{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,11]],"date-time":"2026-11-11T23:36:57Z","timestamp":1794440217926,"version":"4.9.1"},"reference-count":89,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2026,1,29]],"date-time":"2026-01-29T00:00:00Z","timestamp":1769644800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2026,2,19]],"date-time":"2026-02-19T00:00:00Z","timestamp":1771459200000},"content-version":"vor","delay-in-days":21,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R35GM142924"],"award-info":[{"award-number":["R35GM142924"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Genomics"],"DOI":"10.1186\/s12864-026-12585-2","type":"journal-article","created":{"date-parts":[[2026,1,29]],"date-time":"2026-01-29T09:47:20Z","timestamp":1769680040000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["Genome-wide co-occurrence patterns link mobile genetic elements, antimicrobial resistance and defense systems in Pseudomonas aeruginosa"],"prefix":"10.1186","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1179-3072","authenticated-orcid":false,"given":"Samara T.","family":"Choudhury","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4428-0924","authenticated-orcid":false,"given":"Cheryl P.","family":"Andam","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,1,29]]},"reference":[{"key":"12585_CR1","doi-asserted-by":"publisher","first-page":"178","DOI":"10.1016\/j.imj.2023.05.003","volume":"2","author":"N Sathe","year":"2023","unstructured":"Sathe N, Beech P, Croft L, Suphioglu C, Kapat A, Athan E. Pseudomonas aeruginosa: Infections and novel approaches to treatment \u201cKnowing the enemy\u201d the threat of Pseudomonas aeruginosa and exploring novel approaches to treatment. Infectious Medicine. 2023;2:178\u201394. https:\/\/doi.org\/10.1016\/j.imj.2023.05.003.","journal-title":"Infectious Medicine"},{"key":"12585_CR2","doi-asserted-by":"publisher","first-page":"199","DOI":"10.1038\/s41392-022-01056-1","volume":"7","author":"S Qin","year":"2022","unstructured":"Qin S, Xiao W, Zhou C, Pu Q, Deng X, Lan L, et al. Pseudomonas aeruginosa: pathogenesis, virulence factors, antibiotic resistance, interaction with host, technology advances and emerging therapeutics. Signal Transduct Target Ther. 2022;7:199. https:\/\/doi.org\/10.1038\/s41392-022-01056-1.","journal-title":"Signal Transduct Target Ther"},{"key":"12585_CR3","doi-asserted-by":"publisher","first-page":"220","DOI":"10.1111\/apm.13010","volume":"128","author":"S Crone","year":"2020","unstructured":"Crone S, Vives-Fl\u00f3rez M, Kvich L, Saunders AM, Malone M, Nicolaisen MH, et al. The environmental occurrence of Pseudomonas aeruginosa. APMIS. 2020;128:220\u201331. https:\/\/doi.org\/10.1111\/apm.13010.","journal-title":"APMIS"},{"key":"12585_CR4","doi-asserted-by":"publisher","first-page":"848","DOI":"10.1080\/09603123.2019.1691719","volume":"31","author":"E Kaszab","year":"2021","unstructured":"Kaszab E, Rad\u00f3 J, Kriszt B, P\u00e1szti J, Lesinszki V, Szab\u00f3 A, et al. Groundwater, soil and compost, as possible sources of virulent and antibiotic-resistant Pseudomonas aeruginosa. Int J Environ Health Res. 2021;31:848\u201360. https:\/\/doi.org\/10.1080\/09603123.2019.1691719.","journal-title":"Int J Environ Health Res"},{"key":"12585_CR5","doi-asserted-by":"publisher","first-page":"130","DOI":"10.1186\/1471-2334-6-130","volume":"6","author":"A Kramer","year":"2006","unstructured":"Kramer A, Schwebke I, Kampf G. How long do nosocomial pathogens persist on inanimate surfaces? A systematic review. BMC Infect Dis. 2006;6:130. https:\/\/doi.org\/10.1186\/1471-2334-6-130.","journal-title":"BMC Infect Dis"},{"key":"12585_CR6","first-page":"16","volume":"76","author":"TM Jones","year":"2014","unstructured":"Jones TM, Lutz EA. Environmental survivability and surface sampling efficiencies for Pseudomonas aeruginosa on various fomites. J Environ Health. 2014;76:16\u201320.","journal-title":"J Environ Health"},{"key":"12585_CR7","doi-asserted-by":"publisher","first-page":"1412","DOI":"10.1093\/cid\/cix462","volume":"65","author":"H Kanamori","year":"2017","unstructured":"Kanamori H, Rutala WA, Weber DJ. The role of patient care items as a fomite in healthcare-associated outbreaks and infection prevention. Clin Infect Dis. 2017;65:1412\u20139. https:\/\/doi.org\/10.1093\/cid\/cix462.","journal-title":"Clin Infect Dis"},{"key":"12585_CR8","doi-asserted-by":"publisher","first-page":"665759","DOI":"10.3389\/fcimb.2021.665759","volume":"11","author":"RF Langendonk","year":"2021","unstructured":"Langendonk RF, Neill DR, Fothergill JL. The building blocks of antimicrobial resistance in Pseudomonas aeruginosa: implications for current resistance-breaking therapies. Front Cell Infect Microbiol. 2021;11:665759. https:\/\/doi.org\/10.3389\/fcimb.2021.665759.","journal-title":"Front Cell Infect Microbiol"},{"key":"12585_CR9","doi-asserted-by":"publisher","first-page":"598","DOI":"10.1038\/s41579-024-01054-w","volume":"22","author":"WR Miller","year":"2024","unstructured":"Miller WR, Arias CA. ESKAPE pathogens: antimicrobial resistance, epidemiology, clinical impact and therapeutics. Nat Rev Microbiol. 