Biology subjects

Macqueen, D.

Publications and source records attributed to Macqueen, D..

12 recordsLinked to original sources

bioRxiv2026

Transcriptomic view of key events during early embryogenesis in the duplicated Atlantic salmon genome

Early embryogenesis is governed by tightly regulated transcriptional programs, including the maternal-to-zygotic transition (MZT), zygotic genome activation (ZGA), and maintenance of pluripotency. While these processes are well studied in model vertebrates, they remain poorly understood in salmonid fishes, whose genomes are shaped by a relatively recent whole genome duplication (WGD) event. Here, we present a temporally resolved transcriptomic analysis of Atlantic salmon (Salmo salar) embryogenesis using bulk RNA-seq across key stages spanning early embryogenesis. Dimensionality reduction and unsupervised clustering of gene expression revealed stage-specific transitions encompassing maternal RNA clearance, cell cycle regulation, and the onset of metabolic activity. We demonstrate that ZGA occurs early and in multiple phases, beginning soon after fertilization, accompanied by chromatin remodelling and the activation of epigenetic regulators. Duplicated gene pairs retained from the salmonid WGD frequently displayed asynchronous expression, indicative of functional divergence and the evolution of additional regulatory complexity of embryonic development. To gain insights into pluripotency, we integrated analyses of gene expression, transcription factor motifs, and chromatin accessibility, to reveal conserved regulators including genes encoding Pou5f3, Nanog, and Sox19b, alongside divergent functions of Klf family members. Our cross-stage profiling allowed us to define a novel panel of stably-expressed reference genes for normalization during quantitative PCR analyses, which were used to validate pluripotency- and differentiation-associated dynamics inferred by RNA-seq. Together, our findings delineate the transcriptional architecture of early embryogenesis in Atlantic salmon, revealing both conserved and lineage-specific features of pluripotency regulation, and providing a foundational resource for future functional genomics and stem cell applications in salmonids.

developmental biology↗

bioRxiv2026

Spermidine enhances metabolic flexibility and attenuates inflammation associated with ageing in farmed Atlantic salmon

Metabolic ageing and associated changes in lipid mobilisation have been most heavily studied in humans and model taxa, yet remain poorly understood in farmed animals, with potentially important uncharacterised implications for health and welfare outcomes in food production systems. Here, we study both processes in domesticated Atlantic salmon (Salmo salar), the worlds most commercially valuable farmed fish, comparing three stages of aquaculture production. Our sampling captures a key life-cycle change where juvenile fish transition from freshwater into seawater (smoltification), followed by the ongoing ageing process during a final period of growth in seawater. Integrating lipidomics and proteomics of visceral adipose and skeletal muscle tissue, we firstly identified a metabolic-ageing profile akin to that observed in humans, which was distinct from lipid-associated remodelling associated with earlier smoltification. This was marked by impaired triglyceride storage, dysfunctional autophagy-lysosomal pathways, inflammation, fibrosis and reduced pathogen clearance pathways in visceral adipose tissue. In skeletal muscle, ageing was accompanied by reduced metabolic flexibility together with triglyceride and fatty acid accumulation, depletion of phospholipids, and a reduction in free fatty acids required for ATP production. We go on to provide experimental in vivo evidence that dietary spermidine supplementation suppresses adipose inflammation and reverses age-associated metabolic flexibility by re-establishing the buffering role of adipose tissue and enhancing fatty acid metabolism in skeletal muscle. Importantly, spermidine appears to reprogram lipid flux to counter metabolic ageing. As farmed Atlantic salmon exhibit key features of metabolic ageing observed in humans that appear linked to its recent domestication history, this species offers a novel model for ageing related studies of vertebrate metabolism.

molecular biology↗

bioRxiv2025

Salmonids reveal principles of regulatory evolution following autotetraploidization

Early vertebrate autotetraploidization events may have enabled major innovations by expanding the genetic material for functional diversification, yet their ancient timing obscures how genome doubling reshaped gene regulatory evolution. Salmonids provide a unique window to these mechanisms, because they experienced a comparatively recent autotetraploidization and are earlier in the rediploidization process - which creates new genes and regulatory elements during evolution. Here, using large-scale multiomics spanning embryonic and adult tissues in two salmonids, we investigate gene regulatory evolution following genome doubling and rediploidization, which we show is governed by developmental and tissue-specific context, with a period of maximal constraint at advanced stages of embryogenesis. This work advances understanding of vertebrate genome evolution, while providing an open resource supporting salmonid aquaculture and conservation.

