Biology subjects

Robledo, D.

Publications and source records attributed to Robledo, D..

At least 19 recordsLinked to original sources

bioRxiv2026

Untargeted metabolomics reveals a selectively enriched surface metabolome underpinning constitutive chemical defence in the red alga Halymenia floresii (Clemente) C.Agardh, 1817 ((Rhodophyta, Halymeniales)

Abstract: Marine macroalgae rely on chemically mediated surface defences to prevent microbial colonization and fouling, yet the composition of surface-associated metabolites and their ecological roles remain poorly understood. In this study, untargeted liquid chromatography/mass spectrometry (LC/MS) based metabolomics was used to characterize the surface-associated metabolome of the tropical red macroalga Halymenia floresii and identify metabolites potentially involved in chemical defence. Selective dipping extraction (DIP) was used to recover surface-associated metabolites and compared with whole-cell metabolome (WCM) extracts. Across both datasets, 22,455 LC/MS features were detected, including 10,505 features in the surface extracts and 11,495 additional features detected only in the WCM extracts. Statistical filtering identified 722 LC/MS features consistently enriched by at least four-fold in surface extracts relative to WCM extracts. These features yielded 928 putative metabolite annotations using xMSannotator, with biological interpretation supported by KEGG, LIPID MAPS, and MassBank. Pathway reconstruction using the Lilikoi R package identified 44 metabolite pathway associations, predominantly involving lipid-associated metabolism, including steroidogenesis, arachidonic acid metabolism, plasmalogen synthesis, fatty acid biosynthesis, sphingolipid metabolism and sterol biosynthesis. Manual curation further indicated enrichment of fatty acids, oxylipin-like metabolites, sphingolipids, phospholipid precursors and isoprenoid intermediates at the algal surface. Rather than indicating the presence of metabolites unique to the surface, the findings suggest that H. floresii selectively enriches lipid-associated metabolites at the thallus seawater interface. Spatial localization of relatively hydrophobic metabolites may provide an energetically efficient chemical defence strategy by retaining bioactive compounds at the site where microbial attachment and biofilm formation are initiated while minimizing their loss to the surrounding seawater. Overall, this study demonstrates that chemical defence in H. floresii is associated with the selective surface enrichment of lipid-associated metabolites rather than the occurrence of unique surface-specific compounds, providing new insights into the spatial organization of macroalgal chemical defences and the mechanisms underlying resistance to microbial colonization and fouling.

biochemistry↗

bioRxiv2026

MicroRNA modulation of viral nervous necrosis resistance in European seabass

MicroRNAs (miRNAs) are key post-transcriptional regulators of antiviral immunity, controlling gene expression by targeting 3 UTRs of immune-related transcripts. Despite their importance, the role of miRNAs in viral nervous necrosis (VNN) resistance in European seabass (Dicentrarchus labrax) is unexplored. Here, we characterized for the first time the brain miRNome of seabass from three VNN-resistance genotypes (susceptible, intermediate, resistant) across two genetically distinct seabass clusters. Differential expression analyses revealed cluster-specific patterns, with susceptible fish consistently showing overexpression of the differently expressed miRNAs (DEmiRNAs) as compared to the resistant fish. Considering the two genetic clusters in the study, miR-199-5p was differentially expressed between the VNN susceptible and resistant fish. This miRNA was found to be less expressed in the resistant individuals. Functional characterization of the miRNA predicted that it binds to two distinct miRNA recognition elements (MREs) within the ifi27l2a 3 UTR. These MREs flank a SNP (Chr3:10,082,380) previously associated with VNN survival. A strong negative correlation (r= -0.840) between miR-199-5p expression and ifi27l2a mRNA abundance further supports a post-transcriptional repression mechanism. Together, these results propose a regulatory model in which miR-199-5p modulates ifi27l2a expression, contributing to phenotypic variation in VNN resistance and positioning it as a promising biomarker for seabass aquaculture breeding.

genomics↗

bioRxiv2026

The genetic basis of resistance to pathogens in rainbow trout: a meta-QTL analysis

