ArticleGenome biology2021
Comparative regulomics supports pervasive selection on gene dosage following whole genome duplication.
Article in Genome biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
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Who cites it
48 citing papers in PubMed, 83 citations in OpenAlex.
- Developmental contexts of gene-regulatory evolution following whole genome duplication in salmonids.Nature ecology & evolution · 2026Article
- Domestication-Driven Expansion and Structural Convergence of the Porcine Antiviral Interferon Repertoire.Biomolecules · 2026Article
- Article
- Evolutionary causes and consequences of gene duplication.Nature reviews. Genetics · 2026Review
- Distinct evolutionary trajectories of gene duplication modes in 40 diploid cotton genomes.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Evolutionary tuning of a biosynthetic gene cluster drives furanocoumarin accumulation and diversification.Nature communications · 2026Article
- Article
- Splicing retention and enhancer divergence govern the evolutionary fate of ohnologues following whole-genome duplication in rainbow trout.Scientific reports · 2026Article
- Degrees of convergent evolution in rodent adaptations to arid environments.Genome research · 2026Article
- Restoring cytonuclear harmony: Distinct strategies in Arabidopsis auto- and allopolyploids.The Plant journal : for cell and molecular biology · 2025Article
- Seasonal and comparative evidence of adaptive gene expression in mammalian brain size plasticity.eLife · 2025Article
- Cell Type Resolved Expression of Duplicate Genes Retained From Whole Genome Duplication in Atlantic salmon.Genome biology and evolution · 2025Article
- Parallel Selection in Domesticated Atlantic Salmon from Divergent Founders Including on Whole-Genome Duplication-derived Homeologous Regions.Genome biology and evolution · 2025Article
- The role of transposon activity in shapingGenome research · 2025Article
- Evolutionary screening of precision oncology biomarkers and its applications in prognostic model construction.iScience · 2024Article
- Draft genome sequence and tissue expression panel of Pacific saury (Cololabis saira).DNA research : an international journal for rapid publication of reports on genes and genomes · 2024Article
- Gene Function is a Driver of Activin Signaling Pathway Evolution Following Whole-Genome Duplication in Rainbow Trout (Oncorhynchus mykiss).Genome biology and evolution · 2024Article
- Identification and effective regulation ofZoological research · 2024Article
- Article
- Expectations of duplicate gene retention under the gene duplicability hypothesis.BMC ecology and evolution · 2023Article
Corrections and comments
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Authors and funding
13 authors at 4 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundWhole genome duplication (WGD) events have played a major role in eukaryotic genome evolution, but the consequence of these extreme events in adaptive genome evolution is still not well understood. To address this knowledge gap, we used a comparative phylogenetic model and transcriptomic data from seven species to infer selection on gene expression in duplicated genes (ohnologs) following the salmonid WGD 80-100 million years ago.
resultsWe find rare cases of tissue-specific expression evolution but pervasive expression evolution affecting many tissues, reflecting strong selection on maintenance of genome stability following genome doubling. Ohnolog expression levels have evolved mostly asymmetrically, by diverting one ohnolog copy down a path towards lower expression and possible pseudogenization. Loss of expression in one ohnolog is significantly associated with transposable element insertions in promoters and likely driven by selection on gene dosage including selection on stoichiometric balance. We also find symmetric expression shifts, and these are associated with genes under strong evolutionary constraints such as ribosome subunit genes. This possibly reflects selection operating to achieve a gene dose reduction while avoiding accumulation of "toxic mutations". Mechanistically, ohnolog regulatory divergence is dictated by the number of bound transcription factors in promoters, with transposable elements being one likely source of novel binding sites driving tissue-specific gains in expression.
conclusionsOur results imply pervasive adaptive expression evolution following WGD to overcome the immediate challenges posed by genome doubling and to exploit the long-term genetic opportunities for novel phenotype evolution.
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