k-mer spectra and allelic coverage analyses reveal pervasive polymorphic duplications in Ostrea edulis

Marine bivalves are known for their high genetic diversity and potentially high genetic load, as well as their structurally complex genomes. The European flat oyster, Ostrea edulis, is no exception. In this study we performed both k-mer based and reference-based analyses on short-read data with high coverage ([~]70-160X) from five individuals. Up to one-third of heterozygous SNPs showed allelic coverage fractions that deviated from expectation. Despite no evidence of recent whole-genome duplication, we detected significant signals for genomic regions of increased ploidy, and 15% and 25% of k-mer pairs distant by a single nucleotide displayed triploid-like and tetraploid-like profiles respectively. In a diploid species, this indicates the presence of heterozygote and homozygote duplications. These results were confirmed by coverage-based genotype inference, which showed that deviant SNPs are located in polymorphic duplications. While duplications affected genic and non-genic regions similarly, their genomic distribution varied across chromosomes, with a notable enrichment in non-metacentric chromosomes. The latter being prone to somatic aneuploidy, we suggest that aneuploidy could act as an indirect driver, with duplications potentially buffering the expression of recessive deleterious mutations in aneuploid cells. Finally, we consider how such widespread structural variation may complicate population genomic analyses in O. edulis and other marine bivalves.