{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,1]],"date-time":"2026-07-01T11:39:35Z","timestamp":1782905975383,"version":"3.54.5"},"reference-count":35,"publisher":"Public Library of Science (PLoS)","issue":"12","license":[{"start":{"date-parts":[[2025,12,31]],"date-time":"2025-12-31T00:00:00Z","timestamp":1767139200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Russian Government"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS One"],"abstract":"<jats:p>\n                    Tandem amplification of genomic fragments is quite common in bacteria growing under stress conditions, while spontaneous genome amplification events are rare, unstable and generally poorly described. Plague pathogen\n                    <jats:italic>Yersinia pestis<\/jats:italic>\n                    is a unique microorganism that contains an enormous number of short repeat sequences in its genome and as a result is very prone to spontaneous genome rearrangements including large tandem genome amplification events. Eleven\n                    <jats:italic>Y. pestis<\/jats:italic>\n                    strains sequenced during this study and more than thousand read archives from SRA were analyzed in this study. It was shown that genomes of more than half of\n                    <jats:italic>Y. pestis<\/jats:italic>\n                    laboratory isolates contain tandem repeats. They are mainly caused by the presence of multicopy IS-elements but a few of them are associated with multicopy rRNA clusters, so the rearrangement mechanism is most likely RecA-dependent recombination. Four regions with unstable copy number reproduced between different bioprojects were found. One of them was identified as an integrative mobilizable element carrying a probably incomplete Type 4 secretion system. More interesting, two other reproducible regions were not identified as mobile elements but had the length and GC-content almost identical to the length and GC-content of pMT1 and pCD1 plasmids.\n                  <\/jats:p>","DOI":"10.1371\/journal.pone.0338460","type":"journal-article","created":{"date-parts":[[2025,12,31]],"date-time":"2025-12-31T18:24:26Z","timestamp":1767205466000},"page":"e0338460","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":1,"title":["Systematic analysis of spontaneous tandem genome amplification events in Yersinia pestis"],"prefix":"10.1371","volume":"20","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1217-9234","authenticated-orcid":true,"given":"Dmitry N.","family":"Konanov","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Olga N.","family":"Liubimova","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7752-6321","authenticated-orcid":true,"given":"Alexander V.","family":"Kovrizhnikov","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0009-7266-6657","authenticated-orcid":true,"given":"Ignat V.","family":"Sonets","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alina N.","family":"Balykova","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-9452-0406","authenticated-orcid":true,"given":"Alexandra V.","family":"Lukina-Gronskaya","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anna S.","family":"Speranskaya","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Danil V.","family":"Krivonos","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Galina A.","family":"Eroshenko","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0130-5079","authenticated-orcid":true,"given":"Elena N.","family":"Ilina","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vadim M.","family":"Govorun","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vladimir V.","family":"Kutyrev","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2025,12,31]]},"reference":[{"key":"pone.0338460.ref001","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1146\/annurev-genet-102108-134805","article-title":"Gene amplification and adaptive evolution in bacteria","volume":"43","author":"DI Andersson","year":"2009","journal-title":"Annu Rev Genet"},{"issue":"1","key":"pone.0338460.ref002","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1016\/0022-2836(78)90279-6","article-title":"Tandem genetic duplications in Salmonella typhimurium: amplification of the histidine operon","volume":"126","author":"RP Anderson","year":"1978","journal-title":"J Mol Biol"},{"issue":"1","key":"pone.0338460.ref003","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1111\/1574-6976.12036","article-title":"The role of variable DNA tandem repeats in bacterial adaptation","volume":"38","author":"K Zhou","year":"2014","journal-title":"FEMS Microbiol Rev"},{"issue":"7","key":"pone.0338460.ref004","doi-asserted-by":"crossref","first-page":"2324","DOI":"10.1128\/AAC.01502-06","article-title":"Multicopy blaOXA-58 gene as a source of high-level resistance to carbapenems in Acinetobacter baumannii","volume":"51","author":"A Bertini","year":"2007","journal-title":"Antimicrob