{"doi":"10.1002/yea.3912","title":"Telomere‐to‐telomere <i>Schizosaccharomyces japonicus</i> genome assembly reveals hitherto unknown genome features","abstract":"<jats:title>Abstract</jats:title><jats:p><jats:italic>Schizosaccharomyces japonicus</jats:italic> belongs to the single‐genus class Schizosaccharomycetes, otherwise known as “fission yeasts.” As part of a composite model system with its widely studied <jats:italic>S. pombe</jats:italic> sister species, <jats:italic>S. japonicus</jats:italic> has provided critical insights into the workings and the evolution of cell biological mechanisms. Furthermore, its divergent biology makes <jats:italic>S. japonicus</jats:italic> a valuable model organism in its own right. However, the currently available genome assembly contains gaps and has been unable to resolve centromeres and other repeat‐rich chromosomal regions. Here we present a telomere‐to‐telomere long‐read genome assembly of the <jats:italic>S. japonicus</jats:italic> genome. This includes the three megabase‐length chromosomes, with centromeres hundreds of kilobases long, rich in 5S ribosomal RNA genes, transfer RNA genes, long terminal repeats, and short repeats. We identify a gene‐sparse region on chromosome 2 that resembles a 331 kb centromeric duplication. We revise the genome size of <jats:italic>S. japonicus</jats:italic> to at least 16.6 Mb and possibly up to 18.12 Mb, at least 30% larger than previous estimates. Our whole genome assembly will support the growing <jats:italic>S. japonicus</jats:italic> research community and facilitate research in new directions, including centromere and DNA repeat evolution, and yeast comparative genomics.</jats:p>","journal":"Yeast","year":2024,"id":659625,"datarank":0.31191623125197543,"base_score":2.0794415416798357,"endowment":2.0794415416798357,"self_citation_contribution":0.31191623125197543,"citation_network_contribution":0.0,"self_endowment_contribution":0.31191623125197543,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":7,"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":1721903,"name":"Pei‐Shang Wu","orcid":"0000-0002-4587-7848","position":1,"is_corresponding":false},{"id":598617,"name":"Snezhana Oliferenko","orcid":"0000-0002-8138-6851","position":2,"is_corresponding":false},{"id":1037788,"name":"Frank Uhlmann","orcid":"0000-0002-3527-6619","position":3,"is_corresponding":false},{"id":34445,"name":"Conrad A. Nieduszynski","orcid":"0000-0003-2001-076X","position":4,"is_corresponding":false},{"id":399347,"name":"Graham Etherington","orcid":"0000-0002-5003-1425","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Telomere‐to‐telomere <i>Schizosaccharomyces japonicus</i> genome assembly reveals hitherto unknown genome features","abstract":"<jats:title>Abstract</jats:title><jats:p><jats:italic>Schizosaccharomyces japonicus</jats:italic> belongs to the single‐genus class Schizosaccharomycetes, otherwise known as “fission yeasts.” As part of a composite model system with its widely studied <jats:italic>S. pombe</jats:italic> sister species, <jats:italic>S. japonicus</jats:italic> has provided critical insights into the workings and the evolution of cell biological mechanisms. Furthermore, its divergent biology makes <jats:italic>S. japonicus</jats:italic> a valuable model organism in its own right. However, the currently available genome assembly contains gaps and has been unable to resolve centromeres and other repeat‐rich chromosomal regions. Here we present a telomere‐to‐telomere long‐read genome assembly of the <jats:italic>S. japonicus</jats:italic> genome. This includes the three megabase‐length chromosomes, with centromeres hundreds of kilobases long, rich in 5S ribosomal RNA genes, transfer RNA genes, long terminal repeats, and short repeats. We identify a gene‐sparse region on chromosome 2 that resembles a 331 kb centromeric duplication. We revise the genome size of <jats:italic>S. japonicus</jats:italic> to at least 16.6 Mb and possibly up to 18.12 Mb, at least 30% larger than previous estimates. Our whole genome assembly will support the growing <jats:italic>S. japonicus</jats:italic> research community and facilitate research in new directions, including centromere and DNA repeat evolution, and yeast comparative genomics.