Biology subjects

Sandve, S. R.

Publications and source records attributed to Sandve, S. R..

At least 19 recordsLinked to original sources

bioRxiv2025

Large-scale eQTL analyses in Atlantic salmon reveal persistent dosage compensation 100 million years after genome duplication.

Whole-genome duplication (WGD) through autopolyploidization has played a role in genome evolution across eukaryotes. A major consequence of WGD is the rewiring of gene regulatory networks, partly driven by selection on dosage balance. In multicellular organisms, evidence for dosage balance selection has relied on comparative patterns of duplicate gene retention and expression, with few studies directly examining regulatory architecture after WGD. Here, we analysed a large-scale eQTL dataset from Atlantic salmon (Salmo salar), which experienced a WGD 100 million years ago. We found that trans-regulatory connections were enriched between duplicated regions, indicating long-term conservation of ancestral interchromosomal regulatory interactions. Overall, 230 duplicated genes (5%) shared eQTLs, suggesting conserved regulatory control. Moreover, 16 gene pairs showed compensatory expression effects mediated by a common regulator, consistent with predictions of the dosage balance hypothesis. These gene pairs were significantly enriched in recently rediploidized regions. Our results indicate long-term maintenance of dosage balance after WGD. TeaserGenetic regulation in Atlantic salmon shows that duplicated genes can remain dosage-balanced across 100 million years of evolution.

evolutionary biology↗

bioRxiv2025

A major locus on chromosome 14 impacts developmental variation of Atlantic salmon smoltification

BackgroundSmoltification in anadromous Atlantic salmon is a complex developmental process involving physiological and cellular changes that enable freshwater fish to adapt to seawater. Central to this transformation is the functional transformation of the gill to manage osmoregulatory demands. While environmental cues like photoperiod are known to influence smolt development, the genetic architecture underlying smolt development -- particularly related to gill physiology -- remains poorly understood. ResultsA large-scale eQTL analysis across 3,000 Atlantic salmon subjected to three photoperiod regimes, identified over 45,000 significant SNP-gene expression associations in gill tissue. Notably, we discovered a 0.5 Mbp large trans-eQTL hotspot on chromosome 14. This hub-locus was associated with expression of more than 2,000 genes across the genome which were significantly enriched for gill cell type specific markers. In addition we found that the hub-locus was associated with somatic growth. Our findings support a "local tissue effect" model, where cis-regulatory or protein sequence variants within the hub-locus modulate cell proliferation and differentiation of gill cell types. ConclusionThis work advances our understanding of the genetic basis of smoltification in Atlantic salmon and provides a foundation for future studies using single-cell approaches to resolve cell-type specific mechanisms underlying genetic variation in smolt development.

genetics↗

bioRxiv2025

Chromosome-level assembly of the octoploid cloudberry(Rubus chamaemorus)

We describe a chromosome-level genome assembly from an individual male plant of the cloudberry (Rubus chamaemorus). The haplotype-resolved assemblies contain one pseudo-haplotype spanning 1198 megabases and one pseudo-haplotype spanning 1161 megabases. Most of these two assemblies, 93.57% and 96.55% respectively, are each scaffolded into 28 pseudo-chromosomes. Both assemblies show high completeness, with the same BUSCO completeness score of 99.2%. Most BUSCO genes are duplicated in both pseudo-haplotypes, in line with the polyploid nature of the cloudberry genome. The assemblies contain 74,132 and 70,692 predicted protein-coding genes, respectively. Analysis of repetitive sequences classified [~]60% of each haplotype as repeats. Comparative synteny with red raspberry (Rubus idaeus) reveals a 4:1 chromosome correspondence, supporting an octoploid origin. Ks distributions and k-mer clustering indicate a fairly recent polyploidization involving one divergent ({beta}) and three closely related () subgenomes. Low coverage targeted sequencing data mapped to our assembly link the {beta}-subgenome to a relative of R. pedatus or R. lasiococcus, while the -subgenomes might derive from a putative auto-allohexaploid within the main Rubus clade. In conclusion, these results indicate that the cloudberry genome arose through multiple hybridization events, including recurrent allopolyploidy and possibly autopolyploidy. Significance statementCloudberry cultivation has lagged due to unclear origin and genome structure. We present a haplotype-resolved, chromosome-scale assembly that resolves four homologs per ancestral chromosome into 28 pseudo-chromosomes per haplotype and shows a 4:1 correspondence with red raspberry (Rubus idaeus). Genomic analyses indicate a recent polyploidization in which three closely related subgenomes likely derive from a putative hexaploid within the main Rubus clade, associated with R. arcticus (Arctic raspberry), whereas the fourth, more divergent subgenome is linked to relatives of R. pedatus (strawberryleaf raspberry) and R. lasiococcus (dwarf bramble). These results clarify cloudberrys formation and provide a foundation for trait discovery and accelerated breeding.

