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Updated: Oct 18, 2026

High-throughput Physical Mapping of Chromosomes using Automated in situ Hybridization
Published on: June 28, 2012
Assembly-graph-assisted haplotype-resolved scaffolding of polyploid genomes
Wenjie Du1,2, Yanchun Li1,3, Xiaofei Zeng1
1Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, State Key Laboratory of Genome and Multi-omics Technologies, State Key Laboratory of Tropical Crop Breeding, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
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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