Biology subjects

Bouza, C.

Publications and source records attributed to Bouza, C..

8 recordsLinked to original sources

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

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↗

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↗

bioRxiv2022

A chromosome-level genome assembly enables the identification of the follicle stimulating hormone receptor as the master sex determining gene in Solea senegalensis

Sex determination (SD) mechanisms are exceptionally diverse and show high evolutionary rates in fish. Pleuronectiformes is an emblematic fish group characterized by its adaptation to demersal life and its compact genomes. Here, we present a chromosome-level genome assembly of Senegalese sole, a promising European aquaculture species. We combined long- and short-read sequencing and a highly dense genetic map to obtain a contiguous assembly of 613 Mb (N50 = 29.0 Mb, 99% of the assembly in the n = 21 chromosomes of its karyotype). The correspondence between this new assembly and the Senegalese sole chromosomes was established by fluorescence in situ hybridization with BAC probes. Orthology within Pleuronectiformes was assessed by using the chromosome-level genomes of six important commercial flatfishes covering a broad phylogenetic spectrum of the order. A total of 7936 single-gene orthologues, shared by the six species, were used to identify syntenies in Pleuronectiformes and to explore chromosome evolutionary patterns in the order. Whole genome resequencing of six males and six females enabled the identification of 41 fixed allelic variants in the follicle stimulating hormone receptor (fshr) gene, homozygous in females and heterozygous in males, consistent with an XX / XY chromosome system. The observed association between fshr SNPs and sex was confirmed at the species level in a broad sample, which allowed tuning up a molecular sexing tool. Fshr demonstrated differential gene expression between male and female gonads since 86 days post-fertilization, when the gonad was still an undifferentiated primordium, concomitant with the activation of other testis and ovary marker genes, such as amh and cyp19a1a genes, respectively. Interestingly, the Y-linked fshr allele, which included 24 non-synonymous variants, expressed to a higher level than the X-linked allele at all stages. We hypothesize a molecular mechanism hampering the action of the follicle stimulating hormone that would drive the undifferentiated gonad toward testis.

genomics↗

bioRxiv2020

Biotic and abiotic factors shaping the genome of cockle (Cerastoderma edule) in the Northeast Atlantic: a baseline for sustainable management of its wild resources

Knowledge on how environmental factors shape the genome of marine species is crucial for sustainable management of fisheries and wild populations. The edible cockle (Cerastoderma edule) is a marine bivalve distributed along the Northeast Atlantic coast of Europe and is an important resource from both commercial and ecological perspectives. We performed a population genomics screening using 2b-RAD genotyping on 9,309 SNPs localised in the cockles genome on a sample of 536 specimens pertaining to 14 beds in the Northeast Atlantic to ascertain its genetic structure regarding environmental variation. Larval dispersal modelling considering species behaviour and interannual variability in ocean conditions was carried out, as an essential background to compare genetic information with. Cockle populations in the Northeast Atlantic were shown to be panmictic and displayed low but significant geographical differentiation across populations (FST = 0.0240; P < 0.001), albeit not across generations. We identified 441 outlier SNPs related to divergent selection, sea surface temperature being the main environmental driver following a latitudinal axis. Two main genetic groups were identified, northwards and southwards of French Brittany, in accordance with our modelling, which demonstrated a barrier for larval dispersal linked to the Ushant front. Further genetic subdivision was observed using outlier loci and considering larval behaviour. The northern group was divided into the Irish/Celtic Seas and the English Channel/North Sea, while the southern group was divided into three subgroups. This information represents the baseline for management of cockles, designing conservation strategies, founding broodstock for depleted beds, and producing suitable seed for aquaculture production.

genomics↗

bioRxiv2019

Multiple evidences suggest sox2 as the main driver of a young and complex sex determining ZW/ZZ system in turbot (Scophthalmus maximus)

A major challenge in evolutionary biology is to find an explanation for the variation in sex-determining (SD) systems across taxa and to understand the mechanisms driving sex chromosome differentiation. We studied the turbot, holding a ZW/ZZ SD system and no sex chromosome heteromorphism, by combining classical genetics and genomics approaches to disentangle the genetic architecture of this trait. RAD-Seq was used to genotype 18,214 SNPs on 1,135 fish from 36 families and a genome wide association study (GWAS) identified a [~] 6 Mb region on LG5 associated with sex (P < 0.05). The most significant associated markers were located close to sox2, dnajc19 and fxr1 genes. A segregation analysis enabled narrowing down the associated region and evidenced recombination suppression in a region overlapping the candidate genes. A Nanopore/Illumina assembly of the SD region using ZZ and WW individuals identified a single SNP fully associated with Z and W chromosomes. RNA-seq from 5-90 day-old fish detected the expression along the gonad differentiation period of a short non-coding splicing variant (ncRNA) included in a vertebrate-conserved long non-coding RNA overlapping sox2. qPCR showed that sox2 was the only differentially expressed gene between males and females at 50-55 days post fertilization, just prior the beginning of gonad differentiation. More refined information on the involvement of secondary genetic and environmental factors and their interactions on SD was gathered after the analysis of a broad sample of families. Our results confirm the complex nature of SD in turbot and support sox2 as its main driver.

genomics↗

bioRxiv2017

Parallel use of a shared genomic island of speciation in clinal and mosaic hybrid zones between cryptic seahorse lineages

Diverging semi-isolated lineages either meet in narrow clinal hybrid zones, or have a mosaic distribution associated with environmental variation. Intrinsic reproductive isolation is often emphasized in the former and local adaptation in the latter, although both can contribute to isolation. Rarely these two patterns of spatial distribution are reported in the same study system. Here we report that the long-snouted seahorse Hippocampus guttulatus is subdivided into discrete panmictic entities by both types of hybrid zones. Along the European Atlantic coasts, a northern and a southern lineage meet in the southwest of France where they coexist in sympatry with little hybridization. In the Mediterranean Sea, two lineages have a mosaic distribution, associated with lagoon-like and marine habitats. A fifth lineage was identified in the Black Sea. Genetic homogeneity over large spatial scales contrasts with isolation maintained in sympatry or close parapatry at a fine scale. A high variation in locus-specific introgression rates provides additional evidence that partial reproductive isolation must be maintaining the divergence. Surprisingly, fixed differences between lagoon and marine populations in the Mediterranean Sea belong to the most differentiated SNPs between the two Atlantic lineages, against the genome-wide pattern of structure. These parallel outlier SNPs cluster on a single chromosome-wide island of differentiation. Since Atlantic lineages do not match the lagoon-sea habitat variation, genetic parallelism at the genomic island suggests a shared genetic barrier contributes to reproductive isolation in contrasting contexts -i.e. spatial vs. ecological. We discuss how a genomic hotspot of parallel differentiation could have evolved and become associated either with space or with a patchy environment in a single study system.

evolutionary biology↗