Biology subjects

GUINAND, B.

Publications and source records attributed to GUINAND, B..

4 recordsLinked to original sources

bioRxiv2025

Genomic differentiation of the black-chinned tilapia (Sarotherodon melanotheron) along a fresh-to-hypersaline water gradient

The black-chinned tilapia (Sarotherodon melanotheron) is an African fish species, found in freshwater, brackish, marine and especially hypersaline (up to 110 {per thousand}) habitats in Senegambia. Using 16,786 filtered single nucleotide polymorphism (SNP) markers, we investigated whether it has responded adaptively to this fresh-to-hypersaline water gradient. Significant genetic differentiation between samples was observed (FST = 0.0568, p < 0.01), revealing an interplay between geographic and environmental variation. We focused on a set of outlier SNPs (n = 255; FST = 0.320, p < 0.001) indicative of adaptive variation, 119 of which mapped to annotated genes in the Oreochromis niloticus genome. Significant enrichment was found for physiological pathways relevant to osmosensing and osmoregulation (e.g. inositol phosphate, thyroid hormone synthesis pathways), but also for immune-related pathways that could be activated by ion fluxes (e.g. inflammasome). Some outlier loci mapped to genes that are known to respond to salinity variation in other organisms, including genes found to be differentially expressed in black-chinned tilapia. Adaptive variation along a fresh-to-hypersaline water gradient is well supported in black-chinned tilapia, but its association with climate change specifically induced by hypersalinity deserves further attention particularly in the context of increasing cases of inverted estuaries being reported worldwide.

evolutionary biology↗

bioRxiv2020

Spotting genome-wide pigmentation variation in a brown trout admixture context

Variation in body pigmentation attracted fish biologists for a while, but high-throughput genomic studies investigating its molecular basis remain limited to few species and associated conservation issues ignored. Using 75,684 SNPs, we explored the genomic basis of pigmentation pattern variation among individuals of the Atlantic and Mediterranean clades of the brown trout (Salmo trutta), a polytypic species in which Atlantic hatchery individuals are commonly used to supplement local wild populations. Using redundancy analyses and genome-wide association studies, a set of 337 independent "colour patterning loci" (CPLs) significantly associated with pigmentation traits such as the number of red and black spots on flanks, or the presence of a black spot on the pre-opercular bone was identified. CPLs map onto 35 out of 40 brown trout linkage groups indicating a polygenic basis to pigmentation patterns. They are mostly located in coding regions (43.4%) of 223 candidate genes, and correspond to GO-terms known to be involved in pigmentation (e.g. calcium and ion-binding, cell adhesion). Annotated candidates include genes with known pigmentation effects (e.g. SOX10, PEML, SLC45A2), but also the Gap-junction {otimes}2 (GJD2) gene already shown differentially expressed in trout skin. Patterns of admixture were found significantly distinct when using either the full SNP data set or the set of CPLs, indicating that pigmentation patterns accessible to practitioners are not a reliable proxy of genome-wide admixture. Consequences for management are discussed.

evolutionary biology↗

bioRxiv2020

Genome scale epigenomic analysis of response to acute stress in the European sea bass (Dicentrarchus labrax, L.)

BackgroundWhile the stress response inspired genome-wide epigenetic studies in vertebrate models, it remains mostly ignored in fish. We modified the epiGBS (epiGenotyping By sequencing) technique to explore changes in genome-wide cytosine methylation to a repeated acute stress challenge in the nucleated red blood cells (RBCs) of the European sea bass (Dicentrarchus labrax). This species is widely studied in both the natural and farmed environments, including issues regarding health and welfare. ResultsWe retrieved 501,108,033 sequencing reads after trimming, with a mean mapping efficiency of 73.0% (unique best hits). Fifty-seven differentially methylated cytosines (DMCs) close to 51 distinct stress-related genes distributed on 17 of 24 linkage groups (LGs) were detected between RBCs of pre- and post-stress individuals. Literature surveys indicated that thirty-eight of these genes were previously reported as differentially expressed in the brain of zebrafish, most of them involved in stress coping differences. DMC-related genes associated to the Brain Derived Neurotrophic Factor, a protein that favors stress adaptation and fear memory, are especially relevant. ConclusionWe provide an improved epiGBS protocol with increased multiplexing and sequencing capacities that offer new opportunities to improve data acquisition and to investigate important biological processes at a genome-wide level, such as the stress response. Minimally invasive RBCs deserve more attention to investigate the epigenetic response to stress without sacrificing fish.

genomics↗

bioRxiv2018

Genomic consequences of a recent three-way admixture in supplemented wild brown trout populations revealed by ancestry tracts

Understanding the evolutionary consequences of human-mediated introductions of domestic strains into the wild and their subsequent admixture with natural populations is of major concern in conservation biology. In the brown trout Salmo trutta, decades of stocking practices have profoundly impacted the genetic makeup of wild populations. Small local Mediterranean populations in the Orb River watershed (Southern France) have been subject to successive introductions of domestic strains derived from the Atlantic and Mediterranean lineages. However, the genomic impacts of two distinct sources of stocking (locally-derived vs divergent) on the genetic integrity of wild populations remain poorly understood. Here, we evaluate the extent of admixture from both domestic strains within three wild populations of this watershed, using 75,684 mapped SNPs obtained from double-digest restriction-site-associated DNA sequencing (dd-RADseq). Using a local ancestry inference approach, we provide a detailed picture of admixture patterns across the brown trout genome at the haplotype level. By analysing the chromosomal ancestry profiles of admixed individuals, we reveal a wider diversity of hybrid and introgressed genotypes than estimated using classical methods for inferring ancestry and hybrid pedigree. In addition, the length distribution of introgressed tracts retained different timings of introgression between the two domestic strains. We finally reveal opposite consequences of admixture on the level of polymorphism of the recipient populations between domestic strains. Our study illustrates the potential of using the information contained in the genomic mosaic of ancestry tracts in combination with classical methods based on allele frequencies for analysing multiple-way admixture with population genomic data.

genomics↗