genomics↗

bioRxiv2025

Gene gain and loss drive the diversification of gig immune genes in teleosts: structural and regulatory insights from Atlantic salmon

Interferon-stimulated genes (ISGs) are key players in vertebrate antiviral immunity. Among teleost ISGs, the grass carp reovirus-induced gene (gig) families 1 and 2 (gig1 and gig2, respectively) are absent in mammals but conserved in fishes and amphibians, and they have been implicated in resistance to viral infections across several aquaculture species. In particular, gig1 and gig2 genes are transcriptionally induced by viral stimuli in teleosts such as zebrafish, grass carp, and salmonids, and recent studies have highlighted their potential involvement in resistance to economically important diseases like pancreas disease in Atlantic salmon. Yet, the rapid evolution of these genes hinders a comprehensive understanding of their diversification process and regulatory mechanisms. This study investigated gig gene evolution across teleosts, with a focus on Atlantic salmon (Salmo salar). Phylogenetic analysis across representative ray-finned fishes (Actinopterygii), including both teleosts and non-teleost outgroups such as the spotted gar (Holostei), indicated that gig1 is restricted to teleosts, with no identifiable homologs in non-teleost lineages. In contrast, gig2 genes are present in both teleosts and the spotted gar, suggesting an origin prior to the teleost-specific whole genome duplication (Ts3R), likely in early non-amniote vertebrates. Whole-genome duplication drove lineage-specific expansions, particularly of gig2 in salmonids. Structural and transcriptomic analyses showed that gig1 and gig2 differ in domain composition, repeat content, and regulation. Our findings suggest the complex interplay of duplication history, structural divergence, and transcriptional regulation in shaping immune gene repertoires in teleosts, with implications for understanding host-pathogen interactions and aquaculture disease responses. Article summaryThis study investigates the evolutionary history and diversification of the gig immune gene families in aquatic species, with particular focus on Atlantic salmon. Phylogenetic and structural analyses revealed that gig1 and gig2 follow distinct evolutionary trajectories, shaped by whole-genome and tandem duplications. Further analysis of Atlantic salmon gig genes showed divergent structures and regulation, highlighting a general role of gig genes in antiviral Interferon-mediated immunity and additionally suggesting functional specialization across gig paralogs. Together, these findings improve our understanding of immune gene evolution in fishes and provide insights relevant to antiviral defense and disease management in aquaculture species.

genomics↗

bioRxiv2025

OmniCorr: An R-package for visualizing putative host-microbiota interactions using multi-omics data

Holo-omics leverages omics datasets to explore the interactions between hosts and their associated microbiomes. Although the generation of omics data from matching host and microbiome samples is steadily increasing, there remains a scarcity of computational tools capable of integrating and visualizing this data to facilitate the interpretation and prediction of host-microbiota interactions. We present OmniCorr, an R package designed to: (1) manage the complexity of omics data by clustering similar observations into modules, (2) visualize correlations of these modules across different omics layers, host-microbiota interfaces, and meta-data, and (3) identify statistically significant associations indicative of putative host-microbiota interactions. OmniCorrs utility is demonstrated using datasets from two systems: (i) Atlantic salmon, integrating host transcriptomics with metagenomics and metatranscriptomics to explore dietary impacts, and (ii) cattle, combining host proteomics with metaproteomics and metabolomics to investigate methane emission variability. Availability and ImplementationOmniCorr is freely available at: https://github.com/shashank-KU/OmniCorr.

bioinformatics↗

bioRxiv2025

A Nextflow pipeline for molecular quantitative trait loci mapping in small sample size datasets with an application in Atlantic salmon