Agents Chemother"},{"issue":"5","key":"pone.0338460.ref005","doi-asserted-by":"crossref","first-page":"578","DOI":"10.1016\/j.chom.2014.04.003","article-title":"Retracing the evolutionary path that led to flea-borne transmission of Yersinia pestis","volume":"15","author":"Y-C Sun","year":"2014","journal-title":"Cell Host Microbe"},{"issue":"4","key":"pone.0338460.ref006","doi-asserted-by":"crossref","first-page":"319","DOI":"10.1016\/S1473-3099(13)70323-2","article-title":"Yersinia pestis and the plague of Justinian 541-543 AD: a genomic analysis","volume":"14","author":"DM Wagner","year":"2014","journal-title":"Lancet Infect Dis"},{"issue":"1","key":"pone.0338460.ref007","doi-asserted-by":"crossref","first-page":"2234","DOI":"10.1038\/s41467-018-04550-9","article-title":"Analysis of 3800-year-old Yersinia pestis genomes suggests Bronze Age origin for bubonic plague","volume":"9","author":"MA Spyrou","year":"2018","journal-title":"Nat Commun"},{"key":"pone.0338460.ref008","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1016\/j.cell.2018.11.005","article-title":"Emergence and spread of basal lineages of Yersinia pestis during the Neolithic decline.","volume":"1","author":"N Rascovan","year":"2019","journal-title":"Cell 176"},{"issue":"12","key":"pone.0338460.ref009","doi-asserted-by":"crossref","first-page":"5575","DOI":"10.1099\/ijsem.0.001485","article-title":"Genome-based phylogeny and taxonomy of the \u201cEnterobacteriales\u201d: proposal for Enterobacterales ord. nov. divided into the families Enterobacteriaceae, Erwiniaceae fam. nov., Pectobacteriaceae fam. nov., Yersiniaceae fam. nov., Hafniaceae fam. nov., Morganellaceae fam. nov., and Budviciaceae fam. nov","volume":"66","author":"M Adeolu","year":"2016","journal-title":"Int J Syst Evol Microbiol"},{"key":"pone.0338460.ref010","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1007\/978-94-024-0890-4_14","article-title":"Perspectives on Yersinia pestis: A model for studying zoonotic pathogens","volume-title":"Yersinia pestis: Retrospective and Perspective","author":"R Yang","year":"2016"},{"issue":"6855","key":"pone.0338460.ref011","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1038\/35097083","article-title":"Genome sequence of Yersinia pestis, the causative agent of plague","volume":"413","author":"J Parkhill","year":"2001","journal-title":"Nature"},{"issue":"4","key":"pone.0338460.ref012","doi-asserted-by":"crossref","first-page":"722","DOI":"10.4269\/ajtmh.13-0491","article-title":"Chromosomal rearrangement features of Yersinia pestis strains from natural plague foci in China","volume":"91","author":"Y Liang","year":"2014","journal-title":"Am J Trop Med Hyg"},{"issue":"2","key":"pone.0338460.ref013","doi-asserted-by":"crossref","first-page":"682","DOI":"10.1128\/AAC.47.2.682-688.2003","article-title":"Tandem amplification of a 28-kilobase region from the Yersinia enterocolitica chromosome containing the blaA gene","volume":"47","author":"A Seoane","year":"2003","journal-title":"Antimicrob Agents Chemother"},{"issue":"5","key":"pone.0338460.ref014","doi-asserted-by":"crossref","DOI":"10.1128\/genomeA.01207-16","article-title":"Complete genome sequence of pigmentation-negative yersinia pestis strain cadman","volume":"4","author":"S Lovett","year":"2016","journal-title":"Genome Announc"},{"issue":"6","key":"pone.0338460.ref015","doi-asserted-by":"crossref","first-page":"1685","DOI":"10.1128\/JB.01518-09","article-title":"Genome sequence of the deep-rooted Yersinia pestis strain Angola reveals new insights into the evolution and pangenome of the plague bacterium","volume":"192","author":"M Eppinger","year":"2010","journal-title":"J Bacteriol"},{"key":"pone.0338460.ref016","first-page":"1","article-title":"Insights into Yersinia pestis evolution through rearrangement analysis of 242 complete genomes","author":"Y Wu","year":"2025","journal-title":"Nature Genetics"},{"issue":"1","key":"pone.0338460.ref017","doi-asserted-by":"crossref","first-page":"388","DOI":"10.1038\/s41467-024-55581-4","article-title":"Hotspots of genetic change in Yersinia pestis","volume":"16","author":"Y Wu","year":"2025","journal-title":"Nat Commun"},{"issue":"3","key":"pone.0338460.ref018","article-title":"Small Insertions and Deletions Drive Genomic Plasticity during Adaptive Evolution of Yersinia pestis","volume":"10","author":"Y Wu","year":"2022","journal-title":"Microbiol Spectr"},{"key":"pone.0338460.ref019","first-page":"10","article-title":"Thirty-two complete genome assemblies of nine Yersinia species, including Y. pestis, Y. pseudotuberculosis, and Y. enterocolitica.","volume":"2","author":"SL Johnson","year":"2015","journal-title":"Genome announc"},{"key":"pone.0338460.ref020","article-title":"ICEberg 2.0: an updated database of bacterial integrative and conjugative elements","volume":"47","author":"M Liu","year":"2019","journal-title":"Nucleic Acids