Structural variant landscape provides insights into genome organisation and domestication in European seabass

Structural variants (SVs) are genetic polymorphisms including deletions, insertions, inversions, and duplications, with potential to influence traits through impacts on gene function and expression. SVs have not been widely utilized in genetic analysis, owing to the challenge of their accurate detection and genotyping. Addressing this general issue, and the broader demand to understand their role in commercially important taxa, we report a comprehensive analysis of SVs in the genome of European seabass (Dicentrarchus labrax), the most commercially important fish in the Mediterranean region.

Using whole genome sequencing from a farmed population (n = 90 samples), 21,428 SVs were identified using a comprehensive detection and genotyping strategy involving manual curation of every variant. This high-confidence SV atlas was annotated to predict impacts on genes and evolutionarily conserved sequences. We explored the overlap between SVs and repeats, identified heterogeneity in SV density across the genome, and tested if the coding genes disrupted by SVs are enriched for specific biological processes or conserved protein domains. SVs impacting evolutionarily conserved genomic regions were enriched in genes with nervous system and developmental functions. Finally, we performed a comparative analysis incorporating 38,408 high-confidence SVs identified independently for three wild populations (n = 80 samples) using identical methods. An analysis of 41,336 SVs merged across the two datasets provides insights into genes and biological functions targeted during aquaculture domestication, with evidence of shifts in allele frequency for SVs located within or near genes controlling behaviour, enriched for forebrain and synaptic functions, and specifically expressed in the brain.

This study sheds light on the global organisation of SVs across the European seabass genome, revealing a potential role in aquaculture domestication. The reported datasets provide a novel, high-quality reference for future genetic investigations of both farmed and wild European seabass.