BackgroundMolecular quantitative trait loci (molQTL) mapping, particularly for gene expression and chromatin accessibility, provides crucial insights into the regulatory and functional potential of genetic variation. While significant progress has been made in humans and model organisms, aquatic genomics remains underexplored due to the large sample sizes typically required for statistical power. ResultsIn this work, we enhance the scalability, reproducibility, and accessibility of the well-established RASQUAL method, which efficiently detects molQTLs in small datasets, by leveraging the Nextflow workflow framework. This adaptation, named nf-RASQUAL, supports fully automated QTL mapping and incorporates a robust, comprehensive multiple-testing correction process. We apply the pipeline to a comprehensive multi-omics dataset from Atlantic salmon, identifying numerous significant expression and chromatin accessibility QTLs across multiple tissues. Our analysis reveals that a large proportion of lead variants for these loci reside in non-coding regions, with caQTL lead SNPs more likely to disrupt transcription factor motifs. Additionally, the enriched colocalization of eQTL and caQTL lead SNPs in brain, liver, and gonad tissues suggests shared regulatory mechanisms. ConclusionsThese findings highlight the scalability and utility of nf-RASQUAL for advancing genetic regulation research in aquaculture, facilitating molQTL studies in less-explored species, and improving our understanding of molecular phenotypes shaped by genetic diversity.

genomics↗

bioRxiv2025

Gamma radiation-induced molecular toxicity and effects on pluripotent stem cells of the radiosensitive conifer Norway spruce (Picea abies)

Conifers are among the most radiosensitive plant species. Elevated, sublethal levels of ionising radiation result in reduced apical dominance in conifers, indicating a negative effect on shoot apical meristems (SAMs). The SAMs, harbouring the pluripotent stem cells, generate all the cells of the shoot, enabling growth and reproduction. However, knowledge on the effects of ionising radiation on such stem cells is scarce, but important for risk assessment and radioprotection of plants in contaminated ecosystems. Here, we assessed the sensitivity of in vitro-grown stem cells of Norway spruce to 144-h of gamma irradiation at 1-100 mGy h-1, using such cells as a model for molecular toxicity of gamma radiation in conifers. Although there were no visible effects of the gamma irradiation on cell proliferation and subsequent embryo formation, dose rate-dependent DNA damage was observed at [≥]10 mGy h-1, and comprehensive organelle damage at all dose rates. Massive dose rate-dependent transcriptome changes occurred, with downregulation of a range of genes related to cell division, DNA repair and protein folding but upregulation of stress-related hormonal pathways and several antioxidant-related genes. The upregulation of such genes, survival and continued proliferation of at least a subset of cells and the post-irradiation normalisation of expression of DNA repair and protein-folding genes together with somatic embryo formation suggest that stem cells are able to recover from gamma-irradiation-induced stress. Collectively, regardless of cellular abnormalities after gamma irradiation, and huge transcriptomic shifts towards stress management pathways, the pluripotent stem cell cultures were able to retain their stemness. HighlightsO_LINorway spruce stem cells retained stemness after gamma irradiation (1-100 mGy h-1). C_LIO_LIDNA damage was observed at [≥] 10 mGy h-1 and organelle damage at all dose rates. C_LIO_LIHuge dose rate-dependent transcriptomic changes occurred after 144-h irradiation. C_LIO_LIDownregulated key DNA repair-genes recovered post-irradiation. C_LIO_LIInduction of stress-management and antioxidant genes may aid stem cell maintenance. C_LI

plant biology↗

bioRxiv2025

Photoperiodic history modulates the response of the saccus vasculosus transcriptome to SW water exposure in Atlantic salmon

Atlantic salmon (Salmo salar) move from fresh- to seawater environments following a seasonally timed preparative transition called smoltification, which takes place under photoperiodic control in the freshwater environment. In masu salmon (Oncorhynchus masou), coordination of photoperiodic sexual maturation is proposed to involve in a fish-specific circumventricular organ, the saccus vasculosus (SV), through its intrinsic opsin-based light sensitivity, thyrotrophin secretion and modulation of deiodinase activity (TSH-DIO cascade). The saccus vasculosus is a highly vascularized structure located on the ventral side of the hypothalamus and its interface between the blood and cerebrospinal fluid also hints at a role in ionic balance of the cerebrospinal fluid (CSF). Both the potential photoperiodic and ionic functions of the SV led us to perform transcriptome analysis of the SV in smoltification in Atlantic salmon. Our data show that SV response to seawater exposure is highly dependent on photoperiodic history and identifies ependymin as a major secretory output of the SV, consistent with a role in control of CSF composition. Conversely, we could not detect crucial elements of the opsin-TSH-DIO cascade suggesting that the photoperiodic history-dependence of the SV to seawater exposure is unlikely to stem from SV-intrinsic responses to photoperiod.

