{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T15:45:47Z","timestamp":1792079147121,"version":"4.4.0"},"reference-count":83,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2025,11,20]],"date-time":"2025-11-20T00:00:00Z","timestamp":1763596800000},"content-version":"vor","delay-in-days":44,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Medical Research Council Career Development Award","award":["UKRI\/MR\/B000331\/1"],"award-info":[{"award-number":["UKRI\/MR\/B000331\/1"]}]},{"DOI":"10.13039\/100004410","name":"EMBO","doi-asserted-by":"publisher","award":["ALTF 139-2024"],"award-info":[{"award-number":["ALTF 139-2024"]}],"id":[{"id":"10.13039\/100004410","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Wellcome Trust PhD studentship","award":["218518\/Z\/19\/Z"],"award-info":[{"award-number":["218518\/Z\/19\/Z"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,10,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Bacteria use diverse defence systems to resist phage predation, many of which cluster within mobile genetic elements (MGEs) and defence islands. In Pseudomonas aeruginosa, genomic and pathogenicity islands\u2014such as the pathogenicity islands (PAPI), genomic islands (PAGI), and Liverpool epidemic strain islands (LESGI)\u2014have been linked to virulence and adaptation, but their contribution to the organization and spread of defence systems remains unexplored. Here, we show that these islands serve as hubs for the assembly and spread of defence systems, revealing an underappreciated role in shaping the bacterium\u2019s antiviral arsenal. We identify 11 conserved hotspots that encode defence and anti-defence genes, but rarely co-occur with virulence factors, resistance genes, or interbacterial competition modules. The frequent co-occurrence of defence and anti-defence genes within these loci points to an ongoing, intense molecular arms race between bacteria, MGEs, and lytic phages. Notably, these hotspots are found beyond their original island contexts, appearing across diverse Pseudomonas species and, in some cases, other genera. Together, our findings expand the known bacterial immunity landscape in P. aeruginosa, redefine the roles of these islands as defence and anti-defence reservoirs, and establish a framework for scalable discovery and annotation of novel defence and anti-defence systems in bacterial genomes.<\/jats:p>","DOI":"10.1093\/nargab\/lqaf148","type":"journal-article","created":{"date-parts":[[2025,11,20]],"date-time":"2025-11-20T03:04:32Z","timestamp":1763607872000},"source":"Crossref","is-referenced-by-count":2,"title":["Genomic islands in\n                    <i>Pseudomonas<\/i>\n                    encode modular hotspots of defence and anti-defence systems"],"prefix":"10.1093","volume":"7","author":[{"given":"Stephen R","family":"Garrett","sequence":"first","affiliation":[{"name":"Michael DeGroote Institute for Infectious Disease Research , Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1 ,","place":["Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Samantha K","family":"Tucker","sequence":"additional","affiliation":[{"name":"School of Infection and Immunity, 120 University Place, University of Glasgow , Glasgow G12 8TA ,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vojtech","family":"Pavelka","sequence":"additional","affiliation":[{"name":"School of Infection and Immunity, 120 University Place, University of Glasgow , Glasgow G12 8TA ,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3698-6134","authenticated-orcid":false,"given":"Andrew J","family":"Roe","sequence":"additional","affiliation":[{"name":"School of Infection and Immunity, 120 University Place, University of Glasgow , Glasgow G12 8TA ,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1197-2123","authenticated-orcid":false,"given":"Giuseppina","family":"Mariano","sequence":"additional","affiliation":[{"name":"School of Infection and Immunity, 120 University Place, University of Glasgow , Glasgow G12 8TA ,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2025,11,19]]},"reference":[{"key":"2025111922042598800_B1","doi-asserted-by":"crossref","DOI":"10.1016\/j.celrep.2023.112672","article-title":"A host of armor: prokaryotic immune strategies against mobile genetic elements","volume":"42","author":"Mayo-Mu\u00f1oz","year":"2023","journal-title":"Cell Rep"},{"key":"2025111922042598800_B2","doi-asserted-by":"publisher","DOI":"10.1101\/2024.08.21.608784","article-title":"Exploring the diversity of anti-defense systems across prokaryotes, phages, and mobile genetic elements","author":"Tesson","year":"2024"},{"key":"2025111922042598800_B3","doi-asserted-by":"publisher","DOI":"10.1101\/2023.12.18.572097","article-title":"Structure and mechanism of Zorya anti-phage defense system","author":"Hu","year":"2023"},{"key":"2025111922042598800_B4","doi-asserted-by":"publisher","first-page":"2344","DOI":"10.1038\/s41467-025-57397-2","article-title":"Modularity of Zorya defense systems during phage inhibition","volume":"16","author":"Mariano","year":"2025","journal-title":"Nat Commun"},{"key":"2025111922042598800_B5","doi-asserted-by":"publisher","first-page":"e1010784","DOI":"10.1371\/journal.pgen.1010784","article-title":"The novel anti-phage system Shield co-opts an RmuC domain to mediate phage defense across Pseudomonas species","volume":"19","author":"Macdonald","year":"2023","journal-title":"PLoS Genet"},{"key":"2025111922042598800_B6","doi-asserted-by":"publisher","first-page":"1556","DOI":"10.1016\/j.chom.2022.09.017","article-title":"An expanded arsenal of immune systems that protect bacteria from phages","volume":"30","author":"Millman","year":"2022","journal-title":"Cell Host Microbe"},{"key":"2025111922042598800_B7","doi-asserted-by":"publisher","first-page":"1077","DOI":"10.1126\/science.aba0372","article-title":"Diverse enzymatic activities mediate antiviral immunity in prokaryotes","volume":"369","author":"Gao","year":"2020","journal-title":"Science"},{"key":"2025111922042598800_B8","doi-asserted-by":"publisher","first-page":"eaar4120","DOI":"10.1126\/science.aar4120","article-title":"Systematic discovery of antiphage defense systems in the microbial pangenome","volume":"359","author":"Doron","year":"2018","journal-title":"Science"},{"key":"2025111922042598800_B9","doi-asserted-by":"publisher","first-page":"1568","DOI":"10.1038\/s41564-022-01219-4","article-title":"A functional selection reveals previously undetected anti-phage defence systems in the E. coli pangenome","volume":"7","author":"Vassallo","year":"2022","journal-title":"Nat Microbiol"},{"key":"2025111922042598800_B10","doi-asserted-by":"publisher","first-page":"740","DOI":"10.1016\/j.chom.2022.02.018","article-title":"Phages and their satellites encode hotspots of antiviral systems","volume":"30","author":"Rousset","year":"2022","journal-title":"Cell Host Microbe"},{"key":"2025111922042598800_B11","doi-asserted-by":"publisher","first-page":"3619","DOI":"10.1016\/j.cell.2023.07.020","article-title":"A conserved family of immune effectors cleaves cellular ATP upon viral infection","volume":"186","author":"Rousset","year":"2023","journal-title":"Cell"},{"key":"2025111922042598800_B12","doi-asserted-by":"publisher","first-page":"1004","DOI":"10.1016\/j.chom.2025.04.021","article-title":"E. coli prophages encode an arsenal of defense systems to protect against temperate phages","volume":"33","author":"Brenes","year":"2025","journal-title":"Cell Host Microbe"},{"key":"2025111922042598800_B13","doi-asserted-by":"publisher","first-page":"115055","DOI":"10.1016\/j.celrep.2024.115055","article-title":"Multi-conflict