{
  "abstract": "Assembling polyploid genomes at the chromosome level remains a major challenge due to the difficulty of accurately distinguishing homologous chromosomes, leaving a vast number of polyploid species without high-quality genome sequences. Current chromatin conformation capture (3C)-based haplotype-resolved scaffolding methods often produce highly incomplete and mis-phased assemblies of complex polyploids, as short sequences lacking sufficient interaction support and collapsed regions with misleading signals are difficult to resolve. Here we present GPhase, a haplotype-resolved scaffolding algorithm that integrates 3C (for example, Hi-C, Pore-C and Omni-C) data with assembly graphs to enhance accuracy, completeness and contiguity. By leveraging graph connectivity derived from long-read overlaps, GPhase effectively overcomes key limitations of 3C. When applied to 15 complex polyploid genomes, GPhase reduced the sequence missing rate (BUSCO-based) by up to tens-fold, decreased the sequence error rate (k-mer-based) by up to an order of magnitude and improved the contiguity (N50) of gap-free sequences by several-fold compared with existing tools.",
  "abstract_shown": true,
  "affiliations": [
    "State Key Laboratory of Resource Insects, Southwest University, Chongqing, China.",
    "College of Computer Science and Technology, Taiyuan University of Technology, Taiyuan, China.",
    "National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China.",
    "Fruit Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China.",
    "State Key Laboratory of Resource Insects, Southwest University, Chongqing, China. chengtc@swu.edu.cn.",
    "College of Computer Science and Technology, Taiyuan University of Technology, Taiyuan, China. dxli0426@126.com."
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 14,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Wenjie Du"
    },
    {
      "affs": [
        1
      ],
      "name": "Yanchun Li"
    },
    {
      "name": "Xiaofei Zeng",
      "orcid": "0000-0001-8127-3825"
    },
    {
      "name": "Jinbao Yang",
      "orcid": "0000-0003-1650-6981"
    },
    {
      "name": "Xingbin Wang"
    },
    {
      "name": "Xiaohui Zhang"
    },
    {
      "name": "Lianguang Shang",
      "orcid": "0000-0002-4606-2800"
    },
    {
      "affs": [
        2
      ],
      "name": "Xiaopeng Fu",
      "orcid": "0000-0003-2244-4983"
    },
    {
      "name": "Xiaoni Zhang"
    },
    {
      "affs": [
        3
      ],
      "name": "Xiu-Qing Wei"
    },
    {
      "affs": [
        4
      ],
      "name": "Tingcai Cheng",
      "orcid": "0000-0002-3862-0817"
    },
    {
      "affs": [
        5
      ],
      "name": "Dongxi Li",
      "orcid": "0000-0003-2786-8048"
    },
    {
      "name": "Zhiqiang Wu",
      "orcid": "0000-0002-4238-7317"
    },
    {
      "name": "Weihua Pan",
      "orcid": "0000-0002-4796-6895"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/8m6ta9cagfr0m.bib",
  "cited_by": 0,
  "doi": "10.1038/s41477-026-02422-5",
  "fulltext_url": "https://europepmc.org/articles/PMC13680272",
  "id": "8m6ta9cagfr0m",
  "issns": [
    "2055-0278"
  ],
  "landing_url": "https://europepmc.org/article/MED/42888234",
  "language": "eng",
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "1312|Genomics and Phylogenetic Studies"
    ]
  ],
  "openalex": "W7222703169",
  "pdf_url": "https://europepmc.org/articles/PMC13680272?pdf=render",
  "pmcid": "PMC13680272",
  "pmid": "42888234",
  "published": "2026-10-16",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/8m6ta9cagfr0m.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:18:46Z",
      "native_id": "MED:42888234",
      "source": "europepmc",
      "url": "https://europepmc.org/article/MED/42888234"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1312|Genomics and Phylogenetic Studies",
      "subfield": "molecular-biology"
    }
  ],
  "title": "Assembly-graph-assisted haplotype-resolved scaffolding of polyploid genomes.",
  "title_text": "Assembly-graph-assisted haplotype-resolved scaffolding of polyploid genomes.",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:18:46Z",
  "url": "https://research.draconitic.com/paper/8m6ta9cagfr0m",
  "venue": "Nature plants",
  "versions": []
}