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Article
Open AccessIndependent rediploidization masks shared whole genome duplication in the sturgeon-paddlefish ancestor
Whole genome duplication (WGD) is a dramatic evolutionary event generating many new genes and which may play a role in survival through mass extinctions. Paddlefish and sturgeon are sister lineages that both s...
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Article
Open AccessComparative regulomics supports pervasive selection on gene dosage following whole genome duplication
Whole 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 ...
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Open AccessFrom FAANG to fork: application of highly annotated genomes to improve farmed animal production
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Open AccessThe structural variation landscape in 492 Atlantic salmon genomes
Structural variants (SVs) are a major source of genetic and phenotypic variation, but remain challenging to accurately type and are hence poorly characterized in most species. We present an approach for reliab...
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Article
Harnessing genomics to fast-track genetic improvement in aquaculture
Aquaculture is the fastest-growing farmed food sector and will soon become the primary source of fish and shellfish for human diets. In contrast to crop and livestock production, aquaculture production is deri...
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Article
Open AccessEffect of growth rate on transcriptomic responses to immune stimulation in wild-type, domesticated, and GH-transgenic coho salmon
Transcriptomic responses to immune stimulation were investigated in coho salmon (Oncorhynchus kisutch) with distinct growth phenotypes. Wild-type fish were contrasted to strains with accelerated growth arising ei...
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Article
Open AccessSalMotifDB: a tool for analyzing putative transcription factor binding sites in salmonid genomes
Recently developed genome resources in Salmonid fish provides tools for studying the genomics underlying a wide range of properties including life history trait variation in the wild, economically important tr...
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Article
Open AccessThe AMPK system of salmonid fishes was expanded through genome duplication and is regulated by growth and immune status in muscle
5′adenosine monophosphate-activated protein kinase (AMPK) is a master regulator of energy homeostasis in eukaryotes. This study identified expansions in the AMPK-α, -β and -γ families of salmonid fishes due to...
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Article
Open AccessPhylotranscriptomics suggests the jawed vertebrate ancestor could generate diverse helper and regulatory T cell subsets
The cartilaginous fishes diverged from other jawed vertebrates ~ 450 million years ago (mya). Despite this key evolutionary position, the only high-quality cartilaginous fish genome available is for the elepha...
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Open AccessNanopore sequencing for rapid diagnostics of salmonid RNA viruses
Analysis of pathogen genome variation is essential for informing disease management and control measures in farmed animals. For farmed fish, the standard approach is to use PCR and Sanger sequencing to study p...
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Article
Open AccessHigh-throughput proteomic profiling of the fish liver following bacterial infection
High-throughput proteomics was used to determine the role of the fish liver in defense responses to bacterial infection. This was done using a rainbow trout (Oncorhynchus mykiss) model following infection with Ae...
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Open AccessFunctional Annotation of All Salmonid Genomes (FAASG): an international initiative supporting future salmonid research, conservation and aquaculture
We describe an emerging initiative - the ‘Functional Annotation of All Salmonid Genomes’ (FAASG), which will leverage the extensive trait diversity that has evolved since a whole genome duplication event in th...
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Article
Open AccessLineage-specific rediploidization is a mechanism to explain time-lags between genome duplication and evolutionary diversification
The functional divergence of duplicate genes (ohnologues) retained from whole genome duplication (WGD) is thought to promote evolutionary diversification. However, species radiation and phenotypic diversificat...
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Article
Open AccessThe complete salmonid IGF-IR gene repertoire and its transcriptional response to disease
The insulin-like growth factor (IGF) receptor (IGF-IR) is necessary for IGF signalling and has essential roles in cellular growth. In teleost fish, two distinct IGF-IR duplicates are conserved called IGF-IRa a...
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Article
Open AccessCorrection: Corrigendum: Disparate developmental patterns of immune responses to bacterial and viral infections in fish
During early stages of development vertebrates rely on an immature immune system to fight pathogens, but in non mammalian species few studies have taken an in-depth analysis of the transition from reliance on ...
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Article
Open AccessDisparate developmental patterns of immune responses to bacterial and viral infections in fish
During early stages of development vertebrates rely on an immature immune system to fight pathogens, but in non mammalian species few studies have taken an in-depth analysis of the transition from reliance on ...
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Article
Open AccessEvolution of the multifaceted eukaryotic akiringene family
Akirins are nuclear proteins that form part of an innate immune response pathway conserved in Drosophila and mice. This studies aim was to characterise the evolution of akirin gene structure and protein function ...
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Article
Evolution of follistatin in teleosts revealed through phylogenetic, genomic and expression analyses
Follistatin (Fst) inhibits transforming growth factor-β (TGF-B) proteins and is a known regulator of amniote myogenesis. Here, we used phylogenetic, genomic and experimental approaches to study its evolution i...
