{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,7]],"date-time":"2026-07-07T18:19:07Z","timestamp":1783448347354,"version":"3.55.0"},"reference-count":68,"publisher":"Wiley","issue":"4","license":[{"start":{"date-parts":[[2026,5,26]],"date-time":"2026-05-26T00:00:00Z","timestamp":1779753600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"},{"start":{"date-parts":[[2026,5,26]],"date-time":"2026-05-26T00:00:00Z","timestamp":1779753600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Yeast"],"published-print":{"date-parts":[[2026,7]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>\n                    In this study, we introduce a novel approach for analysing long, repetitive genomic sequences. Our methods significantly advance research on rDNA polymorphism. First, we describe a technique for isolating high\u2010molecular\u2010weight DNA from individual chromosomes, enabling selective enrichment of sequencing libraries for extensive genomic regions of interest. Second, we present rDNAmine, a bioinformatic toolkit for capturing and examining large repetitive arrays in Oxford Nanopore sequencing data. This approach facilitates the study of polymorphisms within long repeats, bypassing traditional alignment\u2010based methods and providing a more efficient and scalable solution for investigating repetitive regions. We demonstrate the effectiveness of our approach through the analysis of rDNA arrays in two yeast species,\n                    <jats:italic>Saccharomyces cerevisiae<\/jats:italic>\n                    and\n                    <jats:italic>Candida albicans<\/jats:italic>\n                    . In\n                    <jats:italic>S. cerevisiae<\/jats:italic>\n                    , rDNA arrays show limited polymorphism, while in\n                    <jats:italic>C. albicans<\/jats:italic>\n                    , we observe substantial variation in rDNA module size, with two distinct repeat populations within the array. These findings reveal species\u2010specific differences in the structural organisation of rDNA\n                    <jats:italic>loci<\/jats:italic>\n                    , highlighting the diverse nature of tandem repeat architecture. The rDNAmine toolkit is broadly applicable to various organisms and repetitive genomic contexts, offering a versatile platform for studying repetitive sequences.\n                  <\/jats:p>","DOI":"10.1002\/yea.70023","type":"journal-article","created":{"date-parts":[[2026,5,26]],"date-time":"2026-05-26T13:25:41Z","timestamp":1779801941000},"page":"170-183","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["rDNAmine: A New Tool for the Analysis of Long Repetitive Sequences"],"prefix":"10.1002","volume":"43","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8088-5026","authenticated-orcid":false,"given":"Agnieszka","family":"Czarnocka\u2010Cieciura","sequence":"first","affiliation":[{"name":"Laboratory of RNA Biology, International Institute of Molecular and Cell Biology Warsaw Poland"},{"name":"Institute of Genetics and Biotechnology, Faculty of Biology University of Warsaw Warsaw Poland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Natalia","family":"Gumi\u0144ska","sequence":"additional","affiliation":[{"name":"Laboratory of RNA Biology, International Institute of Molecular and Cell Biology Warsaw Poland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,5,26]]},"reference":[{"key":"e_1_2_9_2_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1009999107"},{"key":"e_1_2_9_3_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0272878"},{"key":"e_1_2_9_4_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2020.107611"},{"key":"e_1_2_9_5_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.sbi.2018.01.008"},{"key":"e_1_2_9_6_1","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-biochem-013118-110817"},{"key":"e_1_2_9_7_1","doi-asserted-by":"publisher","DOI":"10.1093\/femsyr\/foad032"},{"key":"e_1_2_9_8_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.fsigen.2024.103154"},{"key":"e_1_2_9_9_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-10-421"},{"key":"e_1_2_9_10_1","doi-asserted-by":"publisher","DOI":"10.1007\/s10096-023-04590-0"},{"key":"e_1_2_9_11_1","doi-asserted-by":"publisher","DOI":"10.1002\/ctm2.1705"},{"key":"e_1_2_9_12_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.semcdb.2024.01.004"},{"key":"e_1_2_9_13_1","doi-asserted-by":"publisher","DOI":"10.1093\/gigascience\/giab008"},{"key":"e_1_2_9_14_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1574-6968.2001.tb10758.x"},{"key":"e_1_2_9_15_1","doi-asserted-by":"publisher","DOI":"10.1101\/gad.169660"},{"key":"e_1_2_9_16_1","doi-asserted-by":"publisher","DOI":"10.1261\/rna.078925.121"},{"key":"e_1_2_9_17_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkr367"},{"key":"e_1_2_9_18_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2018.11.023"},{"key":"e_1_2_9_19_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.5457707"},{"key":"e_1_2_9_20_1","doi-asserted-by":"publisher","DOI":"10.1128\/MRA.00299-21"},{"key":"e_1_2_9_21_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.protis.2024.126033"},{"key":"e_1_2_9_22_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-025-57787-6"},{"key":"e_1_2_9_23_1","doi-asserted-by":"publisher","DOI":"10.1038\/nprot.2007.94"},{"key":"e_1_2_9_24_1","doi-asserted-by":"publisher","DOI":"10.1002\/1097-0061(200102)18:3<261::AID-YEA670>3.0.CO;2-W"},{"key":"e_1_2_9_25_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.084517.108"},{"key":"e_1_2_9_26_1","doi-asserted-by":"publisher","DOI":"10.1038\/srep28555"},{"key":"e_1_2_9_27_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0401648101"},{"key":"e_1_2_9_28_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1439-0507.2004.01022.x"},{"key":"e_1_2_9_29_1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/mst010"},{"key":"e_1_2_9_30_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-025-94737-0"},{"key":"e_1_2_9_31_1","first-page":"193","volume-title":"Methods