islands are a widespread trend within Serratia spp","volume-title":"Cell Rep","author":"Cummins","year":"2024"},{"key":"2025111922042598800_B14","doi-asserted-by":"publisher","first-page":"e1010694","DOI":"10.1371\/journal.pgen.1010694","article-title":"The defense island repertoire of the Escherichia coli pan-genome","volume":"19","author":"Hochhauser","year":"2023","journal-title":"PLoS Genet"},{"key":"2025111922042598800_B15","doi-asserted-by":"publisher","first-page":"3268","DOI":"10.1038\/s41564-024-01840-5","article-title":"GMT systems define a new class of mobile elements rich in bacterial defensive and offensive tools","author":"Mahata","year":"2024"},{"key":"2025111922042598800_B16","doi-asserted-by":"publisher","first-page":"e3002746","DOI":"10.1371\/journal.pbio.3002746","article-title":"Comprehensive blueprint of Salmonella genomic plasticity identifies hotspots for pathogenicity genes","volume":"22","author":"Krishnakant\u00a0Kushwaha","year":"2024","journal-title":"PLoS Biol"},{"key":"2025111922042598800_B17","doi-asserted-by":"publisher","DOI":"10.1101\/2024.09.11.612399","article-title":"LoVis4u: locus visualisation tool for comparative genomics","author":"Egorov","year":"2024"},{"key":"2025111922042598800_B18","doi-asserted-by":"publisher","first-page":"eabg2166","DOI":"10.1126\/science.abg2166","article-title":"Temporal shifts in antibiotic resistance elements govern phage-pathogen conflicts","volume":"373","author":"LeGault","year":"2021","journal-title":"Science"},{"key":"2025111922042598800_B19","doi-asserted-by":"publisher","first-page":"1133144","DOI":"10.3389\/fmicb.2023.1133144","article-title":"Broadness and specificity: ardB, ArdA, and Ocr against various restriction-modification systems","volume":"14","author":"Kudryavtseva","year":"2023","journal-title":"Front. Microbiol"},{"key":"2025111922042598800_B20","doi-asserted-by":"publisher","first-page":"8129","DOI":"10.1093\/nar\/gks516","article-title":"Exploring the DNA mimicry of the ocr protein of phage T7","volume":"40","author":"Roberts","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"2025111922042598800_B21","doi-asserted-by":"publisher","first-page":"485","DOI":"10.1093\/nar\/gkx1181","article-title":"Crystal structure of an anti-CRISPR protein, AcrIIA1","volume":"46","author":"Ka","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2025111922042598800_B22","doi-asserted-by":"publisher","first-page":"117","DOI":"10.1016\/j.molcel.2017.05.024","article-title":"Inhibition mechanism of an anti-CRISPR suppressor AcrIIA4 targeting SpyCas9","volume":"67","author":"Yang","year":"2017","journal-title":"Mol Cell"},{"key":"2025111922042598800_B23","doi-asserted-by":"publisher","first-page":"326","DOI":"10.1038\/s41586-022-05375-9","article-title":"Viruses inhibit TIR gcADPR signalling to overcome bacterial defence","volume":"611","author":"Leavitt","year":"2022","journal-title":"Nature"},{"key":"2025111922042598800_B24","doi-asserted-by":"publisher","first-page":"375","DOI":"10.1016\/j.molcel.2023.11.026","article-title":"Phage anti-CBASS protein simultaneously sequesters cyclic trinucleotides and dinucleotides","volume":"84","author":"Cao","year":"2024","journal-title":"Mol Cell"},{"key":"2025111922042598800_B25","doi-asserted-by":"crossref","DOI":"10.1101\/2023.05.01.538930","article-title":"Phages overcome bacterial immunity via diverse anti-defense proteins","author":"Yirmiya","year":"2023"},{"key":"2025111922042598800_B26","doi-asserted-by":"publisher","first-page":"124","DOI":"10.1089\/dcbr.2025.0027","article-title":"MGE-acr clusters in Pseudomonas aeruginosa clinical isolates","volume":"6","author":"Arm\u00e1n","year":"2025","journal-title":"DNA and Cell Biology