</jats:p>","is_dataset_classified":null,"base_score":2.0794415416798357,"endowment":2.0794415416798357,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"38451028","pmcid":null,"openalex_id":"https://openalex.org/W4392551680","authors":[],"funders":[{"funder_name":"Wellcome Trust","grant_id":"220244/Z/20/Z","title":null},{"funder_name":"The Francis Crick Institute","grant_id":"CC2137","title":null},{"funder_name":"Biotechnology and Biological Sciences Research Council","grant_id":" BB/CCG1720/1","title":null},{"funder_name":"Biotechnology and Biological Sciences Research Council","grant_id":"BB/T000481/1","title":null},{"funder_name":"Wellcome Trust","grant_id":"220790","title":"Exploiting divergent biology of two fission yeasts to understand membrane function"},{"funder_name":"Wellcome Trust","grant_id":"103741/Z/14/Z","title":null},{"funder_name":"Wellcome Trust","grant_id":"220244","title":"The Molecular Basis of Sister Chromatid Cohesion"},{"funder_name":"Cancer Research UK","grant_id":"","title":null},{"funder_name":"Cancer Research UK","grant_id":"","title":null}],"total_grants":9,"fwci":0.9564,"citation_percentile":0.71992164,"influential_citations":0,"citation_trend":[{"year":2023,"count":1},{"year":2024,"count":3},{"year":2025,"count":1},{"year":2026,"count":2}],"oa_status":"hybrid","license":"cc-by","oa_locations":[{"url":"https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/yea.3912","host_type":"journal"},{"url":"https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/yea.3912","host_type":"publisher"},{"url":"https://onlinelibrary.wiley.com/doi/pdf/10.1002/yea.3912","host_type":"publisher"},{"url":"http://dx.doi.org/10.1002/yea.3912","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/38451028","host_type":"repository"},{"url":"https://kclpure.kcl.ac.uk/portal/en/publications/0a5a6739-4208-4b72-9b90-951259bbaedd","host_type":"repository"},{"url":"https://ueaeprints.uea.ac.uk/id/eprint/97196/1/Etherington_etal_2024_Yeast.pdf","host_type":"repository"},{"url":"https://kclpure.kcl.ac.uk/portal/files/356979883/Telomere-to-telomere_Schizosaccharomyces_japonicus_genome_assembly_reveals_hitherto_unknown_genome_features_Version_of_Record.pdf","host_type":"repository"},{"url":"https://kclpure.kcl.ac.uk/ws/files/356979883/Telomere-to-telomere_Schizosaccharomyces_japonicus_genome_assembly_reveals_hitherto_unknown_genome_features_Version_of_Record.pdf","host_type":"repository"},{"url":"https://doi.org/10.1002/yea.3912","host_type":"Unpaywall"},{"url":"https://doi.org/10.1101/2023.09.04.556195","host_type":""},{"url":"https://dx.doi.org/10.25418/crick.25398640","host_type":""},{"url":"https://dx.doi.org/10.25418/crick.25398640.v1","host_type":""},{"url":"https://www.scopus.com/pages/publications/85180892429","host_type":""},{"url":"https://doi.org/https://doi.org/10.1002/yea.3912","host_type":""}],"fields_of_study":["Genomics and Phylogenetic Studies","Fungal and yeast genetics research","Chromosomal and Genetic Variations","0301 basic medicine","0303 health sciences","03 medical and health sciences","Schizosaccharomyces","Telomere","Centromere","Schizosaccharomyces japonicus"],"mesh_terms":["Centromere","Schizosaccharomyces","Telomere"],"keywords":["Biology","Genome","Centromere","Schizosaccharomyces pombe","Genetics","Telomere","Chromosome","Gene","Schizosaccharomyces","Eukaryotic chromosome fine structure","Genome size","Comparative genomics","Genomics","Saccharomyces cerevisiae","tRNA","rDNA","Fission yeast","Schizosaccharomyces Japonicus","Model organisms","570","500","Cell Biology","Ecology,Evolution &amp; Ethology","Cell Cycle &amp; Chromosomes","Genetics &amp; Genomics","Computational &amp; Systems Biology"],"sdg_mappings":[{"sdg_number":0,"sdg_label":"Life in Land"}],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-12T07:18:08.060763Z","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":[]}