Chromosome-level haplotype-resolved assembly of highly heterozygous grass genomes with PhaseGrass.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 41422104.
- Also identified by DOI 10.1038/s41467-025-66377-5 and PMC identifier 12764793.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
Abstract
Current methods to generate haplotype-resolved assemblies for highly heterozygous genomes suffer from reference bias when relying on reference-based phasing or may generate imbalanced haplomes when relying on graph-based phasing. Here, we report PhaseGrass, an assembly, phasing and scaffolding workflow that is compatible with accurate or error-prone long reads, generating haplotype-resolved assemblies for highly heterozygous genomes. Requiring no parental data, PhaseGrass combines reference-based phasing with haplotype-specific k-mers to partition long reads or unitigs to corresponding haplotypes, thereby avoiding reference bias and uneven haplotype partitioning. Using PhaseGrass, we generated chromosome-level, haplotype-resolved assemblies for the highly heterozygous, allogamous grass species Lolium perenne L. and L. multiflorum Lam. We find that PhaseGrass can bin 20% more reads to haplotypes than WhatsHap and generated balanced haplomes compared to Hifiasm, which produced largely imbalanced haplomes for L. multiflorum due to abundant structural variations between haplotypes. PhaseGrass will facilitate routine generation of haplotype-resolved pangenomes for species with highly heterozygous genomes.
Medical subject headings
- Haplotypes
- Genome, Plant
- Chromosomes, Plant
- Lolium
- Poaceae