Rainbow trout is affected by a broad range of pathogens causing large economic losses and animal welfare concerns. Marker-assisted selection can significantly enhance resistance to pathogens in a few generations, and to this end many studies have focused on identifying quantitative trait loci (QTLs) for resistance traits. The integration of accumulated genetic resources provides an opportunity to uncover important genetic variation and candidate genes crucially involved in rainbow trout immunity. Here, we present a comprehensive meta-QTL (MQTL) analysis based on the integration of 145 QTLs related to pathogen resistance. These QTLs were refined into 26 MQTLs, of which 15 were validated by genome-wide association studies (GWAS). The average confidence interval (CI) of these MQTLs was reduced by 2.03-fold compared to the initial QTL, improving mapping precision. Integration of GWAS results revealed regions along the rainbow trout genome pivotal for pathogen resistance, and a major region in chromosome 3, which could be used in marker-assisted selection. Further, among the validated MQTLs we identified a subset of high-confidence MQTLs, based on those supported by at least three initial QTL from more than two independent studies, with a percentage of variance explained greater than 8% and a LOD score higher than three. Gene annotation identified 11 unique candidate genes within these high-confidence MQTLs involved in immune pathways, encoding proteins involved in the regulation of immune responses, signalling pathways, receptor activity, and direct immune effector production. The MQTLs and candidate genes identified are valuable resources for advancing molecular breeding and unravelling the genetic basis of pathogen resistance in rainbow trout.

genomics↗

bioRxiv2026

A microbiome assessment of healthy and bleached Halymenia floresii (Clemente) C. Agardh (Rhodophyta, Florideophyceae)

Macroalgae serve as critical habitat-formers and primary producers in coastal ecosystems, functioning across near-subtidal and intertidal zones in three distinct states: substrate-attached, free-floating (drift), and beach-cast. While substrate-attached macroalgae are susceptible to infectious diseases with significant ecological implications, diseases affecting drift macroalgal communities remain virtually unstudied. Here, we investigated bleaching disease - one of the most common macroalgal afflictions - in the drift rhodophyte Halymenia floresii from the Gulf of Mexico. Using 16S rRNA gene high-throughput sequencing and scanning electron microscopy, we characterized the bacterial community structure and composition associated with the free-floating healthy, bleached and degrading H. floresii to understand how bacterial partners respond to host health status. Principal Coordinate Analysis based on UniFrac distance revealed distinct clustering of bacterial communities according to host health condition. Shannon diversity indices showed distinct patterns ranging from 1.14 - 3.15 for healthy, bleached, and degrading samples, while Simpson indices ranged from 0.62 to 0.91, reflecting substantial variation in community evenness. In healthy samples, Cyanobacteria (17 - 52%) and Pseudomonadota (previously, Proteobacteria) (41 - 81%) dominated, and the bleached samples were characterized by elevated Bacteroidota (formerly, Bacteroidetes) (5 - 35%) and Pseudomonadota (41 - 88%). Notably, Novosphingobium (25 - 49%) dominated healthy hosts while showing lower abundance in degrading (13 - 17%) and bleached (18 - 22%) specimens. Conversely, Reinekea emerged as a dominant genus (22.5%) specifically in bleached samples, suggesting a potential role in disease pathogenesis. Microbial network analysis using NetCoMi revealed three distinct bacterial clusters corresponding to health states: a healthy-associated cluster dominated by Novosphingobium and uncultured Cyanobacterial with predominantly positive associations, and two disease-associated clusters enriched in opportunistic genera including Reinekea, Vibrio, Colwellia, and Alteromonas, indicating network reorganization from cooperative to exploitative interactions. This study provides the first descriptive assessment of microbiome transitions associated with bleaching disease in a drift macroalga and highlights the importance of considering free-floating macroalgal diseases and their potential impacts on coastal ecosystem health.

microbiology↗

bioRxiv2026

Comparative transcriptomics of immune response to viral and bacterial stimuli in three acanthopterygian bony fish