molecular biology↗

bioRxiv2025

Calcium starvation leads to strain-specific gene regulation of lipid and carotenoid production in Mucor Circinelloides

AO_SCPLOWBSTRACTC_SCPLOWFungi are pivotal in transitioning to a bio-based, circular economy due to their ability to transform organic material into valuable products such as organic acids, enzymes, and drugs. Mucor circinelloides is a model organism for studying lipogenesis and it particularly promising for its metabolic capabilities in producing oils like TAGs and carotenoids, influenced by environmental factors such as nutrient availability. Notably, strains VI04473 and FRR5020 have been identified for their potential in producing single-cell oils and carotenoids, respectively. Calcium starvation have previously been shown to have strain-specific effects, with VI04473 accumulating more lipids and FRR5020 producing more carotenoids. Here we used genome sequencing, comparative genomics, transcriptomics, and metabolite phenotyping to explore the genetic basis of lipid and carotenoid production under calcium starvation in these strains. We found extensive genomic rearrangements between these strains, as well as low conservation of gene regulatory responses to calcium depletion. This lack of conservation also applies to genes involved in lipid and carotenoid production, i.e. the lipidome. Several pathways show divergent regulation between strains, which explains the phenotypic divergence between VI04473 and FRR5020. The complex gene family evolution of several lipidome genes probably also affected specialization of these strains to calcium stress. Our study sheds light on the complexity of the evolution of metabolic networks in M. circinelloides. Understanding these genetic underpinnings can optimize the industrial use of M. circinelloides, enhancing lipid productivity and stress tolerance, and tailoring metabolic profiles for specific applications. This research advances our knowledge on complexity of fungal lipid metabolism and the role of calcium in regulating metabolic pathways.

genomics↗

bioRxiv2025

Sequence-based chromatin activity modeling and regulatory impact prediction of genetic variants in farmed animals using deep learning

Non-coding genomic variations are crucial for the genetic regulation of traits; how-ever, their functional impact in farmed animals remains underexplored due to lim-ited genomic resources and the absence of tailored computational tools. Here, we present a deep learning-based framework that utilizes functional genomics data to generate genome-wide predictions of the regulatory impact of non-coding vari-ants in cattle, chicken, pig, and Atlantic salmon. By leveraging chromatin profiles such as ATAC, DHS, and ChIP-seq data, we train and optimize separate deep networks for each species, achieving robust sequence modeling accuracy specific to each. Motif analysis confirms that the models capture regulatory grammar, while in silico saturation mutagenesis experiments provide meaningful interpretations of the functional impact of putative causal variants. Furthermore, functional scores derived from these models predict eQTL causal variants and enhance genomic prediction performance. Our findings highlight the transformative potential of se-quence to function models in prioritizing causal variants and improving genomic prediction for livestock and aquaculture.

genomics↗

bioRxiv2024

Transcriptomic profiling of gill biopsies to define predictive markers for seawater survival in farmed Atlantic salmon

Wild Atlantic salmon migrate to sea following completion of a developmental process known as parr - smolt transformation (PST), which establishes a seawater (SW) tolerant phenotype. Effective imitation of this aspect of anadromous life-history is a crucial aspect of commercial salmon production, with current industry practice being marred by significant losses during transition from the freshwater (FW) to SW phase of production. The natural photoperiodic control of PST can be mimicked by exposing farmed juvenile fish to a reduced duration photoperiod for at least 6 weeks before increasing the photoperiod in the last 1 - 2 months before SW transfer. While it is known that variations in this general protocol affect subsequent SW performance, there is no uniformly accepted industry standard; moreover, reliable prediction of SW performance from fish attributes in the FW phase remains a major challenge. Here we describe an experiment in which we took gill biopsies 1 week prior to SW transfer from 3000 individually tagged fish raised on 3 different photoperiod regimes during the FW phase. Biopsies were subjected to RNA profiling by Illumina sequencing, while individual fish growth and survival was monitored over 300 days in a SW cage environment, run as a common garden experiment. Using a random forest machine learning algorithm, we developed gene expression-based predictive models for initial survival and stunted growth in SW. Stunted growth phenotypes could not be predicted based on gill transcriptomes, but survival the first 40 days in SW could be predicted with moderate accuracy. While several previously identified marker genes contribute to this model, a surprisingly low weighting is ascribed to sodium potassium ATPase subunit genes, contradicting advocacy for their use as SW readiness markers. However, genes with photoperiod-history sensitive regulation were highly enriched among the genes with highest importance in the prediction model. This work opens new avenues for understanding and exploiting developmental changes in gill physiology during smolt development.

