The structural variation landscape of the flat oyster genome

Structural variants (SV), ranging in size from a few base pairs to entire chromosomes, are important contributors to population structure and evolutionary processes, such as local adaptation or speciation. Despite their impact on gene regulatory mechanisms, SVs remain uncharacterized in non-model organisms due to high sequencing costs and bioinformatic challenges. This work presents a genome-wide characterization of SVs in the European flat oyster (Ostrea edulis), an ecologically and economically important bivalve, using long-read sequencing data from 35 individuals sampled in the Netherlands. A spectrum of SV types and sizes were identified, with many overlapping repetitive elements, highlighting their contribution to within-population genetic structure. Analysis of haplotype divergence across three large inversions revealed signatures of recombination suppression in heterozygote individuals. Together, these findings provide an overview of SV landscape in O. edulis and highlight the potential role of structural variation in shaping genomic diversity, underscoring its relevance for oyster restoration efforts.