Diseases triggered by bacterial and viral infections have caused huge economic losses for three of the most important European aquaculture species: turbot (Scophthalmus maximus), gilthead seabream (Sparus aurata) and European seabass (Dicentrarchus labrax). Understanding how they respond to pathogens is relevant for advancing aquaculture disease management and comprehending evolution of immune response within teleosts. Since mechanisms conserved across species are assumed to perform important roles, comparative analysis provides a powerful approach to pinpoint key elements of the immune defence. Here, we report the first comparative immune-transcriptomic analysis of these three species using bacterial and viral mimics after 20-24 hours post-stimulation with inactivated Vibrio anguillarum and Poly I:C in the head kidney of live fish (in vivo), and in primary leukocyte cultures (in vitro). The transcriptomic response, based on RNA-seq data, revealed a total of 503 differentially expressed orthologous genes in response to in vitro-Poly I:C, 1,472 to in vitro-Vibrio, 920 to in vivo-Poly I:C, and 832 to in vivo-Vibrio. Interestingly, consistent expression patterns were identified in seven genes across all species in both cell culture and live organisms in response to both pathogen stimuli. Functional enrichment analysis revealed associations with immunity, DNA replication and repair, and cytokine pathways, with the Toll-Like Receptor (TLR) pathway common to both conditions and stimuli. Our study suggests conservation of orthologous gene expression during infection across the three species for genes involved in chemokine pathways, interferon signalling, antigen processing and presentation, cell signalling regulators, and MAPK cascades. This study provides insights into key immune defence mechanisms in acanthopterygian bony fish.

genomics↗

bioRxiv2025

Transcriptomic study of WSSV infection in Litopenaeus vannamei lymphoid organ via single nuclei RNA sequencing

BackgroundAquaculture is the fastest growing farmed food sector and is a key part of global food security. Crustacean aquaculture, while being one of the most profitable sectors, is threatened by pathogenic diseases such as white spot disease (WSD), which results in severe stock losses and threatens animal health and welfare. In this study, we used novel techniques to study the impact of white spot syndrome virus (WSSV), the causative agent of WSD, on Pacific whiteleg shrimp (Litopenaeus vannamei), and uncover additional information that may be used in creating WSSV-resistant shrimp stocks. ResultsWe successfully developed a novel nuclei isolation protocol optimized for shrimp tissues to prepare our samples for single nuclei RNA-sequencing following a pathogen challenge comprising of 32 adult whiteleg shrimp infected with WSSV either through their feed or by injection. We constructed the first penaeid shrimp lymphoid organ cell atlas to improve our understanding of the characteristics of this immune organ, constructed the UMAPs and identified marker genes that define distinct cell clusters to reveal the biological functions of different cell types within this organ. ConclusionBy comparing gene expression between the control and WSSV-infected samples we uncovered multiple genes of interest that that have the potential to be used as targets for CRISPR gene editing for WSSV-resistance in Pacific whiteleg shrimp. These genes have the potential to be valuable assets for future gene editing studies in commercially important penaeid shrimp species. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=90 SRC="FIGDIR/small/693182v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@1be071org.highwire.dtl.DTLVardef@2c3da6org.highwire.dtl.DTLVardef@835e67org.highwire.dtl.DTLVardef@aacff1_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2025

Striking olfactory receptor gene repertoire expansion in Senegalese sole (Solea senegalensis)

Chemoreception through olfaction is essential for regulating fish behaviour. Fish olfactory receptor repertoire comprises four multigene families (OlfC, OR, ORA and TAAR), whose diversity strongly shapes species-specific olfactory capabilities. In this study, the olfactory repertoire of the flatfish Solea senegalensis was characterized through orthology analysis with seven species, identifying 455 olfactory receptor genes in S. senegalensis, including large OlfC and TAAR gene expansions. Active functionality was shown in 426 genes of the total repertoire through the olfactory transcriptome and the RNA-seq libraries generated in this study, showing expression correlation within each family. Phylogenetic trees integrating orthologous and paralogous relationships, along with chromosomal locations were constructed. Notable synteny conservation was observed primarily among flatfish, partially lost with phylogenetically distant taxa. Olfactory receptor genes were heterogeneously distributed across twelve S. senegalensis chromosomes, constituting eleven major clusters of paralogous genes. Overall, S. senegalensis exhibits an expanded and specialized olfactory function, emerging as a promising model for studying chemoreception and addressing the reproductive issues in aquaculture.

evolutionary biology↗

bioRxiv2025

Optimization of reference population for imputation of low-density SNPs panel for genomic prediction in Atlantic salmon.