genomics↗

bioRxiv2024

Evolutionary new centromeres in the snowy owl genome putatively seeded from a transposable element

Comparative genomic studies in birds have revealed that bird genomes are relatively repeat-poor and stable in terms of karyotype, size, and gene synteny/collinearity compared to other vertebrates. One notable exception is the owls, with cytogenetic studies demonstrating large variations in karyotypes and the evolution of unusual centromeric satellite repeats in some species. However, there has so far not been an investigation into genome architecture and repeat landscape of owls. Here, we present a chromosome-level genome assembly for the snowy owl (Bubo scandiacus). We find that the repeat DNA content in the relatively large snowy owl genome (1.6 Gb) is among the highest reported for any bird genome to date (28.34% compared to an average of [~]10% in other birds). The bulk of the snowy owl genomic repeat landscape consists of centromeric satellite DNA, which appears to have originated from an endogenous retrovirus (ERV1). Using gene collinearity analyses we show that the position of these evolutionary new centromeres (ECNs) are not homologous with chicken centromeres, and are located in regions with collinearity breaks to other bird genomes due to chromosomal rearrangements. Our results support rapid transposable element-driven evolution of lineage-specific centromeres, which could have played a role in reproductive isolation and speciation of the snowy owl.

genomics↗

bioRxiv2024

Impact of three light smoltification regimes on performance and genetic parameters of traits in Atlantic salmon

2800 Atlantic salmon pre-smolts (50 g on average, the offspring of 53 sires and 100 dams) were individually tagged with PIT-tags and distributed among six circular 1200L tanks with approximately 450 fish per tank. Fish in duplicated tanks were put on three different light regimes, i.e. six weeks on either 8L:16D, 12L:12D or 24L:0D followed by six weeks on 24L:0D. One week prior to their transfer as 1+ smolt to a net cage in the sea in June 2021 their body weight, length, subjectively scored smolt status and fin damage were recorded. Recording of animal traits (body weight, wounds, fin damage, snout damage) were also performed in November 2021 and in April 2022. During the light regimes, fish on the two short day regimes had slower growth compared to fish on continuous light. However, after four (November 2021) and ten (April 2022) months in the sea the effect of light regime on fish size was not significantly different from zero (P>0.05). The fish on the 24L:0D regime showed increased mortality from day two after sea transfer with an accumulated recorded mortality of 8.9% during the two first months while it was only 1.0% and 0.7% for the 12L:12D and the 8L:16D fish, respectively. However, from the third until ten months in the sea recorded mortality was very similar for fish on the three light regimes. The effect of light regime on the recorded welfare traits (fin and snout damage and runts) was not significantly different from zero. For traits measured prior to seawater transfer the difference between fish that survived and those that died during the first two months in the sea were largest in the 24L:0D group indicating a positive effect of the short-day regimes also on the general smolt synchronization (i.e., group level uniformity). Moderate heritability estimates were found for the external smolt indicator traits condition factor, smolt status score and skin silveriness, as well as for snout damage, wounds, runts and body weight, but low estimates fin damage. For survival in the sea heritability on the liability scale was 0.09 after four months in the sea and 0.22 from five to ten months in the sea. The estimated genetic correlations between the same trait of the three different light regimes were moderate to high and thus unimportant genotype by light regime interaction. The genetic correlation of body in June 2021 with survival after two months in the sea was high (0.96), but not significantly different from zero with survival after four months in the sea and survival from five to ten months in the sea. Genetic correlations of survival with the other traits recorded in June 2021, November 2021 and April 2022 were low to medium in magnitude and not significantly different from zero. Therefore, for genetic improvement of survival in the seawater period direct selection for increased survival and growth during the first months is probably a better strategy than to perform indirect selection for smolt indicator traits.

genetics↗

bioRxiv2024

The need for high-resolution gut microbiome characterization to design efficient strategies for sustainable aquaculture production

