Selecting genomes that matter: haplotype-based prioritization for iterative pangenome expansion
SelHap provides a practical framework for targeted pangenome expansion. It facilitates ancestry and germplasm comparisons across diverse panels and offers a scalable, interpretable approach for extending mature pangenomes by explicitly targeting previously unrepresented sequence space. Building on the existing barley pangenome project, we expanded the resource by incorporating an additional 36 high-quality genome assemblies. We obtained HiFi data (~20-fold coverage) and Hi-C sequencing data (~200M read pairs) for each genotype. High molecular weight (HMW) DNA isolation, library preparation and HiFi sequencing using the PacBio Revio device (Pacific Biosciences) were as described previously. Hi-C libraries were generated using the DpnII restriction enzyme as described previously. After obtaining the HiFi and Hi-C data, read quality control was performed using FastQC. PacBio HiFi reads were assembled using hifiasm v.0.24.0. Pseudomolecules were constructed with the TRITEX pipeline using Morex V3 single-copy regions to guide scaffolding. Chimeric contigs and orientation errors were identified through manual inspection of Hi-C contact maps. Heterozygosity was assessed with Jellyfish v.2.2.6 and GenomeScope v.2.0.
SelHap provides a practical framework for targeted pangenome expansion. It facilitates ancestry and germplasm comparisons across diverse panels and offers a scalable, interpretable approach for extending mature pangenomes by explicitly targeting previously unrepresented sequence space. Building on the existing barley pangenome project, we expanded the resource by incorporating an additional 36 high-quality genome assemblies. We obtained HiFi data (~20-fold coverage) and Hi-C sequencing data (~200M read pairs) for each genotype. High molecular weight (HMW) DNA isolation, library preparation and HiFi sequencing using the PacBio Revio device (Pacific Biosciences) were as described previously. Hi-C libraries were generated using the DpnII restriction enzyme as described previously. After obtaining the HiFi and Hi-C data, read quality control was performed using FastQC. PacBio HiFi reads were assembled using hifiasm v.0.24.0. Pseudomolecules were constructed with the TRITEX pipeline using Morex V3 single-copy regions to guide scaffolding. Chimeric contigs and orientation errors were identified through manual inspection of Hi-C contact maps. Heterozygosity was assessed with Jellyfish v.2.2.6 and GenomeScope v.2.0.