In recent years many advances have been made towards developing cost-efficient low-density genomic tools for a wider implementation of genomic selection in aquaculture breeding programmes. Genotype imputation from very low-density (LD) SNP panels of just a few hundred markers to high-density (HD) SNP panels has become a promising strategy to reduce the cost of genotyping while maintaining accurate genomic prediction. The objective of this study is to assess the impact of the makeup of HD-genotyped reference populations on i) the accuracy of imputation for LD-genotyped individuals and ii) the accuracy of genomic prediction for three traits of importance in Atlantic salmon production: growth, resistance to cardiomyopathy syndrome and resistance to pancreas disease. An Atlantic salmon population genotyped with a 47K SNP array was used for the study, along with an in silico LD panel of 554 SNPs. Five reference population scenarios for imputation were tested, which could include only the parents of the candidates for selection, a combination of parents and candidates, or just candidates. All scenarios resulted in highly accurate imputation rates (over 80%) except when the HD reference population was only composed of selection candidates. Nonetheless, the accuracy of imputation barely had an impact on the accuracy of genomic prediction, as the imputed datasets performed very similarly to the HD-panel. Adding a proportion of the offspring to the reference population, in addition to the parents, did not result in any benefit in terms of genomic prediction. Imputation is a cost-effective and robust option for genomic selection in aquaculture.

genetics↗

bioRxiv2025

Impaired Sertoli-Spermatogonia Interactions Contribute to Oligospermia and Infertility in F1 Captive-bred Male Solea senegalensis

Reproductive dysfunction of captive-bred males of the Senegalese sole (Solea senegalensis) represents a significant bottleneck for its aquaculture, as these fish exhibit reduced sperm production and impaired fertility compared to wild-bred counterparts acclimated to farm conditions. To elucidate the cellular and molecular mechanisms underlying this phenomenon, single-nuclei RNA sequencing was performed on gonadal tissue from adult captive-bred and wild-bred males. The analysis yielded a high-quality dataset comprising [~]80.000 cells, which were grouped into eleven distinct clusters representing all major germline and somatic cell types, including spermatogonial stem cells, differentiating spermatogonia, spermatocytes, spermatids, Sertoli cells, Leydig cells, immune cells, and peritubular myoid cells. It is noteworthy that captive-bred males exhibited a marked overrepresentation of proliferative spermatogonia and a significant reduction in mature spermatids, suggesting a disruption in the progression of spermatogenesis. Differential expression and functional enrichment analyses revealed that spermatogonial cells in captive-bred males displayed heightened translational activity alongside downregulation of pathways related to cell-cell communication and interaction. Focused cell-cell communication analyses further indicated defective Sertoli-spermatogonia interactions as a key factor contributing to oligospermia and infertility of captive-bred males. This study provides the first single-nuclei transcriptomic atlas of the Senegalese sole male gonad, offering valuable insights into the molecular basis of reproductive failure in captivity related to gonadal development. The findings of the study will inform future strategies to enhance selective breeding and improve aquaculture productivity for this economically important species.

genomics↗

bioRxiv2025

FULL-LENGTH HYBRID TRANSCRIPTOME OF THE OLFACTORY ROSETTE IN SENEGALESE SOLE (Solea senegalensis): AN ESSENTIAL GENOMIC RESOURCE TO IMPROVE REPRODUCTION AT FARMS

Senegalese sole is a promising European aquaculture species whose main challenge is that captive-born males (F1) are unable to reproduce in farms, hindering breeding programs. Chemical communication through the olfactory system is hypothesized to stem this issue. Although significant advancement in genomic resources has been made over the past decade, scarce information exists on the genomic basis of olfaction, a special sensory system for demersal species like flatfish, which could play a prominent role in reproduction, social and environmental interactions. A full-length transcriptome of the olfactory rosettes including females, males, juveniles and adults, of both F1 and wild origins, was generated at the isoform-level by combining Oxford Nanopore long-read and Illumina short-read sequencing technologies. A total of 20,670 transcripts actively expressed were identified: 13,941 were known transcripts, 5,758 were novel transcripts from known genes, and 971 were novel genes encoding novel transcripts. Special attention was paid to the olfactory receptor gene families (OlfC, OR, ORA and TAAR) expression. Our comprehensive olfactory transcriptome of Senegalese sole provides a foundation for delving into the functional basis of this complex organ in teleost and flatfish. Furthermore, it provides a valuable resource for addressing reproductive management challenges in Senegalese sole aquaculture.