2024;22:598\u2013616. https:\/\/doi.org\/10.1038\/s41579-024-01054-w.","journal-title":"Nat Rev Microbiol"},{"key":"12585_CR10","doi-asserted-by":"publisher","first-page":"e00031\u201319","DOI":"10.1128\/CMR.00031-19","volume":"32","author":"JP Horcajada","year":"2019","unstructured":"Horcajada JP, Montero M, Oliver A, Sorl\u00ed L, Luque S, G\u00f3mez-Zorrilla S, et al. Epidemiology and treatment of multidrug-resistant and extensively drug-resistant Pseudomonas aeruginosa infections. Clin Microbiol Rev. 2019;32:e00031-19. https:\/\/doi.org\/10.1128\/CMR.00031-19.","journal-title":"Clin Microbiol Rev"},{"key":"12585_CR11","doi-asserted-by":"publisher","first-page":"661","DOI":"10.1007\/s40121-022-00591-2","volume":"11","author":"AJ Kunz Coyne","year":"2022","unstructured":"Kunz Coyne AJ, El Ghali A, Holger D, Rebold N, Rybak MJ. Therapeutic strategies for emerging multidrug-resistant Pseudomonas aeruginosa. Infect Dis Ther. 2022;11:661\u201382. https:\/\/doi.org\/10.1007\/s40121-022-00591-2.","journal-title":"Infect Dis Ther"},{"key":"12585_CR12","doi-asserted-by":"publisher","first-page":"621","DOI":"10.1128\/MMBR.00027-10","volume":"74","author":"VL Kung","year":"2010","unstructured":"Kung VL, Ozer EA, Hauser AR. The accessory genome of Pseudomonas aeruginosa. Microbiol Mol Biol Rev. 2010;74:621\u201341. https:\/\/doi.org\/10.1128\/MMBR.00027-10.","journal-title":"Microbiol Mol Biol Rev"},{"key":"12585_CR13","doi-asserted-by":"publisher","first-page":"109","DOI":"10.1093\/gbe\/evy259","volume":"11","author":"L Freschi","year":"2019","unstructured":"Freschi L, Vincent AT, Jeukens J, Emond-Rheault J-G, Kukavica-Ibrulj I, Dupont M-J, et al. The Pseudomonas aeruginosa pan-genome provides new insights on its population structure, horizontal gene transfer, and pathogenicity. Genome Biol Evol. 2019;11:109\u201320. https:\/\/doi.org\/10.1093\/gbe\/evy259.","journal-title":"Genome Biol Evol"},{"key":"12585_CR14","doi-asserted-by":"publisher","first-page":"55","DOI":"10.4161\/mge.1.1.16432","volume":"1","author":"RW Jackson","year":"2011","unstructured":"Jackson RW, Vinatzer B, Arnold DL, Dorus S, Murillo J. The influence of the accessory genome on bacterial pathogen evolution. Mobile Genet Elem. 2011;1:55\u201365. https:\/\/doi.org\/10.4161\/mge.1.1.16432.","journal-title":"Mobile Genet Elem"},{"key":"12585_CR15","doi-asserted-by":"publisher","first-page":"e1002608","DOI":"10.1371\/journal.ppat.1002608","volume":"8","author":"D Croll","year":"2012","unstructured":"Croll D, McDonald BA. The accessory genome as a cradle for adaptive evolution in pathogens. PLoS Pathog. 2012;8:e1002608. https:\/\/doi.org\/10.1371\/journal.ppat.1002608.","journal-title":"PLoS Pathog"},{"key":"12585_CR16","doi-asserted-by":"publisher","first-page":"20231088","DOI":"10.1098\/rspb.2023.1088","volume":"290","author":"N Takeuchi","year":"2023","unstructured":"Takeuchi N, Hamada-Zhu S, Suzuki H. Prophages and plasmids can display opposite trends in the types of accessory genes they carry. Proc Biol Sci. 2023;290:20231088. https:\/\/doi.org\/10.1098\/rspb.2023.1088.","journal-title":"Proc Biol Sci"},{"key":"12585_CR17","doi-asserted-by":"publisher","first-page":"722","DOI":"10.1038\/nrmicro1235","volume":"3","author":"LS Frost","year":"2005","unstructured":"Frost LS, Leplae R, Summers AO, Toussaint A. Mobile genetic elements: the agents of open source evolution. Nat Rev Microbiol. 2005;3:722\u201332. https:\/\/doi.org\/10.1038\/nrmicro1235.","journal-title":"Nat Rev Microbiol"},{"key":"12585_CR18","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1186\/s13100-018-0141-4","volume":"9","author":"J Botelho","year":"2018","unstructured":"Botelho J, Roberts AP, Le\u00f3n-Sampedro R, Grosso F, Peixe L. Carbapenemases on the move: it\u2019s good to be on ICEs. Mob DNA. 2018;9:37. https:\/\/doi.org\/10.1186\/s13100-018-0141-4.","journal-title":"Mob DNA"},{"key":"12585_CR19","doi-asserted-by":"publisher","first-page":"e0169724","DOI":"10.1128\/aac.01697-24","volume":"69","author":"Y Fang","year":"2025","unstructured":"Fang Y, Song M, Zhang Y, Wu Z, Li X, Guo Y, et al. Evolution of XDR Pseudomonas aeruginosa ST463 strains with two plasmids harboring multiple antimicrobial resistance genes. Antimicrob Agents Chemother. 2025;69:e0169724. https:\/\/doi.org\/10.1128\/aac.01697-24.","journal-title":"Antimicrob Agents Chemother"},{"key":"12585_CR20","doi-asserted-by":"publisher","first-page":"000650","DOI":"10.1099\/mgen.0.000650","volume":"7","author":"RJ Hall","year":"2021","unstructured":"Hall RJ, Whelan FJ, Cummins EA, Connor C, McNally A, McInerney JO. Gene-gene relationships in an Escherichia coli accessory genome are linked to function and mobility. Microb Genom. 