Microbiome-directed dietary interventions such as microbiota-directed fibers (MDFs) have a proven track record in eliciting responses in beneficial gut microbes and are increasingly being promoted as an effective strategy to improve animal production systems. Here we used initial metataxonomic data on fish gut microbiomes as well as a wealth of a priori mammalian microbiome knowledge on -MOS and {beta}-mannan-derived MDFs to study effects of such feed supplements in Atlantic salmon (Salmo salar) and their hitherto poorly characterized gut microbiomes. Our multi-omic analysis revealed that the investigated MDFs (two -mannans and an acetylated {beta}-galactoglucomannan), at a dose of 0.2%, had negligible effects on both host gene expression, and gut microbiome structure and function under studied conditions. While a subsequent trial using a higher (4%) dietary inclusion of {beta}-mannan significantly shifted the gut microbiome composition, there were still no biologically relevant effects on salmon metabolism and physiology. Only a single Burkholderia-Caballeronia-Paraburkholderia (BCP) population demonstrated consistent and significant abundance shifts across both feeding trials, although with no evidence of {beta}-mannan utilization capabilities or changes in gene transcripts for producing metabolites beneficial to the host. In light of these findings, we revisited our omics data to predict and outline novel and potentially beneficial endogenous lactic acid bacteria that should be targeted with future, conceivably more suitable, MDF strategies for salmon. IMPORTANCEThis study focuses on the potential of MDFs to improve aquaculture production. Despite preliminary 16S rRNA amplicon data suggested that populations in the salmon gut microbiome could utilize structurally complex mannans, our findings indicates that endogenous microbes could not metabolize it, nor the host responds to its dietary inclusion, at least not under the trial conditions investigated in this study. We highlight that high-resolution and host-specific microbiome characterization can greatly improve trial design and selection of candidate MDFs for future nutritional interventions. Understanding the intricate interplay between host and its gut microbiome is paramount in studies seeking to leverage endogenous microbial communities to benefit the host. While each new condition, whether it is a disease onset or a nutritional stressor, has the potential to profoundly reshape the microbial diversity, composition and outputs, the functional microbiome information gained under healthy conditions represent a pivotal step towards designing more effective trials involving microbiome-reprogramming feed additives. Overall, we envisage that these results will lead to improved focus on coupling fundamental microbiome characterization to the design of next-generation feeds for salmon aquaculture.

microbiology↗

bioRxiv2024

The role of transposon activity in shaping cis-regulatory element evolution after whole genome duplication

Two of the most potent drivers of genome evolution in eukaryotes are whole genome duplications (WGD) and transposable element (TE) activity. These two mutational forces can also play synergistic roles; WGDs result in both cellular stress and functional redundancy, which would allow TEs to escape host-silencing mechanisms and effectively spread with reduced impact on fitness. As TEs can function as, or evolve into, TE-derived cis-regulatory elements (TE-CREs), bursts of TE-activity following WGD are likely to impact evolution of gene regulation. However, the role of TEs in genome regulatory remodelling after WGDs is unclear. Here we used the genome of Atlantic salmon, which is known to have experienced massive expansion of TEs after a WGD [~]100 Mya, as a model system to explore the synergistic roles of TEs and WGDs on genome regulatory evolution. We identified 55,080 putative TE-CREs in Atlantic salmon using chromatin accessibility data from brain and liver. Of these, 80% were tissue specific to liver (43%) or brain (37%) and TE-CREs originating from retroelements were twice as common as those originating from DNA elements. Signatures of selection shaping TE-CRE evolution were evident from depletion of TEs in open chromatin, a bias in tissue-shared TE-CREs towards older TE-insertions, as well as tissue-specific processes shaping the TE-CRE repertoire. A minority of TE-families (16%) accounted for the origin of 46% of all TE-CREs, but the transposition activity of these CRE-superspreader families happened mostly prior to the WGD. Analyses of individual TE-CREs do however support a significantly higher rate of TE-CRE evolution from insertions happening around the time of the salmonid WGD. This pattern was particularly striking for the DTT elements, despite having generally low propensity to evolve into TE-CREs and impact transcription. Furthermore, co-expression based analyses supported the presence of TE-driven gene regulatory network evolution, including DTT elements active at the time of WGD. In conclusion, we find a strong association between TE insertions at the time of WGD and TE-CRE evolution. This association was not driven by particular TE-families with high capability to evolve into TE-CREs but likely a consequence of the concurrent surge of novel TE insertions, mostly from DTT elements, in combination with a shift in selective pressure on genome regulation following the WGD.