evolutionary biology↗

bioRxiv2024

Epigenomics of embryogenesis in turbot (Scophthalmus maximus)

Embryogenesis is the crucial first step of ontogeny, where an organism with a complex body plan arises from a single undifferentiated totipotent cell. This process is orchestrated by dynamic changes in transcriptional regulation, influenced by chromatin accessibility and nucleotide and histone modifications constituting epigenetic signals enabling access to transcription factors. The epigenomic regulation of embryogenesis has been studied in model fishes, but little attention has been paid to farmed fish - where traits of importance to aquaculture rely on early developmental processes. This study, framed within the AQUA-FAANG consortium, reports a comprehensive regulatory atlas of embryogenesis for turbot (Scophthalmus maximus), a farmed flatfish representing order Pleuronectiformes. 14,560 genes were expressed in the embryonic transcriptome with > 90% showing differential expression across consecutive stages. By integrating multi-histone ChIP-Seq marks with ATAC-Seq, we built a genome-wide chromatin state model, defining promoter and enhancer activity across stages. Transcription factor binding motif (TFBM) analysis of differentially active promoters and enhancers revealed dynamism in regulated gene functions, with more than half the TFBM enriched in a single developmental transition. Significant shifts in chromatin accessibility occurred across stages, most notably during the transition from shield to early segmentation, suggesting a profound chromatin reorganization underpins somitogenesis and early organ development. Most changes in chromatin accessibility across stages did not involve promoter regions of differentially expressed genes, suggesting a trend of promoter accessibility preceding gene transcriptional activity. Comparative analyses with zebrafish revealed a global transcriptomic correlation of single copy orthologs at matched stages of embryogenesis across species. While conserved expression dynamics were revealed for many orthologous Hox genes, notable cross-species differences were identified from before zygotic genome activation leading up to hatching. This multi-omics investigation provides a novel atlas of non-coding regulatory elements controlling turbot development, with key applications for flatfish biology and enhancing sustainable aquaculture.

genomics↗

bioRxiv2024

Rapamycin induced autophagy enhances lipid breakdown and ameliorates lipotoxicity in Atlantic salmon cells.

Autophagy is a highly conserved cellular recycling process essential for homeostasis in all eukaryotic cells. Lipid accumulation and its regulation by autophagy are key areas of research for understanding metabolic disorders in human and model mammals. However, the role of autophagy in lipid regulation remains poorly characterised in non-model fish species of importance to food production, which could be important for managing health and welfare in aquaculture. Addressing this knowledge gap, we investigate the role of autophagy in lipid regulation using a macrophage-like cell line (SHK-1) from Atlantic salmon (Salmo salar L.), the worlds most commercially valuable farmed finfish. Multiple lines of experimental evidence reveal that the autophagic pathway responsible for lipid droplet breakdown is conserved in Atlantic salmon cells. We employed global lipidomics and proteomics analyses on SHK-1 cells subjected to lipid overload, followed by treatment with rapamycin to induce autophagy. This revealed that activating autophagy via rapamycin enhances storage of unsaturated triacylglycerols and suppresses key lipogenic proteins, including fatty acid elongase 6 and acid sphingomyelinase. Moreover, fatty acid elongase 6 was identified as cargo for autophagosomes, suggesting a critical role for autophagy in lipid metabolism in fish. Together, this study establishes a novel model of lipotoxicity and advances understanding of lipid autophagy in fish cells, with significant implications for addressing fish health issues in aquaculture.

cell biology↗

bioRxiv2024

Glycophagy is an ancient bilaterian pathway supporting metabolic adaptation through STBD1 structural evolution

The selective autophagy of glycogen (glycophagy) has recently emerged as being crucial to glucose homeostasis in vertebrates, yet its origins remain elusive. Here, we provide evidence that starch-binding domain-containing protein 1 (STBD1), the key glycophagy receptor in vertebrates, is functionally conserved in the Pacific oyster, revealing its conserved position within ancient autophagy networks. We show that STBD1 in oysters - as seen in other invertebrate groups - possesses an N-terminal carbohydrate binding module family 20 (CBM20) domain, representing the ancestral state for this protein, while a shuffling of CBM20 to the C- terminus occurred during early chordate evolution. Structural modelling and functional studies reveal that the N-terminal CBM20 organization of STBD1 enhances glycogen binding. Functional experiments demonstrate that an STBD1-glycogen complex, anchored by GABARAPL2, facilitates an increased glycogen flux into autophagosomes for lysosomal degradation. We conclude that glycophagy is deeply conserved in bilaterians and that STBD1 structural evolution underlies potentially adaptive variation in metabolic strategies across distinct animal clades.