2021;7:000650. https:\/\/doi.org\/10.1099\/mgen.0.000650.","journal-title":"Microb Genom"},{"key":"12585_CR21","doi-asserted-by":"publisher","first-page":"243","DOI":"10.1186\/s12859-023-05363-4","volume":"24","author":"RS Mehta","year":"2023","unstructured":"Mehta RS, Petit RA, Read TD, Weissman DB. Detecting patterns of accessory genome coevolution in Staphylococcus aureus using data from thousands of genomes. BMC Bioinformatics. 2023;24:243. https:\/\/doi.org\/10.1186\/s12859-023-05363-4.","journal-title":"BMC Bioinformatics"},{"key":"12585_CR22","doi-asserted-by":"publisher","first-page":"964","DOI":"10.1186\/s12864-015-2153-5","volume":"16","author":"C Pal","year":"2015","unstructured":"Pal C, Bengtsson-Palme J, Kristiansson E, Larsson DGJ. Co-occurrence of resistance genes to antibiotics, biocides and metals reveals novel insights into their co-selection potential. BMC Genomics. 2015;16:964. https:\/\/doi.org\/10.1186\/s12864-015-2153-5.","journal-title":"BMC Genomics"},{"key":"12585_CR23","doi-asserted-by":"publisher","first-page":"369","DOI":"10.1016\/j.jmb.2012.03.009","volume":"419","author":"I Junier","year":"2012","unstructured":"Junier I, H\u00e9risson J, K\u00e9p\u00e8s F. Genomic organization of evolutionarily correlated genes in bacteria: limits and strategies. J Mol Biol. 2012;419:369\u201386. https:\/\/doi.org\/10.1016\/j.jmb.2012.03.009.","journal-title":"J Mol Biol"},{"key":"12585_CR24","doi-asserted-by":"publisher","first-page":"e2304934120","DOI":"10.1073\/pnas.2304934120","volume":"121","author":"AJS Beavan","year":"2024","unstructured":"Beavan AJS, Domingo-Sananes MR, McInerney JO. Contingency, repeatability, and predictability in the evolution of a prokaryotic pangenome. Proc Natl Acad Sci U S A. 2024;121:e2304934120. https:\/\/doi.org\/10.1073\/pnas.2304934120.","journal-title":"Proc Natl Acad Sci U S A"},{"key":"12585_CR25","doi-asserted-by":"publisher","first-page":"20240070","DOI":"10.1098\/rstb.2024.0070","volume":"380","author":"A Kupczok","year":"2025","unstructured":"Kupczok A, Gavriilidou A, Paulitz E, Guerrero-Garc\u00eda L, Baumdicker F. Gene co-occurrence and its association with phage infectivity in bacterial pangenomes. Philos Trans R Soc Lond B Biol Sci. 2025;380:20240070. https:\/\/doi.org\/10.1098\/rstb.2024.0070.","journal-title":"Philos Trans R Soc Lond B Biol Sci"},{"key":"12585_CR26","doi-asserted-by":"publisher","first-page":"e00135\u201319","DOI":"10.1128\/mSphere.00135-19","volume":"4","author":"P Escudeiro","year":"2019","unstructured":"Escudeiro P, Pothier J, Dionisio F, Nogueira T. Antibiotic resistance gene diversity and virulence gene diversity are correlated in human gut and environmental microbiomes. mSphere. 2019;4:e00135-19. https:\/\/doi.org\/10.1128\/mSphere.00135-19.","journal-title":"mSphere"},{"key":"12585_CR27","doi-asserted-by":"publisher","first-page":"1072","DOI":"10.1093\/bioinformatics\/btt086","volume":"29","author":"A Gurevich","year":"2013","unstructured":"Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics. 2013;29:1072\u20135. https:\/\/doi.org\/10.1093\/bioinformatics\/btt086.","journal-title":"Bioinformatics"},{"key":"12585_CR28","doi-asserted-by":"publisher","first-page":"1043","DOI":"10.1101\/gr.186072.114","volume":"25","author":"DH Parks","year":"2015","unstructured":"Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. Checkm: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25:1043\u201355. https:\/\/doi.org\/10.1101\/gr.186072.114.","journal-title":"Genome Res"},{"key":"12585_CR29","doi-asserted-by":"publisher","first-page":"000685","DOI":"10.1099\/mgen.0.000685","volume":"7","author":"O Schwengers","year":"2021","unstructured":"Schwengers O, Jelonek L, Dieckmann MA, Beyvers S, Blom J, Goesmann A. Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification. Microb Genom. 2021;7:000685. https:\/\/doi.org\/10.1099\/mgen.0.000685.","journal-title":"Microb Genom"},{"key":"12585_CR30","doi-asserted-by":"publisher","first-page":"5114","DOI":"10.1038\/s41467-018-07641-9","volume":"9","author":"C Jain","year":"2018","unstructured":"Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun. 2018;9:5114. https:\/\/doi.org\/10.1038\/s41467-018-07641-9.","journal-title":"Nat Commun"},{"key":"12585_CR31","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkaf1040","author":"DH Parks","year":"2025","unstructured":"Parks DH, Chaumeil P-A, Mussig AJ, Rinke C, Chuvochina M, Hugenholtz P. GTDB release 10: a complete and systematic taxonomy for 715 230 bacterial and 17 245 archaeal genomes. Nucleic Acids Res. 2025. https:\/\/doi.org\/10.1093\/nar\/gkaf1040.","journal-title":"Nucleic Acids Res"},{"key":"12585_CR32","doi-asserted-by":"publisher","unstructured":"Rudra B, Duncan L, Shah AJ, Shah HN, Gupta RS. Phylogenomic and comparative genomic studies robustly demarcate two distinct clades of Pseudomonas aeruginosa strains: proposal to transfer the strains from an outlier clade to a novel species Pseudomonas paraeruginosa sp. nov. Int J Syst Evol Microbiol. 