Haplotype-resolved assembly of auto-polyploid genomes via combining Hi-C and gametic data

• Published in: Scientific reports Vol. 14; no. 1; p. 7892
• Main Authors: Zhang, Xiaohui, Li, Dongxi, Pan, Weihua
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 03-04-2024; Nature Publishing Group; Nature Portfolio
• Subjects: 631/208; 631/208/2491/3933; 631/208/514/2254; 631/208/727/728; 631/208/728; 631/208/742; Alleles; Auto-polyploid; Cultivars; Gametic data; Genomes; Germ Cells; Haplotype-resolved assembly; Haplotypes; Haplotypes - genetics; Hi-C; Humanities and Social Sciences; Humans; multidisciplinary; PacBio HiFi; Polyploidy; Science; Science (multidisciplinary); Sequence Analysis, DNA - methods; Haplotype-resolved assembly; Auto-polyploid; PacBio HiFi; Hi-C; Gametic data
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-024-58623-5

Haplotype-resolved genome assembly plays a crucial role in understanding allele-specific functions. However, obtaining haplotype-resolved assembly for auto-polyploid genomes remains challenging. Existing methods can be classified into reference-based phasing, assembly-based phasing, and gamete binning. Nevertheless, there is a lack of cost-effective and efficient methods for haplotyping auto-polyploid genomes. In this study, we propose a novel phasing algorithm called PolyGH, which combines Hi-C and gametic data. We conducted experiments on tetraploid potato cultivars and divided the method into three steps. Firstly, gametic data was utilized to bin non-collapsed contigs, followed by merging adjacent fragments of the same type within the same contig. Secondly, accurate Hi-C signals related to differential genomic regions were acquired using unique k-mers. Finally, collapsed fragments were assigned to haplotigs based on combined Hi-C and gametic signals. Comparing PolyGH with Hi-C-based and gametic data-based methods, we found that PolyGH exhibited superior performance in haplotyping auto-polyploid genomes when integrating both data types. This approach has the potential to enhance haplotype-resolved assembly for auto-polyploid genomes.