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Such misjoins were widespread, involved the connection of both small and large contigs, and even overlapped annotated genes. We conclude that the integration of optical mapping data after, not before, Hi-C-based scaffolding, improves the quality of the assembly and limits reconstruction errors by highlighting misjoins that can then be subjected to further investigation.</jats:p>","journal":"Plants","year":2023,"id":597391,"datarank":0.24141568686511508,"base_score":1.6094379124341003,"endowment":1.6094379124341003,"self_citation_contribution":0.24141568686511508,"citation_network_contribution":0.0,"self_endowment_contribution":0.24141568686511508,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":4,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1530481,"name":"Leonardo Vincenzi","orcid":null,"position":1,"is_corresponding":false},{"id":1530482,"name":"Matteo Ballottari","orcid":"0000-0001-8410-3397","position":2,"is_corresponding":false},{"id":1530483,"name":"Michela Cecchin","orcid":"0000-0002-9970-7174","position":3,"is_corresponding":false},{"id":1530484,"name":"Emanuela Cosentino","orcid":"0000-0001-5379-9491","position":4,"is_corresponding":false},{"id":1530485,"name":"Thomas Mignani","orcid":null,"position":5,"is_corresponding":false},{"id":1530486,"name":"Antonina Limongi","orcid":null,"position":6,"is_corresponding":false},{"id":1530487,"name":"Irene Ferraris","orcid":null,"position":7,"is_corresponding":false},{"id":1530488,"name":"Matteo Orlandi","orcid":null,"position":8,"is_corresponding":false},{"id":1074599,"name":"Marzia Rossato","orcid":"0000-0002-6101-1550","position":9,"is_corresponding":false},{"id":1521683,"name":"Massimo Delledonne","orcid":"0000-0002-7100-4581","position":10,"is_corresponding":false},{"id":1530480,"name":"Luca Marcolungo","orcid":"0000-0002-2366-5684","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Structural Refinement by Direct Mapping Reveals Assembly Inconsistencies near Hi-C Junctions","abstract":"<jats:p>High-throughput chromosome conformation capture (Hi-C) is widely used for scaffolding in de novo assembly because it produces highly contiguous genomes, but its indirect statistical approach can introduce connection errors. We employed optical mapping (Bionano Genomics) as an orthogonal scaffolding technology to assess the structural solidity of Hi-C reconstructed scaffolds. Optical maps were used to assess the correctness of five de novo genome assemblies based on long-read sequencing for contig generation and Hi-C for scaffolding. Hundreds of inconsistencies were found between the reconstructions generated using the Hi-C and optical mapping approaches. Manual inspection, exploiting raw long-read sequencing data and optical maps, confirmed that several of these conflicts were derived from Hi-C joining errors. Such misjoins were widespread, involved the connection of both small and large contigs, and even overlapped annotated genes. We conclude that the integration of optical mapping data after, not before, Hi-C-based scaffolding, improves the quality of the assembly and limits reconstruction errors by highlighting misjoins that can then be subjected to further investigation.</jats:p>","is_dataset_classified":null,"base_score":1.3862943611198906,"endowment":1.3862943611198906,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"36679033","pmcid":"PMC9861903","openalex_id":"https://openalex.org/W4315487151","authors":[],"funders":[{"funder_name":"ERC","grant_id":"679814","title":"IMPROVING PHOTOSYNTHETIC SOLAR ENERGY CONVERSION IN MICROALGAL CULTURES FOR THE PRODUCTION OF BIOFUELS AND HIGH VALUE PRODUCTS"},{"funder_name":"ERC","grant_id":"JPVR18RY8Y","title":null},{"funder_name":"ERC","grant_id":"RBVR17WKNJ","title":null}],"total_grants":3,"fwci":0.2809,"citation_percentile":0.48388966,"influential_citations":0,"citation_trend":[{"year":2026,"count":3}],"oa_status":"gold","license":"cc-by","oa_locations":[{"url":"https://www.mdpi.com/2223-7747/12/2/320/pdf?version=1673332853","host_type":"journal"},{"url":"https://www.mdpi.com/2223-7747/12/2/320/pdf?version=1673332853","host_type":"publisher"},{"url":"https://www.mdpi.com/2223-7747/12/2/320/pdf","host_type":"publisher"},{"url":"https://doi.org/10.3390/plants12020320","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/36679033","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9861903","host_type":"repository"},{"url":"https://doaj.org/article/03c64934714040b898694d83f3e99599","host_type":"repository"},{"url":"https://dx.doi.org/10.3390/plants12020320","host_type":"repository"},{"url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC9861903/pdf/plants-12-00320.pdf","host_type":"repository"},{"url":"https://europepmc.org/articles/PMC9861903","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC9861903?pdf=render","host_type":"Europe_PMC"},{"url":"http://dx.doi.org/10.3390/plants12020320","host_type":""},{"url":"https://hdl.handle.net/11562/1093507","host_type":""}],"fields_of_study":["Genomics and Phylogenetic Studies","Chromosomal and Genetic Variations","Molecular Biology Techniques and Applications","0301 basic medicine","0303 health sciences","03 medical and health sciences"],"mesh_terms":[],"keywords":["Contig","Sequence assembly","Optical mapping","Correctness","Computer science","Scaffold","Genome","Computational biology","Algorithm","Biology","Genetics","Gene","Database","De Novo Genome Assembly","Hi-c","Assembly Refinement","de novo genome assembly; optical mapping; Hi-C; assembly refinement","QK1-989","Botany","Article"],"sdg_mappings":[],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[{"name":"bioproject"}],"source":"live","citation_network_status":"fetched"},"created_at":"2026-07-28T13:07:27.910360Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}