Year: 2026
Type: preprint
Abstract: Here, we present Dipler, a two-step strategy that combines the identification of group-specific k-mers from whole-genome sequencing data with de novo assembly of PacBio reads enriched for those k-mers. Using a Gg/gg presence/absence-like model in Juglans hindsii, we recovered the structurally distinct "G" allele from PacBio reads at coverage as low as 9×. Using the exceptional GG genotype of J. regia "Sharkey" as a complementary diploid model, we further show that two divergent "G" alleles of the same locus can be resolved and assembled separately from 13× coverage. Dipler therefore provides a rapid, reference-independent framework for identifying structurally complex loci, with potential applicability across eukaryotic species.
Institution: University of Tartu
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
Funders: European Commission, Tartu Ülikool
OpenAlex ID: W7222019905