Biology subjects

Aramburu, O.

Publications and source records attributed to Aramburu, O..

4 recordsLinked to original sources

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

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↗

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

Multiomics uncovers the epigenomic and transcriptomic response to viral and bacterial stimulation in turbot

Uncovering the epigenomic regulation of immune responses is essential for a comprehensive understanding of host defence mechanisms, though remains poorly investigated in farmed fish. We report the first annotation of the innate immune regulatory response in the turbot genome (Scophthalmus maximus), integrating RNA-Seq with ATAC-Seq and ChIP-Seq (H3K4me3, H3K27ac and H3K27me3) data from head kidney (in vivo) and primary leukocyte cultures (in vitro) 24 hours post-stimulation with viral (poly I:C) and bacterial (inactive Vibrio anguillarum) mimics. Among the 8,797 differentially expressed genes (DEGs), we observed enrichment of transcriptional activation pathways in response to Vibrio and immune pathways - including interferon stimulated genes - for poly I:C. We identified notable differences in chromatin accessibility (20,617 in vitro, 59,892 in vivo) and H3K4me3-bound regions (11,454 in vitro, 10,275 in vivo) between stimulations and controls. Overlap of DEGs with promoters showing differential accessibility or histone mark binding revealed significant coupling of the transcriptome and chromatin state. DEGs with activation marks in their promoters were enriched for similar functions to the global DEG set, but not always, suggesting key regulatory genes being in poised state. Active promoters and putative enhancers were enriched in specific transcription factor binding motifs, many common to viral and bacterial responses. Finally, an in-depth analysis of immune response changes in chromatin state surrounding key DEGs encoding transcription factors was performed. This multi-omics investigation provides an improved understanding of the epigenomic basis for the turbot immune responses and provides novel functional genomic information, leverageable for disease resistance selective breeding.

genomics↗