evolutionary biology↗

bioRxiv2024

Haplotype-resolved genomes provide insights into the origin and function of genome diversity in bivalves

Bivalves are famed for exhibiting vast genetic diversity of poorly understood origins and functional significance. Within bivalves, oysters are an ancient group showing remarkable genetic and phenotypic variability alongside extensive adaptability, serving as an ideal system to understand the origins and functional significance of genomic diversity. Here, we reveal the divergent genomic landscape of Crassostrea oysters, characterized by a history of genome size reduction associated with transposable elements (TEs). By constructing a haplotype-resolved genome for Kumamoto oyster C. sikamea, we demonstrate the widespread presence of haplotype divergent sequences (HDS); genomic regions present in just one haplotype. Combined with population resequencing, we define the role of genomic divergence driven by TEs in shaping oyster genetic diversity. Comparisons of haplotype-resolved genomes across four bivalve orders reveal that while extensive HDS is common, its origins may differ markedly. We show that HDS are a hotspot of genetic innovation, harboring rapidly evolving genes of various evolutionary ages, while also strongly influencing gene expression phenotypes. A widespread lack of allele-specific expression shared among oyster individuals indicates that haplotype polymorphism provides a key source of expression variation, promoting phenotypic plasticity and adaptation. These findings advance understanding on the origins of genomic diversity and its role in adaptive evolution.

genomics↗

bioRxiv2023

High performance imputation of structural and single nucleotide variants in Atlantic salmon using low-coverage whole genome sequencing

BackgroundWhole genome sequencing (WGS), despite its advantages, is yet to replace standard? methods for genotyping single nucleotide variants (SNVs) such as SNP arrays and targeted genotyping assays. Structural variants (SVs) have larger effects on traits than SNVs, but are more challenging to accurately genotype. Using low-coverage WGS with genotype imputation offers a cost-effective strategy to achieve genome-wide variant coverage, but is yet to be tested for SVs. MethodsHere, we investigate combined SNV and SV imputation with low-coverage WGS data in Atlantic salmon (Salmo salar). As the reference panel, we used genotypes for high-confidence SVs and SNVs for n=365 wild individuals sampled from diverse populations. We also generated 15x WGS data (n=20 samples) for a commercial population external to the reference panel, and called SVs and SNVs with gold-standard approaches. An imputation method selected for its established performance using low-coverage sequencing data (GLIMPSE) was tested at WGS depths of 1x, 2x, 3x, and 4x for samples within and external to the reference panel. ResultsSNVs were imputed with high accuracy and recall across all WGS depths, including for samples out-with the reference panel. For SVs, we compared imputation based purely on linkage disequilibrium (LD) with SNVs, to that supplemented with SV genotype likelihoods (GLs) from low-coverage WGS. Including SV GLs increased imputation accuracy, but as a trade-off with recall, requiring 3-4x depth for best performance. Combining strategies allowed us to capture 84% of the reference panel deletions with 87% accuracy at 1x depth. We also show that SV length affects imputation performance, with provision of SV GLs greatly enhancing accuracy for the longest SVs in the dataset. ConclusionsThis study highlights the promise of reference panel imputation using low-coverage WGS, including novel opportunities to enhance the resolution of genome-wide association studies by capturing SVs.

genetics↗

bioRxiv2022

Genome-wide association and genomic prediction of growth traits in the European flat oyster (Ostrea edulis)

