Aim: Bivalves are aquatic filter-feeding molluscs characterized by a highly rich and diverse set of transposable elements (TEs) as well as by high levels of heterozygosity. In this study, we used five high-quality, long-read chromosome-level oyster assemblies and whole-genome resequencing data to investigate the impact of TEs in the emergence of within- and between-individual structural variants (SVs). We hypothesize that transposons can be an overlooked but important source of genetic variability both within and between individuals in bivalves and that they can contribute to population differentiation.

Methods: We combined multiple long-read pipelines and simulations to characterize high-confidence within-individual SVs. We have then estimated the role of TEs in their emergence. To characterize between-individual SVs we used 120 publicly available Crassostrea ariakensis short read resequenced samples encompassing the entire Chinese coasts. This SV set was used in classical population genomics analyses to detect population structure, differentiation, and putative variants under selection.

Results: Between 4% and 14% of oyster genomes exhibit structural variability between homologous chromosomes. Most of these regions are enriched in transposable elements, including both putative TE insertions and deletions, but are depleted of host genes. Similar results were obtained when analyzing SVs between individuals. Population structure based on more than 60,000 high-confidence SVs reflects the geographic origin of samples, reflecting what can be recovered using SNPs. Among these SVs, we identified multiple loci under putative diversifying selection between southern and northern populations.