Res"},{"issue":"4","key":"pone.0338460.ref021","doi-asserted-by":"crossref","first-page":"57","DOI":"10.21055\/0370-1069-2022-4-57-62","article-title":"Variability of <i>pgm<\/i>\u2011Region Genes in <i>Yersinia pestis<\/i> Strains from the Caspian Sandy and Adjacent Plague Foci","author":"PA Goryunova","year":"2023","journal-title":"Problemy Osobo Opasnykh Infektsii"},{"key":"pone.0338460.ref022","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkae909","article-title":"KEGG: biological systems database as a model of the real world","volume":"53","author":"M Kanehisa","year":"2025","journal-title":"Nucleic Acids Res"},{"issue":"4","key":"pone.0338460.ref023","first-page":"598","article-title":"Overview of Yersinia pestis Metallophores: Yersiniabactin and Yersinopine","volume":"12","author":"T Chaaban","year":"2023","journal-title":"Biology (Basel)"},{"issue":"1","key":"pone.0338460.ref024","doi-asserted-by":"crossref","first-page":"11","DOI":"10.2323\/jgam.51.11","article-title":"Genetic variations in the pgm locus among natural isolates of Yersinia pestis","volume":"51","author":"Z-Z Tong","year":"2005","journal-title":"J Gen Appl Microbiol"},{"key":"pone.0338460.ref025","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1007\/978-94-024-0890-4_6","volume-title":"Yersinia pestis: Retrospective and perspective","author":"Y Cui","year":"2016"},{"issue":"2","key":"pone.0338460.ref026","doi-asserted-by":"crossref","DOI":"10.1101\/cshperspect.a016592","article-title":"Mechanisms of gene duplication and amplification","volume":"7","author":"AB Reams","year":"2015","journal-title":"Cold Spring Harb Perspect Biol"},{"issue":"16","key":"pone.0338460.ref027","doi-asserted-by":"crossref","first-page":"4896","DOI":"10.1128\/JB.181.16.4896-4904.1999","article-title":"High-frequency RecA-dependent and -independent mechanisms of Congo red binding mutations in Yersinia pestis","volume":"181","author":"JM Hare","year":"1999","journal-title":"J Bacteriol"},{"issue":"1","key":"pone.0338460.ref028","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1534\/genetics.113.158519","article-title":"Recombination and annealing pathways compete for substrates in making rrn duplications in Salmonella enterica","volume":"196","author":"AB Reams","year":"2014","journal-title":"Genetics"},{"issue":"4","key":"pone.0338460.ref029","doi-asserted-by":"crossref","DOI":"10.1128\/microbiolspec.MDNA3-0031-2014","article-title":"Copy-out-Paste-in Transposition of IS911: A Major Transposition Pathway","volume":"3","author":"M Chandler","year":"2015","journal-title":"Microbiol Spectr"},{"issue":"23","key":"pone.0338460.ref030","doi-asserted-by":"crossref","first-page":"7945","DOI":"10.1128\/JB.187.23.7945-7954.2005","article-title":"Enterobacterial repetitive intergenic consensus sequence repeats in yersiniae: genomic organization and functional properties","volume":"187","author":"E De Gregorio","year":"2005","journal-title":"J Bacteriol"},{"issue":"3","key":"pone.0338460.ref031","doi-asserted-by":"crossref","first-page":"595","DOI":"10.1128\/JB.186.3.595-600.2004","article-title":"Lysogeny at mid-twentieth century: P1, P2, and other experimental systems","volume":"186","author":"G Bertani","year":"2004","journal-title":"J Bacteriol"},{"issue":"5","key":"pone.0338460.ref032","doi-asserted-by":"crossref","first-page":"834","DOI":"10.1128\/am.18.5.834-837.1969","article-title":"Congo red-agar plating medium for detecting pigmentation in Pasteurella pestis","volume":"18","author":"MJ Surgalla","year":"1969","journal-title":"Appl Microbiol"},{"key":"pone.0338460.ref033","volume-title":"Laboratory diagnostics of particularly dangerous infectious diseases. Practice guidelines","author":"GG Onishchenko","year":"2013"},{"issue":"19","key":"pone.0338460.ref034","doi-asserted-by":"crossref","first-page":"4321","DOI":"10.1093\/nar\/8.19.4321","article-title":"Rapid isolation of high molecular weight plant DNA","volume":"8","author":"MG Murray","year":"1980","journal-title":"Nucleic Acids Res"},{"issue":"3","key":"pone.0338460.ref035","doi-asserted-by":"crossref","first-page":"1365","DOI":"10.1128\/jb.145.3.1365-1373.1981","article-title":"Rapid procedure for detection and isolation of large and small plasmids","volume":"145","author":"CI Kado","year":"1981","journal-title":"J Bacteriol"}],"container-title":["PLOS One"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0338460","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,12,31]],"date-time":"2025-12-31T18:24:31Z","timestamp":1767205471000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0338460"}},"subtitle":[],"editor":[{"given":"Javier Antonio","family":"Benavides-Monta\u00f1o","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2025,12,31]]},"references-count":35,"journal-issue":{"issue":"12","published-online":{"date-parts":[[2025,12,31]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0338460","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,12,31]]}}}