2022;72. https:\/\/doi.org\/10.1099\/ijsem.0.005542.","DOI":"10.1099\/ijsem.0.005542"},{"key":"12585_CR33","doi-asserted-by":"publisher","first-page":"e0014925","DOI":"10.1128\/jb.00149-25","volume":"207","author":"M D\u00e9raspe","year":"2025","unstructured":"D\u00e9raspe M, Burrows LL, Voulhoux R, Centr\u00f3n D, Corbeil J, Roy PH. Comparative genomics of Pseudomonas paraeruginosa. J Bacteriol. 2025;207:e0014925. https:\/\/doi.org\/10.1128\/jb.00149-25.","journal-title":"J Bacteriol"},{"key":"12585_CR34","doi-asserted-by":"publisher","first-page":"589","DOI":"10.1016\/j.gde.2005.09.006","volume":"15","author":"D Medini","year":"2005","unstructured":"Medini D, Donati C, Tettelin H, Masignani V, Rappuoli R. The microbial pan-genome. Curr Opin Genet Dev. 2005;15:589\u201394. https:\/\/doi.org\/10.1016\/j.gde.2005.09.006.","journal-title":"Curr Opin Genet Dev"},{"issue":"1","key":"12585_CR35","doi-asserted-by":"publisher","first-page":"180","DOI":"10.1186\/s13059-020-02090-4","volume":"21","author":"G Tonkin-Hill","year":"2020","unstructured":"Tonkin-Hill G, MacAlasdair N, Ruis C, Weimann A, Horesh G, Lees JA, et al. Producing polished prokaryotic pangenomes with the Panaroo pipeline. Genome Biol. 2020;21(1):180. https:\/\/doi.org\/10.1186\/s13059-020-02090-4.","journal-title":"Genome Biol"},{"key":"12585_CR36","doi-asserted-by":"publisher","first-page":"772","DOI":"10.1093\/molbev\/mst010","volume":"30","author":"K Katoh","year":"2013","unstructured":"Katoh K, Standley DM. Mafft multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30:772\u201380. https:\/\/doi.org\/10.1093\/molbev\/mst010.","journal-title":"Mol Biol Evol"},{"key":"12585_CR37","doi-asserted-by":"publisher","first-page":"e000056","DOI":"10.1099\/mgen.0.000056","volume":"2","author":"AJ Page","year":"2016","unstructured":"Page AJ, Taylor B, Delaney AJ, Soares J, Seemann T, Keane JA, et al. Snp-sites: rapid efficient extraction of SNPs from multi-FASTA alignments. Microb Genom. 2016;2:e000056. https:\/\/doi.org\/10.1099\/mgen.0.000056.","journal-title":"Microb Genom"},{"key":"12585_CR38","doi-asserted-by":"publisher","first-page":"1530","DOI":"10.1093\/molbev\/msaa015","volume":"37","author":"BQ Minh","year":"2020","unstructured":"Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD, von Haeseler A, et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol. 2020;37:1530\u20134. https:\/\/doi.org\/10.1093\/molbev\/msaa015.","journal-title":"Mol Biol Evol"},{"key":"12585_CR39","first-page":"57","volume":"17","author":"S Tavar\u00e9","year":"1986","unstructured":"Tavar\u00e9 S. Some probabilistic and statistical problems in the analysis of DNA sequences. Lectures on mathematics in the life sciences. 1986;17:57\u201386.","journal-title":"Lectures on mathematics in the life sciences"},{"key":"12585_CR40","doi-asserted-by":"publisher","first-page":"5539","DOI":"10.1093\/nar\/gkz361","volume":"47","author":"G Tonkin-Hill","year":"2019","unstructured":"Tonkin-Hill G, Lees JA, Bentley SD, Frost SDW, Corander J. Fast hierarchical Bayesian analysis of population structure. Nucleic Acids Res. 2019;47:5539\u201349. https:\/\/doi.org\/10.1093\/nar\/gkz361.","journal-title":"Nucleic Acids Res"},{"key":"12585_CR41","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkae268","author":"I Letunic","year":"2024","unstructured":"Letunic I, Bork P. Interactive tree of life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool. Nucleic Acids Res. 2024. https:\/\/doi.org\/10.1093\/nar\/gkae268.","journal-title":"Nucleic Acids Res"},{"key":"12585_CR42","doi-asserted-by":"publisher","first-page":"124","DOI":"10.12688\/wellcomeopenres.14826.1","volume":"3","author":"KA Jolley","year":"2018","unstructured":"Jolley KA, Bray JE, Maiden MCJ. Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications. Wellcome Open Res. 2018;3:124. https:\/\/doi.org\/10.12688\/wellcomeopenres.14826.1.","journal-title":"Wellcome Open Res"},{"key":"12585_CR43","doi-asserted-by":"publisher","first-page":"5644","DOI":"10.1128\/JCM.42.12.5644-5649.2004","volume":"42","author":"B Curran","year":"2004","unstructured":"Curran B, Jonas D, Grundmann H, Pitt T, Dowson CG. Development of a multilocus sequence typing scheme for the opportunistic pathogen Pseudomonas aeruginosa. J Clin Microbiol. 2004;42:5644\u20139. https:\/\/doi.org\/10.1128\/JCM.42.12.5644-5649.2004.","journal-title":"J Clin Microbiol"},{"issue":"1","key":"12585_CR44","doi-asserted-by":"publisher","first-page":"12728","DOI":"10.1038\/s41598-021-91456-0","volume":"11","author":"M Feldgarden","year":"2021","unstructured":"Feldgarden M, Brover V, Gonzalez-Escalona N, Frye JG, Haendiges J, Haft DH, et al. AMRFinderPlus and the reference gene catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence. Sci Rep. 2021;11(1):12728. https:\/\/doi.org\/10.1038\/s41598-021-91456-0.","journal-title":"Sci Rep"},{"key":"12585_CR45","doi-asserted-by":"publisher","first-page":"D690","DOI":"10.1093\/nar\/gkac920","volume":"51","author":"BP Alcock","year":"2023","unstructured":"Alcock BP, Huynh W, Chalil R, Smith KW, Raphenya AR, Wlodarski MA, et al. CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database. Nucleic Acids Res. 2023;51:D690\u20139. https:\/\/doi.org\/10.1093\/nar\/gkac920.","journal-title":"Nucleic Acids Res"},{"key":"12585_CR46","doi-asserted-by":"publisher","first-page":"e000206","DOI":"10.1099\/mgen.0.000206","volume":"4","author":"J Robertson","year":"2018","unstructured":"Robertson J, Nash JHE. MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies. Microb Genom. 