The European flat oyster (Ostrea edulis) is a bivalve mollusc that was once widely distributed in Europe and represented an important food resource for humans for centuries. Populations of O. edulis experienced a severe decline across their biogeographic range mainly due to anthropogenic activities and disease outbreaks. To restore the economic and ecological benefits of European flat oyster populations, extensive protection and restoration efforts are in place within Europe. In line with the increasing interest in supporting restoration and oyster farming through the breeding of stocks with enhanced performance, the present study aimed to evaluate the potential of genomic selection for improving growth traits in a European flat oyster population obtained from successive mass-spawning events. Four growth-related traits were evaluated: total weight (TW), shell height (SH), shell width (SW) and shell length (SL). The heritability of the growth traits was moderate-low, with estimates of 0.45, 0.37, 0.22, and 0.32 for TW, SH, SW and SL, respectively. A genome-wide association analysis revealed a largely polygenic genetic architecture for the four growth traits, with two distinct QTLs detected on chromosome 4. To investigate whether genomic selection can be implemented in flat oyster breeding at a reduced cost, the utility of low-density SNP panels (down to 100 SNPs) was assessed. Genomic prediction accuracies using the full density panel were high (>0.83 for all traits). The evaluation of the effect of reducing the number of markers used to predict genomic breeding values revealed that similar selection accuracies could be achieved for all traits with 2K SNPs as for a full panel containing 4,577 SNPs. Only slight reductions in accuracies were observed at the lowest SNP density tested (i.e. 100 SNPs), likely due to a high relatedness between individuals being included in the training and validation sets during cross-validation. Overall, our results suggest that the genetic improvement of growth traits in oysters is feasible. Nevertheless, and although low-density SNP panels appear as a promising strategy for applying GS at a reduced cost, additional populations with different degrees of genetic relationship should be assessed to derive estimates of prediction accuracies to be expected in practical breeding programmes.

genetics↗

bioRxiv2020

Comparative regulomics reveals 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 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. We 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. Although ohnolog expression levels have evolved mostly asymmetrically, by diverting one ohnolog copy down a path towards pseudogenization, strong evolutionary constraints have frequently also favoured symmetric shifts in gene dosage of both copies, likely to achieve 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 source of novel binding sites driving tissue-specific gains in expression. Our 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.

evolutionary biology↗

bioRxiv2017

Growth hormone transgenesis disrupts immune function in muscle of coho salmon (Oncorhynchus kisutch) impacting cross-talk with growth systems

The suppression of growth during infection should facilitate resource allocation towards effective immune function. Work supporting this hypothesis has been recently reported in teleosts, demonstrating immune-responsive regulation of the insulin-like growth factor (IGF) system - a key endocrine growth pathway that acts downstream of growth hormone (GH). Skeletal muscle is the main target for growth and energetic storage in fish, yet little is known about how growth is regulated in this tissue during an immune response. We addressed this knowledge gap by characterizing muscle immune responses in size-matched coho salmon (Oncorhynchus kisutch) achieving different growth rates. We compared a wild-type strain with two GH transgenic groups achieving either maximal or highly-suppressed growth - an experimental design that separates GHs direct effects from its influence on growth rate. Fish were sampled 30h post-injection with PBS (control) or mimics of bacterial (peptidoglycan) or viral (Poly:IC) infection. We quantified the mRNA level expression of genes from the GH, GH receptor (GHR), IGF hormone, IGF1 receptor (IGF-1R) and IGF binding protein (IGFBP) families, along with marker genes for muscle growth and host defence genes involved in inflammatory or antiviral responses. We provide strong evidence for dampened immunity in the GH transgenics compared to wild-type animals. Strikingly, the muscle of GH transgenics achieving rapid growth showed no detectable antiviral response, coupled with evidence of a constitutive inflammatory state. GH and IGF system gene expression was also strongly altered by GH transgenesis and fast growth, both for baseline expression levels and responses to immune stimulation. Overall, our findings demonstrate that GH transgenesis disrupts normal immune function and growth-immune cross-talk in muscle, with implications for the health and welfare of farmed salmon.

physiology↗

bioRxiv2017

Lineage-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 diversification is often highly temporally-detached from WGD. Salmonid fish, whose ancestor experienced WGD by autotetraploidization ~95 Ma (i.e. Ss4R), 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 called Lineage-specific Ohnologue Resolution (LORe) to address the phylogenetic and functional consequences of delayed rediploidization. Under LORe, speciation precedes rediploidization, allowing independent ohnologue divergence in sister lineages sharing an ancestral WGD event. 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 4,500 ohnologues, has evolved under LORe, with rediploidization and functional divergence occurring on multiple independent occasions > 50 Myr post-WGD. We demonstrate the existence and regulatory divergence of many LORe ohnologues with functions in lineage-specific physiological adaptations that promoted salmonid species radiation. We show that LORe ohnologues are enriched for different functions than older ohnologues that began diverging in the salmonid ancestor. 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 Myr, promoting lineage-specific diversification regimes under prevailing ecological pressures.

genomics↗