Lineage-specific rediploidization is a mechanism to explain time-lags between genome duplication and evolutionary diversification
| Autor: | Anthony K. Redmond, Manu Kumar Gundappa, Fabian Grammes, Peter W. H. Holland, Fiona M. Robertson, Sigbjørn Lien, Daniel J. Macqueen, Torgeir R. Hvidsten, Simen Rød Sandve, Samuel A.M. Martin |
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| Jazyk: | angličtina |
| Rok vydání: | 2017 |
| Předmět: |
0301 basic medicine
0106 biological sciences Salmonidae/genetics 01 natural sciences Genome Whole genome duplication Divergence Phylogenomics lcsh:QH301-705.5 Phylogeny Genetics Lineage-specific Ohnologue Resolution (LORe) 0303 health sciences Phylogenetic tree Biochemistry and Molecular Biology Adaptation Physiological/genetics Genomics Adaptation Physiological Duplicate genes Salmonidae Synteny/genetics lcsh:QH426-470 Genetic Speciation Species radiation Rediploidization Biology Synteny 010603 evolutionary biology Autotetraploidization Evolution Molecular 03 medical and health sciences Genes Duplicate Phylogenetics Genetic algorithm Functional divergence Animals Genetik 030304 developmental biology Research lcsh:Genetics Genes Duplicate/genetics 030104 developmental biology lcsh:Biology (General) Evolutionary biology Genome/genetics Salmonid fish Adaptation Biokemi och molekylärbiologi |
| Zdroj: | Robertson, F M, Gundappa, M K, Grammes, F, Hvidsten, T R, Redmond, A K, Lien, S, Martin, S A M, Holland, P W H, Sandve, S R & Macqueen, D J 2017, ' Lineage-specific rediploidization is a mechanism to explain time-lags between genome duplication and evolutionary diversification ', Genome Biology, vol. 18, no. 1, 111 . https://doi.org/10.1186/s13059-017-1241-z Genome Biology Genome Biology, Vol 18, Iss 1, Pp 1-14 (2017) |
| DOI: | 10.1186/s13059-017-1241-z |
| Popis: | Background The functional divergence of duplicate genes (ohnologues) retained from whole genome duplication (WGD) is thought to promote evolutionary diversification. However, species radiation and phenotypic diversification are often temporally separated from WGD. Salmonid fish, whose ancestor underwent WGD by autotetraploidization ~95 million years ago, fit such a ‘time-lag’ model of post-WGD radiation, which occurred alongside a major delay in the rediploidization process. Here we propose a model, ‘lineage-specific ohnologue resolution’ (LORe), to address the consequences of delayed rediploidization. Under LORe, speciation precedes rediploidization, allowing independent ohnologue divergence in sister lineages sharing an ancestral WGD event. Results Using cross-species sequence capture, phylogenomics and genome-wide analyses of ohnologue expression divergence, we demonstrate the major impact of LORe on salmonid evolution. One-quarter of each salmonid genome, harbouring at least 4550 ohnologues, has evolved under LORe, with rediploidization and functional divergence occurring on multiple independent occasions >50 million years post-WGD. We demonstrate the existence and regulatory divergence of many LORe ohnologues with functions in lineage-specific physiological adaptations that potentially facilitated salmonid species radiation. We show that LORe ohnologues are enriched for different functions than ‘older’ ohnologues that began diverging in the salmonid ancestor. Conclusions LORe has unappreciated significance as a nested component of post-WGD divergence that impacts the functional properties of genes, whilst providing ohnologues available solely for lineage-specific adaptation. Under LORe, which is predicted following many WGD events, the functional outcomes of WGD need not appear ‘explosively’, but can arise gradually over tens of millions of years, promoting lineage-specific diversification regimes under prevailing ecological pressures. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1241-z) contains supplementary material, which is available to authorized users. |
| Databáze: | OpenAIRE |
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