genomics↗

bioRxiv2025

Amoebic gill disease (AGD) in Atlantic Salmon investigated through a holo-omic lens

Interactions between host genetics and the resident microbiota are complex. Understanding these interactions offers interesting alternatives for addressing gill health and disease resistance in salmonids. Amoebic gill disease (AGD), caused by Neoparamoeba perurans, remains a threat to Atlantic salmon, particularly in aquaculture settings where prevention and treatment options are scant. Selective breeding or genetic engineering towards increased AGD resilience present viable prevention strategies. While a number of studies have addressed AGD resistance in Atlantic salmon using transcriptomic and quantitative genetic approaches, the role of the Atlantic salmon gill microbiota in influencing AGD resilience and susceptibility needs further investigation. Addressing this, we leveraged a holo-omic approach using 16S rRNA bacterial profiling, and quantitative genetics, by considering the microbiota as an extended resistance trait of the salmon. We investigated the microbiota of AGD challenged Atlantic salmon in terms of two common resistance indicator traits: gill score and amoebic load. Subsequently we performed a GWAS using both the traditional indicator traits and traits of the microbiota. We found that the gill microbiota of the AGD affected salmon in this study was dominated by two bacterial families Simkaniaceae and Arcobacteracea. We found that microbial diversity and the relative abundance of Simkaniaceae, potentially derived from the amoeba, varied moderately with indicator traits. Additionally we identified several genomic regions that showed suggestive association with gill score and traits of the microbiota, and explored potential candidate genes for AGD resistance. Although much is still unclear regarding gill microbiota dynamics in gill disease, this study highlights the potential of addressing AGD through an integrative approach that considers the interplay between host genetics, the microbiota, and their roles in disease resistance.

genomics↗

bioRxiv2024

Differential Ubiquitination of Host Proteins in Response to IPNV and ISAV viruses in Atlantic salmon

Viral diseases remain a major barrier to the sustainable production of farmed fish, primarily attributable to the absence of effective prevention and treatment options. Understanding host-pathogen interactions can guide the development of vaccines, antiviral therapies, or gene editing strategies. Ubiquitination is a key cell signalling molecule, known to regulate many aspects of immune functions but currently understudied in fish. This study leverages ubiquitin-enriched mass spectroscopy complemented with RNA sequencing to characterize the role of ubiquitination in response to infection. A challenge experiment was conducted by infecting Atlantic salmon head kidney (SHK-1) cells with Infectious salmon anaemia virus (ISAV) and Infectious pancreatic necrosis virus (IPNV). At 24- and 48 hours post-infection dramatic changes were observed in the global ubiquitination state of host proteins. Many post-translational modifying proteins increased in abundance upon ISAV infection, whilst IPNV infection resulted in a reduction in abundance of many of these proteins. Transcriptomics showed a delay in the activation of the antiviral response to ISAV infection, with major upregulation of genes associated with immune pathways only at 48h. On the contrary, IPNV infection resulted in upregulation of classic innate immune response genes at both timepoints. Clear activation of Rig-like receptor pathways is demonstrated in both infections, in addition to upregulation of both conserved and novel antiviral TRIM E3 ubiquitin ligate genes. Network analysis identified clusters of immune genes and putatively regulatory proteins showing differential ubiquitination upon viral infection. This study highlights the importance of post-translational control of the host innate immune response to viruses in Atlantic salmon. Clear differences in ubiquitination between two viruses indicate either virus-specific post-translational regulation or viral antagonism of the immune response. Additionally, the ubiquitination of various proteins was linked to the regulation of innate immune pathways, suggesting a direct role of ubiquitination in the regulation of antiviral responses. AUTHOR SUMMARYUbiquitination is a main cellular regulatory mechanism in all animal species, controlling the activity of many proteins within the cell. The role of ubiquitination in the regulation of immunity is well-established, and several direct interactions with viruses have been described, either as part of a strategy of the host to fight the infection or as a viral mechanism to evade the host immune response. In aquaculture, viral diseases currently represent the most important threat to the sustainability of the industry. However, very little is known about the interplay between ubiquitination and viral pathogens in fish species. In our study, we have assessed the ubiquitination response of Atlantic salmon to two production-relevant viruses, Infectious salmon anaemia virus (ISAV) and Infectious pancreatic necrosis virus (IPNV). We found remarkable differences in the ubiquitination profiles between the two infections, suggesting a key role of ubiquitination on the early immune response. We also discovered an association between the ubiquitination of certain regulatory proteins and the activation of antiviral pathways. This information could help develop new strategies to tackle viral diseases in aquaculture, such as the development of more effective vaccines or antiviral therapies, or inform gene editing efforts to generate disease resistant fish.