2018;4:e000206. https:\/\/doi.org\/10.1099\/mgen.0.000206.","journal-title":"Microb Genom"},{"key":"12585_CR47","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1186\/s40168-020-00990-y","volume":"9","author":"J Guo","year":"2021","unstructured":"Guo J, Bolduc B, Zayed AA, Varsani A, Dominguez-Huerta G, Delmont TO, et al. Virsorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses. Microbiome. 2021;9:37. https:\/\/doi.org\/10.1186\/s40168-020-00990-y.","journal-title":"Microbiome"},{"key":"12585_CR48","doi-asserted-by":"publisher","first-page":"3340","DOI":"10.1093\/bioinformatics\/btx433","volume":"33","author":"Z Xie","year":"2017","unstructured":"Xie Z, Tang H. Isescan: automated identification of insertion sequence elements in prokaryotic genomes. Bioinformatics. 2017;33:3340\u20137. https:\/\/doi.org\/10.1093\/bioinformatics\/btx433.","journal-title":"Bioinformatics"},{"key":"12585_CR49","doi-asserted-by":"publisher","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","volume":"26","author":"AR Quinlan","year":"2010","unstructured":"Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26:841\u20132. https:\/\/doi.org\/10.1093\/bioinformatics\/btq033.","journal-title":"Bioinformatics"},{"key":"12585_CR50","doi-asserted-by":"publisher","first-page":"649969","DOI":"10.3389\/fmicb.2021.649969","volume":"12","author":"X Hua","year":"2021","unstructured":"Hua X, Liang Q, Deng M, He J, Wang M, Hong W, et al. BacAnt: a combination annotation server for bacterial DNA sequences to identify antibiotic resistance genes, integrons, and transposable elements. Front Microbiol. 2021;12:649969. https:\/\/doi.org\/10.3389\/fmicb.2021.649969.","journal-title":"Front Microbiol"},{"key":"12585_CR51","doi-asserted-by":"publisher","first-page":"mgen000798","DOI":"10.1099\/mgen.0.000798","volume":"8","author":"S Bloomfield","year":"2022","unstructured":"Bloomfield S, Duong VT, Tuyen HT, Campbell JI, Thomson NR, Parkhill J, et al. Mobility of antimicrobial resistance across serovars and disease presentations in non-typhoidal Salmonella from animals and humans in Vietnam. Microb Genom. 2022;8:mgen000798. https:\/\/doi.org\/10.1099\/mgen.0.000798.","journal-title":"Microb Genom"},{"key":"12585_CR52","doi-asserted-by":"publisher","first-page":"2561","DOI":"10.1038\/s41467-022-30269-9","volume":"13","author":"F Tesson","year":"2022","unstructured":"Tesson F, Herv\u00e9 A, Mordret E, Touchon M, d\u2019Humi\u00e8res C, Cury J, et al. Systematic and quantitative view of the antiviral arsenal of prokaryotes. Nat Commun. 2022;13:2561. https:\/\/doi.org\/10.1038\/s41467-022-30269-9.","journal-title":"Nat Commun"},{"key":"12585_CR53","unstructured":"R Core Team. R: A language and environment for statistical computing. 2025.\u00a0https:\/\/www.R-project.org\/."},{"key":"12585_CR54","doi-asserted-by":"crossref","unstructured":"Wickham H. ggplot2: Elegant Graphics for Data Analysis. https:\/\/ggplot2.tidyverse.org. New York, NY, USA: Springer-Verlag; 2016.","DOI":"10.1007\/978-3-319-24277-4_9"},{"key":"12585_CR55","doi-asserted-by":"publisher","first-page":"2847","DOI":"10.1093\/bioinformatics\/btw313","volume":"32","author":"Z Gu","year":"2016","unstructured":"Gu Z, Eils R, Schlesner M. Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics. 2016;32:2847\u20139. https:\/\/doi.org\/10.1093\/bioinformatics\/btw313.","journal-title":"Bioinformatics"},{"key":"12585_CR56","doi-asserted-by":"publisher","first-page":"2498","DOI":"10.1101\/gr.1239303","volume":"13","author":"P Shannon","year":"2003","unstructured":"Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, et al. Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13:2498\u2013504. https:\/\/doi.org\/10.1101\/gr.1239303.","journal-title":"Genome Res"},{"key":"12585_CR57","doi-asserted-by":"publisher","first-page":"2473","DOI":"10.1093\/bioinformatics\/btab007","volume":"37","author":"CLM Gilchrist","year":"2021","unstructured":"Gilchrist CLM, Chooi Y-H. Clinker & clustermap.js: automatic generation of gene cluster comparison figures. Bioinformatics. 2021;37:2473\u20135. https:\/\/doi.org\/10.1093\/bioinformatics\/btab007.","journal-title":"Bioinformatics"},{"key":"12585_CR58","doi-asserted-by":"publisher","first-page":"45","DOI":"10.1186\/s12864-016-2364-4","volume":"17","author":"J Mosquera-Rend\u00f3n","year":"2016","unstructured":"Mosquera-Rend\u00f3n J, Rada-Bravo AM, C\u00e1rdenas-Brito S, Corredor M, Restrepo-Pineda E, Ben\u00edtez-P\u00e1ez A. Pangenome-wide and molecular evolution analyses of the Pseudomonas aeruginosa species. BMC Genomics. 