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Peer-reviewedCC BYNature plants

Assembly-graph-assisted haplotype-resolved scaffolding of polyploid genomes.

  • Wenjie Du1
  • Yanchun Li2
  • Xiaofei Zeng
  • Jinbao Yang
  • Xingbin Wang
  • Xiaohui Zhang
  • Lianguang Shang
  • Xiaopeng Fu3
  • Xiaoni Zhang
  • Xiu-Qing Wei4
  • Tingcai Cheng5
  • Dongxi Li6
2 more authors
  • Zhiqiang Wu
  • Weihua Pan
6 affiliations
  1. 1State Key Laboratory of Resource Insects, Southwest University, Chongqing, China.
  2. 2College of Computer Science and Technology, Taiyuan University of Technology, Taiyuan, China.
  3. 3National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China.
  4. 4Fruit Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China.
  5. 5State Key Laboratory of Resource Insects, Southwest University, Chongqing, China. [email protected].
  6. 6College of Computer Science and Technology, Taiyuan University of Technology, Taiyuan, China. [email protected].
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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.

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Cite

BibTeXRIS
BibTeX
@article{du2026assemblygraphassisted,
  title = {{Assembly-graph-assisted haplotype-resolved scaffolding of polyploid genomes.}},
  author = {Wenjie Du and Yanchun Li and Xiaofei Zeng and Jinbao Yang and Xingbin Wang and Xiaohui Zhang and Lianguang Shang and Xiaopeng Fu and Xiaoni Zhang and Xiu-Qing Wei and Tingcai Cheng and Dongxi Li and Zhiqiang Wu and Weihua Pan},
  journal = {Nature plants},
  year = {2026},
  month = oct,
  doi = {10.1038/s41477-026-02422-5},
  url = {https://europepmc.org/article/MED/42888234},
  note = {CC BY},
}
RIS
TY  - JOUR
TI  - Assembly-graph-assisted haplotype-resolved scaffolding of polyploid genomes.
AU  - Wenjie Du
AU  - Yanchun Li
AU  - Xiaofei Zeng
AU  - Jinbao Yang
AU  - Xingbin Wang
AU  - Xiaohui Zhang
AU  - Lianguang Shang
AU  - Xiaopeng Fu
AU  - Xiaoni Zhang
AU  - Xiu-Qing Wei
AU  - Tingcai Cheng
AU  - Dongxi Li
AU  - Zhiqiang Wu
AU  - Weihua Pan
PY  - 2026
DA  - 2026/10/16
JO  - Nature plants
DO  - 10.1038/s41477-026-02422-5
UR  - https://europepmc.org/article/MED/42888234
AB  - 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.
SN  - 2055-0278
ER  -