evolutionary biology↗

bioRxiv2023

The Salmon Microbial Genome Atlas enables novel insights into bacteria-host interactions via functional mapping

The essential role of the gut microbiota for host health and nutrition is well established for many terrestrial animals, while its importance for fish and particularly Atlantic salmon is unclear. Here, we present the Salmon Microbial Genome Atlas (SMGA) originating from wild and farmed fish both in freshwater and seawater, and consisting of 211 high-quality bacterial genomes, recovered by cultivation (n=131) and gut metagenomics (n=80). Bacterial genomes were taxonomically assigned into 14 different orders, including 28 distinctive genera and 31 potentially novel species. Benchmarking the SMGA, we functionally characterized key populations in the salmon gut that were detected in vivo. This included the ability to degrade diet-derived fibers and release vitamins and other exo-metabolites with known beneficial effects, which were validated by in vitro cultivation and untargeted metabolomics. Together, the SMGA enables high resolution functional insight into salmon gut microbiota with relevance for salmon nutrition and health.

microbiology↗

bioRxiv2023

High radiosensitivity in Norway spruce (Picea abies) is rendered by less comprehensive mobilisation of protection, repair and stress responses compared to the radiotolerant A. thaliana

Risk assessment and protection of plant communities in contaminated ecosystems require in-depth understanding of differential sensitivity to chronic ionising radiation in plants. However, the contributing molecular factors to differential radiosensitivity among plant species are poorly understood. To shed light on this, we compared early events associated with protection, repair, and stress responses in gamma-irradiated (1-290 mGy h-1) seedlings of the radiosensitive conifer Norway spruce (Picea abies) and the radiotolerant Arabidopsis thaliana, by analysing growth, organelle and DNA damage, transcriptomes and the dynamics of antioxidant activities and expression of relevant genes. After 48 h of gamma radiation exposure, Norway spruce showed significantly reduced growth at 100-290 mGy h-1 and organelle damage, especially in mitochondria, at [≥] 1 mGy h-1 whereas A. thaliana showed normal vegetative growth at all dose rates, transiently delayed reproductive development at 290 mGy h-1 only, minor organelle damage only at [≥] 100 mGy h-1 and significantly less DNA damage than in Norway spruce at all dose rates. Comparative transcriptomics revealed that A. thaliana showed massive activation of genes related to DNA damage repair, antioxidants, and other stress responses at [≥] 1 mGy h-1 while Norway spruce mobilized transcription of such pathways only at [≥] 40 mGy h-1. The transcriptional activation of repair and protection responses at higher gamma dose-rates only and its absence in lower dose-rates, correlates with high radiosensitivity of Norway spruce, compared to the massive transcriptional activation from low dose-rates in the radiotolerant A. thaliana.

plant biology↗

bioRxiv2023

Linking genomic prediction for muscle fat content in Atlantic salmon to underlying changes in lipid metabolism regulation

Muscle fat content is an important production trait in Atlantic salmon (Salmo salar) because it influences the flavor, texture, and nutritional properties of the fillet. Genomic selection can be applied to alter muscle fat content, however how such selection changes the underlying molecular physiology of these animals is unknown. Here, we examine the link between genomic prediction and underlying molecular physiology by correlating genomic breeding values for fat content to liver gene expression in 184 fish. We found that Salmon with higher genomic breeding values had higher expression of genes in lipid metabolism pathways. This included key lipid metabolism genes hmgcrab, fasn-b, fads2d5, and fads2d6, and lipid transporters fatp2f, fabp7b, and apobc. We also found several regulators of lipid metabolism with negative correlation to genomic breeding vales, including pparg-b, fxr-a, and fxr-b. A quantitative trait loci analysis for variation in gene expression levels (eQTLs) for 167 trait associated genes found that 71 genes had at least one eQTL, and that most were trans eQTLs. Closer examination revealed distinct eQTL clustering on chromosomes 3 and 6, indicating the presence of putative common regulator in these regions. Taken together, these results suggest that increased fat content in high genomic breeding value salmon is associated with elevated lipid synthesis, elevated lipid transport, and reduced glycerolipid breakdown; and that this is at least partly achieved by selection on genetic variants that impact the function of top-level transcription factors involved in liver metabolism. Our study sheds light on how genomic selection alters lipid content in Atlantic salmon, and the results could be used to prioritize SNPs to improve the efficiency of genomic selection in the future.

genomics↗