, and minority cytotype exclusion 35, 36, the polyploidy events observed in plants highlight their evolutionary potential. Genomic data have revealed at least 18 independent WGT events in eudicots 11, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, indicating a prevalence higher than previously assumed (Supplementary Fig. One specific type of WGD, known as whole-genome triplication (WGT) or hexaploidy, originated through hybridization between tetraploid and diploid species 17, 18, 19. WGDs have also occurred in various lineages, even recurrently, like Arabidopsis 12, 13, soybean 14, carrot 15, and Utricularia 16. Furthermore, core eudicots, a major clade within angiosperms, experienced a well-known paleo-hexaploidization event 11. Early WGD events in plants can be traced back to the common ancestors of extant seed plants and angiosperms, respectively 10. Presently, angiosperms encompass over 90% of all living plant species, with approximately 350,000 known species, making them the most successful land plants on Earth ( There is growing consensus that whole-genome duplication (WGD) events, also known as polyploidy, have played a widespread and significant role in the evolutionary history of angiosperms 3, 4, 5, 6, 7, 8, 9. The origin and radiation of flowering plants (angiosperms) in the mid-Cretaceous was famously referred to by Charles Darwin as “an abominable mystery” 1, 2. 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. Strong selection acting on three-copy retentions indicates adaptive value in response to new environments. We observe the WGT retentions display sequence and expression divergence, suggesting potential neo- and sub-functionalization.
Sonneratia, adapting mangrove habitats, experienced extensive chromosome rearrangements post-WGT. Their common ancestor has experienced a whole-genome triplication (WGT) approximately 64 million years ago coinciding with a period of dramatic global climate change. Here we present chromosome-scale genomes of the mangrove tree Sonneratia alba and the related inland plant Lagerstroemia speciosa. However, empirical evidence for rediploidization, the major process where polyploids give rise to diploid descendants, is still lacking at the genomic level. Whole-genome duplication (WGD), or polyploidy, events are widespread and significant in the evolutionary history of angiosperms.