molecular biology↗

bioRxiv2024

Integrated functional genomic analysis identifies the regulatory variants underlying a major QTL for disease resistance in European sea bass

BackgroundViral nervous necrosis (VNN) is a viral disease threatening the sustainability of global aquaculture, and affecting over 50 of farmed and ecologically important species. A major QTL for resistance to VNN has been previously described in European sea bass, but the underlying causal gene(s) and mutation(s) are unknown. To identify the mechanisms and genetic factors underpinning resistance to VNN, we integrated farmed and wild genetic data with multiple functional genomics assays in a farmed European sea bass population. ResultsA high heritability (h2 [~] 0.40) was estimated for VNN resistance. A major QTL for this trait was confirmed on chromosome 3, and whole-genome resequencing narrowed its location to a small region containing 4 copies of interferon alpha inducible protein 27-like 2A (IFI27L2A) genes, and one copy of the interferon alpha inducible protein 27-like 2 (IFI27L2) gene. RNA sequencing revealed a clear association between the QTL genotype and the expression of two of the IFI27L2A genes, and the IFI27L2 gene. Integration with chromatin accessibility and histone modification data pinpointed two SNPs in active regulatory regions of two of these genes (IFI27L2A and IFI27L2), and transcription factor binding site gains for the resistant alleles were predicted. These alleles, particularly the SNP variant CHR3:10077301, exhibited higher frequency in Eastern Mediterranean sea bass populations, which show considerably higher levels of resistance to VNN. ConclusionsThe SNP variant CHR3:10077301, through modulation of IFI27L2 and IFI27L2A genes, is likely the causative mutation underlying resistance to VNN in European sea bass. This is one of the first causative mutations discovered for disease resistance traits, and paves the way for marker-assisted selection as well as biotechnological approaches to enhance resistance to VNN in European sea bass and other susceptible species.

genetics↗

bioRxiv2024

A single-nucleus RNA sequencing atlas of the postnatal retina of the shark Scyliorhinus canicula

The retina, whose basic cellular structure is highly conserved across vertebrates, constitutes an accessible system for studying the central nervous system. In recent years, single-cell RNA-sequencing studies have uncovered cellular diversity in the retina of a variety of species, providing new insights on retinal evolution and development. However, similar data in cartilaginous fishes, the sister group to all other extant jawed vertebrates, are still lacking. Here, we present a single-nucleus RNA-sequencing atlas of the postnatal retina of the catshark Scyliorhinus canicula, consisting of the expression profiles for 17,438 individual cells from three female, juvenile catshark specimens. Unsupervised clustering revealed 22 distinct cell types comprising all major retinal cell classes, as well as retinal progenitor cells (whose presence reflects the persistence of proliferative activity in postnatal stages in sharks) and oligodendrocytes. Thus, our dataset serves as a foundation for further studies on the development and function of the catshark retina. Moreover, integration of our atlas with data from other species will allow for a better understanding of vertebrate retinal evolution.

