Abstract

Abstract The current swine reference genome, based on a single Duroc individual, has contributed to many significant advances but also carries limitations in many applications. Reference alleles receive substantial bias from alignment-based approaches. Additionally, structural DNA variants are difficult to identify and represent relative to the linear reference genome. As a result, DNA variants more likely to affect complex quantitative traits are understudied and warrant further investigation. In this study, a trio-binning approach was utilized to produce haplotype-resolved assemblies of a Duroc x Landrace hybrid. The Duroc sire and Landrace dam were sequenced via short-read technology (Illumina), and the hybrid offspring was sequenced via long-read technology (PacBio HiFi). A total of 117 Gb HiFi data was produced, equivalent to approximately 47X coverage of the swine genome. Two highly contiguous and high-quality assemblies were produced using hifiasm. The assembled maternal (Landrace) and paternal (Duroc) genomes had a contig N50 of 76.7 Mb and 55.0 Mb, respectively, both of which surpass that of the current reference genome Sscrofa11.1 (48.2 Mb). Furthermore, the maternal and paternal genomes contained 113.6 Mb and 116.0 Mb of novel sequences relative to the reference, respectively. The Benchmarking Universal Single-Copy Orthologue (BUSCO) scores were approximately 96%, indicating high completeness. The computed assembly QVs were found to be >Q40. Compared with short-read technology, whole genome mapping identified substantially more large SVs (> 50bp). These haplotype-resolved assemblies and additional existing assemblies will serve as the basis for the production of a swine pangenome.