Genome-Wide Reconstruction of Rediploidization Following Autopolyploidization across One Hundred Million Years of Salmonid Evolution
| Autor: | Simen Rød Sandve, Samuel A.M. Martin, Lars Grønvold, Juergen Geist, David G. Hazlerigg, Sigbjørn Lien, Thu-Hien To, Manu Kumar Gundappa, Daniel J. Macqueen |
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| Jazyk: | angličtina |
| Rok vydání: | 2021 |
| Předmět: |
Biology
genome evolution AcademicSubjects/SCI01180 Genome Evolution Molecular Hucho hucho Gene Duplication Genetics Animals Clade Molecular clock Molecular Biology Gene Ecology Evolution Behavior and Systematics Discoveries ohnolog Phylogeny Whole genome sequencing Phylogenetic tree AcademicSubjects/SCI01130 phylogenomics biology.organism_classification rediploidization Evolutionary biology whole-genome duplication Ploidy Salmonidae |
| Zdroj: | Molecular Biology and Evolution Gundappa, M K, To, T H, Grønvold, L, Martin, S A M, Lien, S, Geist, J, Hazlerigg, D, Sandve, S R & Macqueen, D 2021, ' Genome-wide reconstruction of rediploidization following autopolyploidization across one hundred million years of salmonid evolution ', Molecular Biology and Evolution . https://doi.org/10.1093/molbev/msab310 Molecular Biology and Evolution (MBE) |
| ISSN: | 1537-1719 0737-4038 |
| DOI: | 10.1093/molbev/msab310 |
| Popis: | The long-term evolutionary impacts of whole genome duplication (WGD) are strongly influenced by the ensuing rediploidization process. Following autopolyploidization, rediploidization involves a transition from tetraploid to diploid meiotic pairing, allowing duplicated genes (ohnologues) to diverge genetically and functionally. Our understanding of autopolyploid rediploidization has been informed by a WGD event ancestral to salmonid fishes, where large genomic regions are characterized by temporally delayed rediploidization, allowing lineage-specific ohnologue sequence divergence in the major salmonid clades. Here, we investigate the long-term outcomes of autopolyploid rediploidization at genome-wide resolution, exploiting a recent ‘explosion’ of salmonid genome assemblies, including a new genome sequence for the huchen (Hucho hucho). We developed a genome alignment approach to capture duplicated regions across multiple species, allowing us to create 121,864 phylogenetic trees describing ohnologue divergence across salmonid evolution. Using molecular clock analysis, we show that 61% of the ancestral salmonid genome experienced an initial ‘wave’ of rediploidization in the late Cretaceous (85-106 Mya). This was followed by a period of relative genomic stasis lasting 17-39 My, where much of the genome remained in a tetraploid state. A second rediploidization wave began in the early Eocene and proceeded alongside species diversification, generating predictable patterns of lineage-specific ohnologue divergence, scaling in complexity with the number of speciation events. Finally, using gene set enrichment, gene expression, and codon-based selection analyses, we provide insights into potential functional outcomes of delayed rediploidization. Overall, this study enhances our understanding of delayed autopolyploid rediploidization and has broad implications for future studies of WGD events. |
| Databáze: | OpenAIRE |
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