ArticleNature plants2024
Chromosome-level scaffolding of haplotype-resolved assemblies using Hi-C data without reference genomes.
Article in Nature plants, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 128 papers.
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128 citing papers in PubMed.
- Haplotype-resolved genome of a dry-preservable cell line reveals chromosome evolution and DNA damage.Life science alliance · 2026Article
- Assembly-graph-assisted haplotype-resolved scaffolding of polyploid genomes.Nature plants · 2026Article
- A chromosome-level genome assembly of Thecaphora frezzii, cause of peanut smut, reveals the largest genome of the true smut fungi.G3 (Bethesda, Md.) · 2026Article
- The heterozygous pineapple genome demonstrates the importance of haplotype-resolved plant genomes.Horticulture research · 2026Article
- Chromosome-scale genomes and population resequencing resolve subgenome diversity and halophyte adaptation in Salicornia.Nature communications · 2026Article
- Allelic expression and subgenome bias influence plant height in cultivated hybrid sugarcane.aBIOTECH · 2026Article
- Characterization of a draft chromosome-scale genome assembly for the mutton snapper, Lutjanus analis.Genes & genomics · 2026Article
- Article
- A high-quality haplotype-resolved genome of Pyrus calleryana provides insights into adaptive gene families.The plant genome · 2026Article
- Complete telomere-to-telomere genome assembly of Guazuma ulmifolia uncovers evolutionary mechanisms, drought adaptation, and flavonoid biosynthesis.Plant cell reports · 2026Article
- Archipelago architecture and evolution of paclitaxel biosynthesis revealed by the Pseudotaxus chienii haplotype-resolved genome.Nature communications · 2026Article
- Unveiling centromeric retrotransposon dynamics through a high-quality rye genome assembly.Nature communications · 2026Article
- A near-complete genome assembly of onion resolves its genomic architecture, origin, and evolution.Plant communications · 2026Article
- Near telomere-to-telomere genome assembly of the rainbow trout (Oncorhynchus mykiss).Scientific data · 2026Article
- De novo haplotype-resolved genome assembly of the endemic kiwifruit Actinidia hubeiensis.Scientific data · 2026Article
- Chromosome-scale Genome Assembly and Annotation of Anise Hyssop (Agastache foeniculum).Scientific data · 2026Article
- A Personalized Haplotype-Resolved Near-Gapless Genome Framework for Somatic Variant Discovery in Hepatocellular Carcinoma.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Two telomere-to-telomere Nelumbo genome assemblies reveal domestication history and empower precision breeding.Nature communications · 2026Article
- Genome assemblies and annotations are not static and need support for tracking their evolution.Briefings in bioinformatics · 2026Review
- Haplotype-resolved genome assembly sheds light on the evolutionary history of autohexaploid Tripidium arundinaceum.Nature communications · 2026Article
68 more citing papers are in PubMed but not listed here.
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Abstract
Scaffolding is crucial for constructing most chromosome-level genomes. The high-throughput chromatin conformation capture (Hi-C) technology has become the primary scaffolding strategy due to its convenience and cost-effectiveness. As sequencing technologies and assembly algorithms advance, constructing haplotype-resolved genomes is increasingly preferred because haplotypes can provide additional genetic information on allelic and non-allelic variations. ALLHiC is a widely used allele-aware scaffolding tool designed for this purpose. However, its dependence on chromosome-level reference genomes and a higher chromosome misassignment rate still impede the unravelling of haplotype-resolved genomes. Here we present HapHiC, a reference-independent allele-aware scaffolding tool with superior performance on chromosome assignment as well as contig ordering and orientation. In addition, we provide new insights into the challenges in allele-aware scaffolding by conducting comprehensive analyses on various adverse factors. Finally, with the help of HapHiC, we constructed the haplotype-resolved allotriploid genome for Miscanthus × giganteus, an important lignocellulosic bioenergy crop.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.