2016;17:45. https:\/\/doi.org\/10.1186\/s12864-016-2364-4.","journal-title":"BMC Genomics"},{"key":"12585_CR59","doi-asserted-by":"publisher","first-page":"e0126468","DOI":"10.1371\/journal.pone.0126468","volume":"10","author":"B Valot","year":"2015","unstructured":"Valot B, Guyeux C, Rolland JY, Mazouzi K, Bertrand X, Hocquet D. What it takes to be a Pseudomonas aeruginosa? The core genome of the opportunistic pathogen updated. PLoS ONE. 2015;10:e0126468. https:\/\/doi.org\/10.1371\/journal.pone.0126468.","journal-title":"PLoS ONE"},{"key":"12585_CR60","doi-asserted-by":"publisher","first-page":"270","DOI":"10.1186\/s13059-019-1890-1","volume":"20","author":"A Vasquez-Rifo","year":"2019","unstructured":"Vasquez-Rifo A, Veksler-Lublinsky I, Cheng Z, Ausubel FM, Ambros V. The Pseudomonas aeruginosa accessory genome elements influence virulence towards Caenorhabditis elegans. Genome Biol. 2019;20:270. https:\/\/doi.org\/10.1186\/s13059-019-1890-1.","journal-title":"Genome Biol"},{"key":"12585_CR61","doi-asserted-by":"publisher","first-page":"236","DOI":"10.1093\/nar\/gkac1220","volume":"51","author":"J Botelho","year":"2023","unstructured":"Botelho J, Cazares A, Schulenburg H. The ESKAPE mobilome contributes to the spread of antimicrobial resistance and CRISPR-mediated conflict between mobile genetic elements. Nucleic Acids Res. 2023;51:236\u201352. https:\/\/doi.org\/10.1093\/nar\/gkac1220.","journal-title":"Nucleic Acids Res"},{"key":"12585_CR62","doi-asserted-by":"publisher","first-page":"1335096","DOI":"10.3389\/fcimb.2024.1335096","volume":"14","author":"M Dolgusevs","year":"2024","unstructured":"Dolgusevs M, Jain N, Savicka O, Vangravs R, Bodrenko J, Bergmanis E, et al. Genomic and phenotypic inconsistencies in Pseudomonas aeruginosa resistome among intensive care patients. Front Cell Infect Microbiol. 2024;14:1335096. https:\/\/doi.org\/10.3389\/fcimb.2024.1335096.","journal-title":"Front Cell Infect Microbiol"},{"key":"12585_CR63","doi-asserted-by":"publisher","first-page":"e0051922","DOI":"10.1128\/msystems.00519-22","volume":"7","author":"B Mahmud","year":"2022","unstructured":"Mahmud B, Wallace MA, Reske KA, Alvarado K, Muenks CE, Rasmussen DA, et al. Epidemiology of plasmid lineages mediating the spread of extended-spectrum beta-lactamases among clinical Escherichia coli. mSystems. 2022;7:e0051922. https:\/\/doi.org\/10.1128\/msystems.00519-22.","journal-title":"mSystems"},{"key":"12585_CR64","doi-asserted-by":"publisher","first-page":"e0062621","DOI":"10.1128\/mSystems.00626-21","volume":"6","author":"V Mateo-Estrada","year":"2021","unstructured":"Mateo-Estrada V, Fern\u00e1ndez-V\u00e1zquez JL, Moreno-Manj\u00f3n J, Hern\u00e1ndez-Gonz\u00e1lez IL, Rodr\u00edguez-Noriega E, Morf\u00edn-Otero R, et al. Accessory genomic epidemiology of cocirculating Acinetobacter baumannii clones. mSystems. 2021;6:e0062621. https:\/\/doi.org\/10.1128\/mSystems.00626-21.","journal-title":"mSystems"},{"key":"12585_CR65","doi-asserted-by":"publisher","first-page":"R1094","DOI":"10.1016\/j.cub.2019.08.012","volume":"29","author":"MA Brockhurst","year":"2019","unstructured":"Brockhurst MA, Harrison E, Hall JPJ, Richards T, McNally A, MacLean C. The ecology and evolution of pangenomes. Curr Biol. 2019;29:R1094\u2013103. https:\/\/doi.org\/10.1016\/j.cub.2019.08.012.","journal-title":"Curr Biol"},{"key":"12585_CR66","doi-asserted-by":"publisher","first-page":"e0075123","DOI":"10.1128\/msphere.00751-23","volume":"9","author":"KR Piper","year":"2024","unstructured":"Piper KR, Ikhimiukor OO, Souza SSR, Garcia-Aroca T, Andam CP. Evolutionary dynamics of the accessory genomes of Staphylococcus aureus. mSphere. 2024;9:e0075123. https:\/\/doi.org\/10.1128\/msphere.00751-23.","journal-title":"mSphere"},{"key":"12585_CR67","doi-asserted-by":"publisher","first-page":"msac232","DOI":"10.1093\/molbev\/msac232","volume":"40","author":"JO McInerney","year":"2023","unstructured":"McInerney JO. Prokaryotic pangenomes act as evolving ecosystems. Mol Biol Evol. 2023;40:msac232. https:\/\/doi.org\/10.1093\/molbev\/msac232.","journal-title":"Mol Biol Evol."},{"key":"12585_CR68","doi-asserted-by":"publisher","first-page":"102282","DOI":"10.1016\/j.mib.2023.102282","volume":"73","author":"T Horne","year":"2023","unstructured":"Horne T, Orr VT, Hall JP. How do interactions between mobile genetic elements affect horizontal gene transfer? Curr Opin Microbiol. 2023;73:102282. https:\/\/doi.org\/10.1016\/j.mib.2023.102282.","journal-title":"Curr Opin Microbiol"},{"key":"12585_CR69","doi-asserted-by":"publisher","first-page":"442","DOI":"10.1080\/22221751.2021.1894903","volume":"10","author":"X Zhang","year":"2021","unstructured":"Zhang X, Wang L, Li D, Li P, Yuan L, Yang F, et al. An incP-2 plasmid sublineage associated with dissemination of blaIMP-45 among carbapenem-resistant Pseudomonas aeruginosa. Emerg Microbes Infect. 