ArticleGenome biology and evolution2018
The Grayling Genome Reveals Selection on Gene Expression Regulation after Whole-Genome Duplication.
Article in Genome biology and evolution, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Developmental contexts of gene-regulatory evolution following whole genome duplication in salmonids.Nature ecology & evolution · 2026Article
- Evolutionary diversification and immunoprofiling of cathepsin L toolkit in common carp.Frontiers in cellular and infection microbiology · 2026Article
- The role of transposon activity in shapingGenome research · 2025Article
- A multi-tissue de novo transcriptome assembly and relative gene expression of the vulnerable freshwater salmonid Thymallus ligericus.Genetica · 2024Article
- Whole-genome Sequencing Reveals Autooctoploidy in Chinese Sturgeon and Its Evolutionary Trajectories.Genomics, proteomics & bioinformatics · 2024Article
- Independent rediploidization masks shared whole genome duplication in the sturgeon-paddlefish ancestor.Nature communications · 2023Article
- Environment and genotype predict the genomic nature of domestication of salmonids as revealed by gene expression.Proceedings. Biological sciences · 2022Review
- Review
- Salinity-induced transcriptome profiles in marine and freshwater threespine stickleback after an abrupt 6-hour exposure.Ecology and evolution · 2022Article
- Genome-Wide Reconstruction of Rediploidization Following Autopolyploidization across One Hundred Million Years of Salmonid Evolution.Molecular biology and evolution · 2022Article
- Diverse Molecular Mechanisms Contribute to Differential Expression of Human Duplicated Genes.Molecular biology and evolution · 2021Article
- Genetic Drift Dominates Genome-Wide Regulatory Evolution Following an Ancient Whole-Genome Duplication in Atlantic Salmon.Genome biology and evolution · 2021Article
- Comparative regulomics supports pervasive selection on gene dosage following whole genome duplication.Genome biology · 2021Article
- Rhythmic Clock Gene Expression in Atlantic Salmon Parr Brain.Frontiers in physiology · 2021Article
- Comparative Genomic Analyses and a Novel Linkage Map for Cisco (G3 (Bethesda, Md.) · 2020Article
- Evaluating the effect of reference genome divergence on the analysis of empirical RADseq datasets.Ecology and evolution · 2020Article
- A de novo chromosome-level genome assembly of Coregonus sp. "Balchen": One representative of the Swiss Alpine whitefish radiation.Molecular ecology resources · 2020Article
- The Genome of the Great Gerbil Reveals Species-Specific Duplication of an MHCII Gene.Genome biology and evolution · 2020Article
- Article
- Parallel selection on ecologically relevant gene functions in the transcriptomes of highly diversifying salmonids.BMC genomics · 2019Article
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11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Whole-genome duplication (WGD) has been a major evolutionary driver of increased genomic complexity in vertebrates. One such event occurred in the salmonid family ∼80 Ma (Ss4R) giving rise to a plethora of structural and regulatory duplicate-driven divergence, making salmonids an exemplary system to investigate the evolutionary consequences of WGD. Here, we present a draft genome assembly of European grayling (Thymallus thymallus) and use this in a comparative framework to study evolution of gene regulation following WGD. Among the Ss4R duplicates identified in European grayling and Atlantic salmon (Salmo salar), one-third reflect nonneutral tissue expression evolution, with strong purifying selection, maintained over ∼50 Myr. Of these, the majority reflect conserved tissue regulation under strong selective constraints related to brain and neural-related functions, as well as higher-order protein-protein interactions. A small subset of the duplicates have evolved tissue regulatory expression divergence in a common ancestor, which have been subsequently conserved in both lineages, suggestive of adaptive divergence following WGD. These candidates for adaptive tissue expression divergence have elevated rates of protein coding- and promoter-sequence evolution and are enriched for immune- and lipid metabolism ontology terms. Lastly, lineage-specific duplicate divergence points toward underlying differences in adaptive pressures on expression regulation in the nonanadromous grayling versus the anadromous Atlantic salmon. Our findings enhance our understanding of the role of WGD in genome evolution and highlight cases of regulatory divergence of Ss4R duplicates, possibly related to a niche shift in early salmonid evolution.
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