Kinetochore and ionomic adaptation to whole-genome duplication in Cochlearia shows evolutionary convergence in three autopolyploids

A longstanding question in plant evolution is why ferns have many more chromosomes than angiosperms. The leading hypothesis proposes that ferns have ancient polyploidy without chromosome loss or gene deletion to explain the high chromosome numbers of ferns. Here, we test this hypothesis by estimating ancient polyploidy frequency, chromosome evolution, protein evolution in meiosis genes, and patterns of gene retention in ferns. We found similar rates of paleopolyploidy in ferns and angiosperms from independent phylogenomic and chromosome number evolution analyses, but lower rates of chromosome loss in ferns. We found elevated evolutionary rates in meiosis genes in angiosperms, but not in ferns. Finally, we found some evidence of parallel and biased gene retention in ferns, but this was comparatively weak to patterns in angiosperms. This work provides genomic evidence supporting a decades-old hypothesis on fern genome evolution and provides a foundation for future work on plant genome structure.

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Polyploids broadly generate novel haplotypes from trans-specific variation in Arabidopsis arenosa and Arabidopsis lyrata

Bohutínská,

Petříková,

Booker

et al. 2024

PLoS Genet

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Polyploidy, the result of whole genome duplication (WGD), is widespread across the tree of life and is often associated with speciation and adaptability. It is thought that adaptation in autopolyploids (within-species polyploids) may be facilitated by increased access to genetic variation. This variation may be sourced from gene flow with sister diploids and new access to other tetraploid lineages, as well as from increased mutational targets provided by doubled DNA content. Here, we deconstruct in detail the origins of haplotypes displaying the strongest selection signals in established, successful autopolyploids, Arabidopsis lyrata and Arabidopsis arenosa. We see strong signatures of selection in 17 genes implied in meiosis, cell cycle, and transcription across all four autotetraploid lineages present in our expanded sampling of 983 sequenced genomes. Most prominent in our results is the finding that the tetraploid-characteristic haplotypes with the most robust signals of selection were completely absent in all diploid sisters. In contrast, the fine-scaled variant ‘mosaics’ in the tetraploids originated from highly diverse evolutionary sources. These include widespread novel reassortments of trans-specific polymorphism from diploids, new mutations, and tetraploid-specific inter-species hybridization–a pattern that is in line with the broad-scale acquisition and reshuffling of potentially adaptive variation in tetraploids.

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Kinetochore and ionomic adaptation to whole-genome duplication in Cochlearia shows evolutionary convergence in three autopolyploids

Cited by 3 publications

References 135 publications

Does nascent polyploidy employ common mechanisms to stabilize and establish?

Does nascent polyploidy employ common mechanisms to stabilize and establish?

Ancient polyploidy and low rate of chromosome loss explain the high chromosome numbers of homosporous ferns

Polyploids broadly generate novel haplotypes from trans-specific variation in Arabidopsis arenosa and Arabidopsis lyrata

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