2021;10:442\u20139. https:\/\/doi.org\/10.1080\/22221751.2021.1894903.","journal-title":"Emerg Microbes Infect"},{"key":"12585_CR70","doi-asserted-by":"publisher","first-page":"44","DOI":"10.3389\/fmicb.2013.00044","volume":"4","author":"M Popowska","year":"2013","unstructured":"Popowska M, Krawczyk-Balska A. Broad-host-range IncP-1 plasmids and their resistance potential. Front Microbiol. 2013;4:44. https:\/\/doi.org\/10.3389\/fmicb.2013.00044.","journal-title":"Front Microbiol"},{"key":"12585_CR71","doi-asserted-by":"publisher","first-page":"e02122\u201320","DOI":"10.1128\/AAC.02122-20","volume":"65","author":"P Urbanowicz","year":"2021","unstructured":"Urbanowicz P, Bitar I, Izdebski R, Baraniak A, Literacka E, Hrab\u00e1k J, et al. Epidemic territorial spread of IncP-2-type VIM-2 carbapenemase-encoding megaplasmids in nosocomial Pseudomonas aeruginosa populations. Antimicrob Agents Chemother. 2021;65:e02122-20. https:\/\/doi.org\/10.1128\/AAC.02122-20.","journal-title":"Antimicrob Agents Chemother"},{"key":"12585_CR72","doi-asserted-by":"publisher","first-page":"1623241","DOI":"10.3389\/fcimb.2025.1623241","volume":"15","author":"Y Ma","year":"2025","unstructured":"Ma Y, Lei Z, Zhang Y, Liu Q, Zhang F, Zu H, et al. Tracing the evolutionary trajectory of the IncP-2 plasmid co-harboring bla IMP-45 and bla VIM-1: an outbreak of Pseudomonas aeruginosa co-producing IMP-45 and VIM-1 carbapenemases in China. Front Cell Infect Microbiol. 2025;15:1623241. https:\/\/doi.org\/10.3389\/fcimb.2025.1623241.","journal-title":"Front Cell Infect Microbiol"},{"key":"12585_CR73","doi-asserted-by":"publisher","first-page":"4385","DOI":"10.1093\/nar\/gkad282","volume":"51","author":"J Botelho","year":"2023","unstructured":"Botelho J. Defense systems are pervasive across chromosomally integrated mobile genetic elements and are inversely correlated to virulence and antimicrobial resistance. Nucleic Acids Res. 2023;51:4385\u201397. https:\/\/doi.org\/10.1093\/nar\/gkad282.","journal-title":"Nucleic Acids Res"},{"key":"12585_CR74","doi-asserted-by":"publisher","first-page":"889","DOI":"10.3390\/genes11080889","volume":"11","author":"J Botelho","year":"2020","unstructured":"Botelho J, Grosso F, Peixe L. ICEs are the main reservoirs of the ciprofloxacin-modifying crpP gene in Pseudomonas aeruginosa. Genes. 2020;11:889. https:\/\/doi.org\/10.3390\/genes11080889.","journal-title":"Genes"},{"key":"12585_CR75","doi-asserted-by":"publisher","first-page":"57","DOI":"10.1038\/s42003-018-0064-0","volume":"1","author":"Y Ding","year":"2018","unstructured":"Ding Y, Teo JWP, Drautz-Moses DI, Schuster SC, Givskov M, Yang L. Acquisition of resistance to carbapenem and macrolide-mediated quorum sensing inhibition by Pseudomonas aeruginosa via ICETn4371 6385. Commun Biol. 2018;1:57. https:\/\/doi.org\/10.1038\/s42003-018-0064-0.","journal-title":"Commun Biol"},{"key":"12585_CR76","doi-asserted-by":"publisher","first-page":"674974","DOI":"10.3389\/fmicb.2021.674974","volume":"12","author":"H Cai","year":"2021","unstructured":"Cai H, Zhu Y, Hu D, Li Y, Leptihn S, Loh B, et al. Co-harboring of novel bla KPC-2 plasmid and integrative and conjugative element carrying Tn6203 in multidrug-resistant Pseudomonas aeruginosa. Front Microbiol. 2021;12:674974. https:\/\/doi.org\/10.3389\/fmicb.2021.674974.","journal-title":"Front Microbiol"},{"key":"12585_CR77","doi-asserted-by":"publisher","unstructured":"Al-Nayyef H, Guyeux C, Petitjean M, Hocquet D, Bahi JM. Relation between insertion sequences and genome rearrangements in Pseudomonas aeruginosa. In: Ortu\u00f1o F, Rojas I, editors. Bioinformatics and Biomedical Engineering. Cham: Springer International Publishing; 2015. p. 426\u201337. https:\/\/doi.org\/10.1007\/978-3-319-16483-0_42.","DOI":"10.1007\/978-3-319-16483-0_42"},{"key":"12585_CR78","doi-asserted-by":"publisher","first-page":"e0305224","DOI":"10.1128\/mbio.03052-24","volume":"16","author":"WY Ngan","year":"2025","unstructured":"Ngan WY, Parab L, Bertels F, Gallie J. A more significant role for insertion sequences in large-scale rearrangements in bacterial genomes. mBio. 2025;16:e0305224. https:\/\/doi.org\/10.1128\/mbio.03052-24.","journal-title":"mBio."},{"key":"12585_CR79","doi-asserted-by":"publisher","first-page":"e00418","DOI":"10.1128\/mSphere.00418-20","volume":"5","author":"M Razavi","year":"2020","unstructured":"Razavi M, Kristiansson E, Flach C-F, Larsson DGJ. The association between insertion sequences and antibiotic resistance genes. mSphere. 2020;5:e00418-e420. https:\/\/doi.org\/10.1128\/mSphere.00418-20.","journal-title":"mSphere"},{"key":"12585_CR80","doi-asserted-by":"publisher","first-page":"2057","DOI":"10.3389\/fmicb.2018.02057","volume":"9","author":"A van der Zee","year":"2018","unstructured":"van der Zee A, Kraak WB, Burggraaf A, Goessens WHF, Pirovano W, Ossewaarde JM, et al. Spread of carbapenem resistance by transposition and conjugation among Pseudomonas aeruginosa. Front Microbiol. 