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

文献类型： 外文期刊

第一作者： Zhang, Xiaohui

作者： Zhang, Xiaohui;Li, Dongxi;Zhang, Xiaohui;Pan, Weihua

作者机构：

关键词： Haplotype-resolved assembly; Auto-polyploid; PacBio HiFi; Hi-C; Gametic data

期刊名称：SCIENTIFIC REPORTS （ 影响因子：3.8； 五年影响因子：4.3 ）

ISSN： 2045-2322

年卷期： 2024 年 14 卷 1 期

页码：

收录情况： SCI

摘要： 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.

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