Impact of whole-genome duplications on structural variant evolution in Cochlearia

Hämälä, Tuomas; Moore, Christopher; Cowan, Laura; Carlile, Matthew; Gopaulchan, David; K. Brandrud, Marie; Birkeland, Siri; Loose, Matthew; Kolář, Filip; A. Koch, Marcus; Yant, Levi

Abstract

Polyploidy, the result of whole-genome duplication (WGD), is a major driver of eukaryote evolution. Yet WGDs are hugely disruptive mutations, and we still lack a clear understanding of their fitness consequences. Here, we study whether WGDs result in greater diversity of genomic structural variants (SVs) and how they influence evolutionary dynamics in a plant genus, Cochlearia (Brassicaceae). By using long-read sequencing and a graph-based pangenome, we find both negative and positive interactions between WGDs and SVs. Masking of recessive mutations due to WGDs leads to a progressive accumulation of deleterious SVs across four ploidal levels (from diploids to octoploids), likely reducing the adaptive potential of polyploid populations. However, we also discover putative benefits arising from SV accumulation, as more ploidy-specific SVs harbor signals of local adaptation in polyploids than in diploids. Together, our results suggest that SVs play diverse and contrasting roles in the evolutionary trajectories of young polyploids.

Citation

Hämälä, T., Moore, C., Cowan, L., Carlile, M., Gopaulchan, D., K. Brandrud, M., Birkeland, S., Loose, M., Kolář, F., A. Koch, M., & Yant, L. (2024). Impact of whole-genome duplications on structural variant evolution in Cochlearia. Nature Communications, 15, Article 5377. https://doi.org/10.1038/s41467-024-49679-y

• Journal Article Type: Article
• Acceptance Date: Jun 14, 2024
• Online Publication Date: Jun 25, 2024
• Publication Date: Jun 25, 2024
• Deposit Date: Nov 20, 2024
• Publicly Available Date: Nov 21, 2024
• Journal: Nature Communications
• Electronic ISSN: 2041-1723
• Publisher: Nature Publishing Group
• Peer Reviewed: Peer Reviewed
• Volume: 15
• Article Number: 5377
• DOI: https://doi.org/10.1038/s41467-024-49679-y
• Public URL: https://nottingham-repository.worktribe.com/output/36578517
• Publisher URL: https://www.nature.com/articles/s41467-024-49679-y