neuroscience↗

bioRxiv2024

Characterisation of mesenchymal stromal cells in the skin of Atlantic salmon

BackgroundThe skin serves as the first line of defence for an organism against the external environment. Despite the global significance of salmon in aquaculture, a critical component of this first line of defence, mesenchymal stromal cells, remains unexplored. These pluripotent cells can differentiate into various tissues, including bone, cartilage, tendon, ligament, adipocytes, dermis, muscle and connective tissue within the skin. These cells are pivotal for preserving the integrity of skin tissue throughout an organisms lifespan and actively participate in wound healing processes. ResultsIn this study, we characterise mesenchymal stromal cells in detail for the first time in healthy Atlantic salmon tissue and during the wound healing process. Single-nucleus sequencing and spatial transcriptomics revealed the transcriptional dynamics of these cells, elucidating the differentiation pathways leading to osteogenic and fibroblast lineages in the skin of Atlantic salmon. We charted their activity during an in vivo wound healing time course, showing clear evidence of their active role during this process, as they become transcriptionally more active during the remodelling stage of wound healing. ConclusionsFor the first time, we chart the activity of sub-clusters of differentiating stromal cells during the process of wound healing, revealing different spatial niches of the various MSC subclusters, and setting the stage for investigations into the manipulation of MSCs to improve fish health.

genomics↗

bioRxiv2023

Keratinocytes Drive the Epithelial Hyperplasia Key to Sea Lice Resistance in Coho Salmon

BackgroundSalmonid species have followed markedly divergent evolutionary trajectories in their interactions with sea lice. While sea lice parasitism poses significant economic, environmental, and animal welfare challenges for Atlantic salmon (Salmo salar) aquaculture, coho salmon (Oncorhynchus kisutch) exhibit near-complete resistance to sea lice, achieved through a potent epithelial hyperplasia response leading to rapid louse detachment. The molecular mechanisms underlying these divergent responses to sea lice are unknown. ResultsWe characterised the cellular and molecular responses of Atlantic salmon and coho salmon to sea lice using single-nuclei RNA sequencing. Juvenile fish were exposed to copepodid sea lice (Lepeophtheirus salmonis), and lice-attached pelvic fin and skin samples were collected 12h, 24h, 36h, 48h, and 60h after exposure, along with control samples. Comparative analysis of control and treatment samples revealed an immune and wound-healing response that was common to both species, but attenuated in Atlantic salmon, potentially reflecting greater sea louse immunomodulation. Our results revealed unique but complementary roles of three layers of keratinocytes in the epithelial hyperplasia response leading to rapid sea lice rejection in coho salmon. Our results suggest that basal keratinocytes direct the expansion and mobility of intermediate and, especially, superficial keratinocytes, which eventually encapsulate the parasite. ConclusionOur results highlight the key role of keratinocytes to coho salmons sea lice resistance, and the diverged biological response of the two salmonid host species when interacting with this parasite. This study has identified key pathways and candidate genes that could be manipulated using various biotechnological solutions to improve Atlantic salmon sea lice resistance.

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↗

bioRxiv2023

Potential of imputation for cost-efficient genomic selection for resistance to Flavobacterium columnare in rainbow trout (Oncorhynchus mykiss)

BackgroundFlavobacterium columnare is the pathogen agent of columnaris disease, a major emerging disease affecting rainbow trout aquaculture. Selective breeding using genomic selection has potential to achieve cumulative improvement of host resistance. However, genomic selection is expensive partly due to the cost of genotyping high numbers of animals using high-density SNP arrays. The objective of this study was to assess the efficiency of genomic selection for resistance to F. columnare using in silico low-density (LD) panels combined with imputation. After a natural outbreak of columnaris disease, 2,874 challenged fish and 469 fish from the parental generation (n=81 parents) were genotyped with 27,907 SNPs. The efficiency of genomic prediction using LD-panels was assessed for panels of 10 different densities, created in silico using two sampling methods, random and equally spaced. All LD-panels were also imputed to the full 28K HD-panel using the parental generation as the reference population, and genomic predictions were reevaluated. The potential of prioritizing SNPs showing association with resistance to F. columnare was also tested for the six lower densities. ResultsSimilar results were obtained with random and equally spaced sampling of SNPs for accuracy of both imputation and genomic predictions. Using LD-panels of at least 3,000 makers or lower density panels (as low as 300 markers) combined with imputation resulted in comparable accuracy to the 28K HD-panel and 11% higher accuracy than pedigree-based predictions. ConclusionsCompared to using the commercial HD-panel, LD-panels with imputation may provide a more affordable route to genomic prediction of breeding values, supporting wider adoption of genomic selection in aquaculture breeding programmes.

genetics↗