ArticleGigaScience2020
Multifaceted Hi-C benchmarking: what makes a difference in chromosome-scale genome scaffolding?
Article in GigaScience, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers, 1 of them a synthesis that pooled it.
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Who cites it
39 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Meta-analysis of gonadal transcriptome provides novel insights into sex change mechanism across protogynous fishes.Genes to cells : devoted to molecular & cellular mechanisms · 2024Pooled it
- Cell-cycle-resolved Hi-C reveals unexpected plasticity of A/B compartments across interphase.eLife · 2026Article
- Nuclear compartmentalization at the G1/S transition plays a key role in DNA replication control.Nature communications · 2026Article
- Genome-Wide Analysis Successfully Resolves Population Structure Shaped by Recent Divergence in the Endangered Bagrid CatfishEcology and evolution · 2026Article
- Silver chimaera genome highlights lineage-specific sex chromosome and opsin gene evolution in holocephalans.DNA research : an international journal for rapid publication of reports on genes and genomes · 2026Article
- The genome of the medicinal plant Uncaria rhynchophylla provides new insights into monoterpenoid indole alkaloid metabolism and its molecular regulatory mechanism.Molecular horticulture · 2026Article
- 3D Genome Constrains Breakpoints of Inversions That Can Act as Barriers to Gene Flow in the Stickleback.Molecular ecology · 2025Article
- Chromosome-level genome assembly and Oligo-FISH confirmation of chromosome models for the Tasmanian snow skink Carinascincus ocellatus (Scincidae, Eugongylinae).BMC biology · 2025Article
- Sharks and rays have the oldest vertebrate sex chromosome with unique sex determination mechanisms.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- H3K27me3 and the PRC1-H2AK119ub pathway cooperatively maintain heterochromatin and transcriptional silencing after the loss of H3K9 methylation.Epigenetics & chromatin · 2025Article
- Establishing genome sequencing and assembly for non-model and emerging model organisms: a brief guide.Frontiers in zoology · 2025Review
- Comparative genomics and multiomics analyses reveal the evolution and physiological basis of rubber biosynthesis in Hevea species.GigaScience · 2025Article
- Read Mapping for Hi-C Analysis.Methods in molecular biology (Clifton, N.J.) · 2025Article
- CWL-Based Analysis Pipeline for Hi-C Data: From FASTQ Files to Matrices.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Footprint-C reveals transcription factor modes in local clusters and long-range chromatin interactions.Nature communications · 2024Article
- A high-quality genome assembly and annotation of Thielaviopsis punctulata DSM102798.Scientific data · 2024Article
- Chromosomal DNA sequences of the Pacific saury genome: versatile resources for fishery science and comparative biology.DNA research : an international journal for rapid publication of reports on genes and genomes · 2024Article
- Elasmobranch genome sequencing reveals evolutionary trends of vertebrate karyotype organization.Genome research · 2023Article
- GreenHill: a de novo chromosome-level scaffolding and phasing tool using Hi-C.Genome biology · 2023Article
- Epigenetic plasticity safeguards heterochromatin configuration in mammals.Nucleic acids research · 2023Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundHi-C is derived from chromosome conformation capture (3C) and targets chromatin contacts on a genomic scale. This method has also been used frequently in scaffolding nucleotide sequences obtained by de novo genome sequencing and assembly, in which the number of resultant sequences rarely converges to the chromosome number. Despite its prevalent use, the sample preparation methods for Hi-C have not been intensively discussed, especially from the standpoint of genome scaffolding.
resultsTo gain insight into the best practice of Hi-C scaffolding, we performed a multifaceted methodological comparison using vertebrate samples and optimized various factors during sample preparation, sequencing, and computation. As a result, we identified several key factors that helped improve Hi-C scaffolding, including the choice and preparation of tissues, library preparation conditions, the choice of restriction enzyme(s), and the choice of scaffolding program and its usage.
conclusionsThis study provides the first comparison of multiple sample preparation kits/protocols and computational programs for Hi-C scaffolding by an academic third party. We introduce a customized protocol designated "inexpensive and controllable Hi-C (iconHi-C) protocol," which incorporates the optimal conditions identified in this study, and demonstrate this technique on chromosome-scale genome sequences of the Chinese softshell turtle Pelodiscus sinensis.
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