Allelic coverage analyses reveal a high proportion and uneven chromosomal distribution of SNPs associated with polymorphic duplications in the oyster Ostrea edulis

Oysters are known for their high genetic diversity, potentially high genetic load, and structurally complex genomes. The European flat oyster, Ostrea edulis, is no exception. Here, we combined a reference-free analysis of pairs of k-mers differing by a single nucleotide (hereafter: het-mers) with a reference-based analysis of allelic coverage using high-coverage short-read sequencing data (70-160X) from five individuals. Up to one-third of SNPs called as heterozygous within an individual exhibited allelic coverage fractions departing from the expected 0.5 ratio. Despite no evidence of recent whole-genome duplication, 40% of het-mers displayed coverage profiles consistent with duplicated genomic segments. We classified AAB het-mers as CN3 and AAAB or AABB het-mers as CN4, corresponding to nucleotide variants located within segments present in three and four copies, respectively, and interpreted as heterozygous and homozygous duplications. These CN3 and CN4 het-mers were typically observed in only a subset of individuals and mostly switched among CN3, CN4, or absence from the het-mer catalog, providing evidence for pervasive paralogous variants associated with rampant polymorphic duplications of genomic segments that vary in copy number among individuals. Reference-based analysis of sequencing depth and allelic coverage fraction similarly showed that SNPs with deviant allelic coverage are frequently associated with duplicated genomic segments segregating within populations, predominantly at low frequencies. Despite their different principles and potential biases, both approaches converged on a minimum estimate of 15% of nucleotide variants being associated with polymorphic duplications. Duplication-associated SNPs occurred in coding and non-coding regions to a similar extent, but their distribution was heterogeneous across chromosomes, with the highest densities on three of the ten chromosomes. These three chromosomes are non-metacentric and particularly prone to chromosome loss in oysters, which are known for their high incidence of somatic aneuploidy. This pattern supports two non-exclusive hypotheses: an architecture-driven model in which chromosome properties prone to structural instability promote both duplications and somatic aneuploidy, and a compensation-driven model in which duplications evolve to buffer dosage imbalance in aneuploid cells. Finally, we discuss how extensive polymorphic duplication may bias population genomic analyses in O. edulis and other ostreids.