2018;9:2057. https:\/\/doi.org\/10.3389\/fmicb.2018.02057.","journal-title":"Front Microbiol"},{"key":"12585_CR81","doi-asserted-by":"publisher","first-page":"4366","DOI":"10.1038\/s41467-023-39964-7","volume":"14","author":"Y Sheng","year":"2023","unstructured":"Sheng Y, Wang H, Ou Y, Wu Y, Ding W, Tao M, et al. Insertion sequence transposition inactivates CRISPR-cas immunity. Nat Commun. 2023;14:4366. https:\/\/doi.org\/10.1038\/s41467-023-39964-7.","journal-title":"Nat Commun"},{"key":"12585_CR82","doi-asserted-by":"publisher","first-page":"1240","DOI":"10.1038\/s42003-025-08611-w","volume":"8","author":"S Du","year":"2025","unstructured":"Du S, Wu Z, Wu Y, Yang M, Deng C, Zhang Y, et al. Marine Autographiviridae phages exhibit high genetic diversity and global-scale biogeographic patterns. Commun Biol. 2025;8:1240. https:\/\/doi.org\/10.1038\/s42003-025-08611-w.","journal-title":"Commun Biol"},{"key":"12585_CR83","doi-asserted-by":"publisher","first-page":"6959403","DOI":"10.1155\/2024\/6959403","volume":"2024","author":"LE Romero-Gonz\u00e1lez","year":"2024","unstructured":"Romero-Gonz\u00e1lez LE, Montelongo-Mart\u00ednez LF, Gonz\u00e1lez-Valdez A, Quiroz-Morales SE, Cocotl-Ya\u00f1ez M, Franco-Cendejas R, et al. Pseudomonas aeruginosa isolates from water samples of the Gulf of Mexico show smilar virulence properties but different antibiotic susceptibility profiles than clinical isolates. Int J Microbiol. 2024;2024:6959403. https:\/\/doi.org\/10.1155\/2024\/6959403.","journal-title":"Int J Microbiol"},{"key":"12585_CR84","doi-asserted-by":"publisher","first-page":"1108","DOI":"10.3389\/fmicb.2017.01108","volume":"8","author":"A Colavecchio","year":"2017","unstructured":"Colavecchio A, Cadieux B, Lo A, Goodridge LD. Bacteriophages contribute to the spread of antibiotic resistance genes among foodborne pathogens of the Enterobacteriaceae family - a review. Front Microbiol. 2017;8:1108. https:\/\/doi.org\/10.3389\/fmicb.2017.01108.","journal-title":"Front Microbiol"},{"key":"12585_CR85","doi-asserted-by":"publisher","first-page":"195","DOI":"10.1038\/s41396-022-01338-0","volume":"17","author":"P Blanco-Picazo","year":"2023","unstructured":"Blanco-Picazo P, Morales-Cortes S, Ramos-Barbero MD, Garc\u00eda-Aljaro C, Rodr\u00edguez-Rubio L, Muniesa M. Dominance of phage particles carrying antibiotic resistance genes in the viromes of retail food sources. ISME J. 2023;17:195\u2013203. https:\/\/doi.org\/10.1038\/s41396-022-01338-0.","journal-title":"ISME J"},{"key":"12585_CR86","doi-asserted-by":"publisher","first-page":"e0118922","DOI":"10.1128\/msystems.01189-22","volume":"8","author":"L Putzeys","year":"2023","unstructured":"Putzeys L, Poppeliers J, Boon M, Lood C, Vallino M, Lavigne R. Transcriptomics-driven characterization of LUZ100, a T7-like Pseudomonas phage with temperate features. mSystems. 2023;8:e0118922. https:\/\/doi.org\/10.1128\/msystems.01189-22.","journal-title":"mSystems."},{"key":"12585_CR87","doi-asserted-by":"publisher","first-page":"153","DOI":"10.1186\/s12862-018-1272-4","volume":"18","author":"L-M Bobay","year":"2018","unstructured":"Bobay L-M, Ochman H. Factors driving effective population size and pan-genome evolution in bacteria. BMC Evol Biol. 2018;18:153. https:\/\/doi.org\/10.1186\/s12862-018-1272-4.","journal-title":"BMC Evol Biol"},{"key":"12585_CR88","doi-asserted-by":"publisher","first-page":"evab234","DOI":"10.1093\/gbe\/evab234","volume":"13","author":"GM Douglas","year":"2021","unstructured":"Douglas GM, Shapiro BJ. Genic selection within prokaryotic pangenomes. Genome Biol Evol. 2021;13:evab234. https:\/\/doi.org\/10.1093\/gbe\/evab234.","journal-title":"Genome Biol Evol"},{"key":"12585_CR89","doi-asserted-by":"publisher","first-page":"e0090424","DOI":"10.1128\/msphere.00904-24","volume":"10","author":"TH Chang","year":"2025","unstructured":"Chang TH, Pourtois JD, Haddock NL, Furukawa D, Kelly KE, Amanatullah DF, et al. Prophages are infrequently associated with antibiotic resistance in Pseudomonas aeruginosa clinical isolates. mSphere. 2025;10:e0090424. https:\/\/doi.org\/10.1128\/msphere.00904-24.","journal-title":"mSphere"}],"container-title":["BMC Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12864-026-12585-2","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12864-026-12585-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12864-026-12585-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,2,19]],"date-time":"2026-02-19T14:29:24Z","timestamp":1771511364000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1186\/s12864-026-12585-2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,1,29]]},"references-count":89,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,12]]}},"alternative-id":["12585"],"URL":"https:\/\/doi.org\/10.1186\/s12864-026-12585-2","relation":{},"ISSN":["1471-2164"],"issn-type":[{"value":"1471-2164","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,1,29]]},"assertion":[{"value":"3 November 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"22 January 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"29 January 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"226"}}