{"doi":"10.1101/gr.280274.124","title":"CGC1, a new reference genome for <i>Caenorhabditis elegans</i>","abstract":"The original 100.3 Mb reference genome for Caenorhabditis elegans , generated from the wild-type laboratory strain N2, has been crucial for analysis of C. elegans since 1998 and has been considered complete since 2005. Unexpectedly, this long-standing reference was shown to be incomplete in 2019 by a genome assembly from the N2-derived strain VC2010. Moreover, genetically divergent versions of N2 have arisen over decades of research and hindered reproducibility of C. elegans genetics and genomics. Here we provide a 106.4 Mb gap-free, telomere-to-telomere genome assembly of C. elegans , generated from CGC1, an isogenic derivative of the N2 strain. We use improved long-read sequencing and manual assembly of 43 recalcitrant genomic regions to overcome deficiencies of prior N2 and VC2010 assemblies and to assemble tandem repeat loci, including a 772 kb sequence for the 45S rRNA genes. Although many differences from earlier assemblies come from repeat regions, unique additions to the genome are also found. Of 19,972 protein-coding genes in the N2 assembly, 19,790 (99.1%) encode products that are unchanged in the CGC1 assembly. The CGC1 assembly also may encode 183 new protein-coding and 163 new ncRNA genes. CGC1 thus provides both a completely defined reference genome and corresponding isogenic wild-type strain for C. elegans , allowing unique opportunities for model and systems biology.","journal":"Genome Research","year":2025,"id":554829,"datarank":0.34454068310334696,"base_score":2.0794415416798357,"endowment":2.0794415416798357,"self_citation_contribution":0.31191623125197543,"citation_network_contribution":0.03262445185137152,"self_endowment_contribution":0.31191623125197543,"citer_contribution":0.03262445185137152,"corpus_percentile":49.12199272839793,"corpus_rank":6578,"citation_count":7,"citer_count":7,"citers_with_citation_signal":3,"citers_with_endowment":3,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9535,"is_data_producer":true,"deposit_databanks":{"BioProject":["PRJDB19205"]},"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":390890,"name":"Massa J. Shoura","orcid":"0000-0003-3278-296X","position":1,"is_corresponding":false},{"id":1175848,"name":"Karen L. Artiles","orcid":"0000-0002-1674-064X","position":2,"is_corresponding":false},{"id":1108214,"name":"Dae‐Eun Jeong","orcid":"0000-0002-9229-4717","position":3,"is_corresponding":false},{"id":1328853,"name":"Chie Owa","orcid":"0000-0002-5241-5414","position":4,"is_corresponding":false},{"id":1329334,"name":"Haruka Kobayashi","orcid":null,"position":5,"is_corresponding":false},{"id":1328854,"name":"Yoshihiko Suzuki","orcid":"0000-0002-8807-2206","position":6,"is_corresponding":false},{"id":1329335,"name":"Manami Kanamori","orcid":null,"position":7,"is_corresponding":false},{"id":1328855,"name":"Yu Toyoshima","orcid":"0000-0001-5239-2235","position":8,"is_corresponding":false},{"id":867401,"name":"Yuichi Iino","orcid":"0000-0002-0936-2660","position":9,"is_corresponding":false},{"id":1328856,"name":"Ann E. Rougvie","orcid":"0000-0002-8743-6143","position":10,"is_corresponding":false},{"id":528578,"name":"Lamia Wahba","orcid":"0000-0001-8369-6864","position":11,"is_corresponding":false},{"id":55768,"name":"Andrew Fire","orcid":"0000-0001-6217-8312","position":12,"is_corresponding":false},{"id":287863,"name":"Erich M. Schwarz","orcid":"0000-0003-3151-4381","position":13,"is_corresponding":false},{"id":24517,"name":"Shinichi Morishita","orcid":"0000-0002-6201-8885","position":14,"is_corresponding":false},{"id":1328852,"name":"Kazuki Ichikawa","orcid":"0009-0003-7884-5126","position":0,"is_corresponding":true}],"reference_count":101,"raw_metadata":null,"created_at":"2026-07-19T02:54:54.542303Z","pmid":"40664475","pmcid":"PMC12315879","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":[]}