in Molecular Biology","author":"Krawczyk P. S.","year":"2024"},{"key":"e_1_2_9_32_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1003329"},{"key":"e_1_2_9_33_1","unstructured":"Li H.2013. Seqtk: A fast and lightweight tool for processing FASTA or FASTQ Sequences [Computer Software]. GitHub.https:\/\/github.com\/lh3\/seqtk."},{"key":"e_1_2_9_34_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btw152"},{"key":"e_1_2_9_35_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty191"},{"key":"e_1_2_9_36_1","doi-asserted-by":"publisher","DOI":"10.1534\/g3.117.044016"},{"key":"e_1_2_9_37_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-023-09343-z"},{"key":"e_1_2_9_38_1","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.3930"},{"key":"e_1_2_9_39_1","doi-asserted-by":"publisher","DOI":"10.1002\/yea.3676"},{"key":"e_1_2_9_40_1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msad048"},{"key":"e_1_2_9_41_1","doi-asserted-by":"publisher","DOI":"10.1099\/00207713-48-1-295"},{"key":"e_1_2_9_42_1","doi-asserted-by":"publisher","DOI":"10.1534\/g3.119.400771"},{"key":"e_1_2_9_43_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1508825112"},{"key":"e_1_2_9_44_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btw369"},{"key":"e_1_2_9_45_1","doi-asserted-by":"publisher","DOI":"10.1093\/ve\/veaf010"},{"key":"e_1_2_9_46_1","doi-asserted-by":"publisher","DOI":"10.1016\/s0168-9525(00)02024-2"},{"key":"e_1_2_9_47_1","doi-asserted-by":"publisher","DOI":"10.1093\/gbe\/evw307"},{"key":"e_1_2_9_48_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-022-02617-x"},{"key":"e_1_2_9_49_1","doi-asserted-by":"publisher","DOI":"10.3390\/biom14050568"},{"key":"e_1_2_9_50_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ygeno.2022.110430"},{"key":"e_1_2_9_51_1","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-0716-2501-9_9"},{"key":"e_1_2_9_52_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-20728-6"},{"key":"e_1_2_9_53_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0092-8674(00)80493-6"},{"key":"e_1_2_9_54_1","doi-asserted-by":"publisher","DOI":"10.3390\/cells10020196"},{"key":"e_1_2_9_55_1","doi-asserted-by":"publisher","DOI":"10.1101\/GR.260836.120"},{"key":"e_1_2_9_56_1","doi-asserted-by":"publisher","DOI":"10.3897\/mbmg.8.121817"},{"key":"e_1_2_9_57_1","doi-asserted-by":"publisher","DOI":"10.1002\/pmic.202000125"},{"key":"e_1_2_9_58_1","doi-asserted-by":"publisher","DOI":"10.3390\/genes10050345"},{"key":"e_1_2_9_59_1","doi-asserted-by":"publisher","DOI":"10.3390\/microorganisms11030804"},{"key":"e_1_2_9_60_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/28.18.3524"},{"key":"e_1_2_9_61_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41437-023-00634-5"},{"key":"e_1_2_9_62_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-13-185"},{"key":"e_1_2_9_63_1","doi-asserted-by":"publisher","DOI":"10.3390\/microorganisms8030316"},{"key":"e_1_2_9_64_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-021-01108-x"},{"key":"e_1_2_9_65_1","unstructured":"Wickham H. D.Navarro andT. L.Pedersen.2016.ggplot2: Elegant Graphics for Data Analysis.2nd ed. 2016 edition.New York NY:Springer.https:\/\/ggplot2-book.org."},{"key":"e_1_2_9_66_1","unstructured":"Wickham H. R.Fran\u00e7ois L.Henry K.M\u00fcller andD.Vaughan.2023.dplyr: A Grammar of Data Manipulation (R package version 1.1.4) [Computer Software].https:\/\/CRAN.R-project.org\/package=dplyr."},{"key":"e_1_2_9_67_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-020-07227-0"},{"key":"e_1_2_9_68_1","doi-asserted-by":"publisher","DOI":"10.1128\/aem.00605-23"},{"key":"e_1_2_9_69_1","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbac146"}],"container-title":["Yeast"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/yea.70023","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/full-xml\/10.1002\/yea.70023","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/yea.70023","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,7]],"date-time":"2026-07-07T18:03:05Z","timestamp":1783447385000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/yea.70023"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,5,26]]},"references-count":68,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2026,7]]}},"alternative-id":["10.1002\/yea.70023"],"URL":"https:\/\/doi.org\/10.1002\/yea.70023","archive":["Portico"],"relation":{"has-preprint":[{"id-type":"doi","id":"10.64898\/2026.02.24.707673","asserted-by":"object"}]},"ISSN":["0749-503X","1097-0061"],"issn-type":[{"value":"0749-503X","type":"print"},{"value":"1097-0061","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,5,26]]},"assertion":[{"value":"2024-05-23","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-05-05","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-05-26","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}