Reports"},{"key":"2025111922042598800_B27","doi-asserted-by":"publisher","first-page":"186","DOI":"10.1038\/s41586-024-07994-w","article-title":"Diverse anti-defence systems are encoded in the leading region of plasmids","volume":"635","author":"Samuel","year":"2024","journal-title":"Nature"},{"key":"2025111922042598800_B28","doi-asserted-by":"publisher","first-page":"1370","DOI":"10.1038\/s41598-020-80592-8","article-title":"Estimation of pathogenic potential of an environmental Pseudomonas aeruginosa isolate using comparative genomics","volume":"11","author":"Berger","year":"2021","journal-title":"Sci Rep"},{"key":"2025111922042598800_B29","doi-asserted-by":"publisher","first-page":"1210","DOI":"10.3389\/fmicb.2016.01210","article-title":"Identification of novel genomic islands in Liverpool epidemic strain of Pseudomonas aeruginosa using segmentation and clustering","volume":"7","author":"Jani","year":"2016","journal-title":"Front. Microbiol"},{"key":"2025111922042598800_B30","doi-asserted-by":"publisher","first-page":"70","DOI":"10.1111\/j.1574-6968.2008.01406.x","article-title":"Genomic islands of Pseudomonas aeruginosa","volume":"290","author":"Battle","year":"2009","journal-title":"FEMS Microbiol Lett"},{"key":"2025111922042598800_B31","doi-asserted-by":"publisher","first-page":"3249","DOI":"10.1128\/JB.00041-10","article-title":"The Pseudomonas aeruginosa pathogenicity island PAPI-1 is transferred via a novel type IV Pilus","volume":"192","author":"Carter","year":"2010","journal-title":"J Bacteriol"},{"key":"2025111922042598800_B32","doi-asserted-by":"publisher","first-page":"1437","DOI":"10.1128\/IAI.00621-09","article-title":"Pathogenicity islands PAPI-1 and PAPI-2 contribute individually and synergistically to the virulence of Pseudomonas aeruginosa strain PA14","volume":"78","author":"Harrison","year":"2010","journal-title":"Infect Immun"},{"key":"2025111922042598800_B33","doi-asserted-by":"publisher","first-page":"19830","DOI":"10.1073\/pnas.0606810104","article-title":"Interstrain transfer of the large pathogenicity island (PAPI-1) of Pseudomonas aeruginosa","volume":"103","author":"Qiu","year":"2006","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2025111922042598800_B34","doi-asserted-by":"publisher","first-page":"4037","DOI":"10.1128\/JB.02000-05","article-title":"Acquisition and evolution of the exoU locus in Pseudomonas aeruginosa","volume":"188","author":"Kulasekara","year":"2006","journal-title":"J Bacteriol"},{"key":"2025111922042598800_B35","article-title":"Diversity and evolution of an abundant ICEclc-Family of integrative and conjugative elements in Pseudomonas aeruginosa","author":"Benigno","year":"2023"},{"key":"2025111922042598800_B36","doi-asserted-by":"publisher","first-page":"621","DOI":"10.1128\/MMBR.00027-10","article-title":"The accessory genome of Pseudomonas aeruginosa","volume":"74","author":"Kung","year":"2010","journal-title":"Microbiol Mol Biol Rev"},{"key":"2025111922042598800_B37","doi-asserted-by":"publisher","first-page":"2443","DOI":"10.1128\/JB.01688-06","article-title":"Diversity of the abundant pKLC102\/PAGI-2 Family of genomic islands in Pseudomonas aeruginosa","volume":"189","author":"Klockgether","year":"2007","journal-title":"J Bacteriol"},{"key":"2025111922042598800_B38","doi-asserted-by":"publisher","first-page":"4995","DOI":"10.1093\/nar\/gkad317","article-title":"Core defense hotspots within Pseudomonas aeruginosa are a consistent and rich source of anti-phage defense systems","volume":"51","author":"Johnson","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2025111922042598800_B39","doi-asserted-by":"publisher","first-page":"12","DOI":"10.1186\/1745-6150-7-12","article-title":"Domain enhanced lookup time accelerated BLAST","volume":"7","author":"Boratyn","year":"2012","journal-title":"Biol Direct"},{"key":"2025111922042598800_B40","doi-asserted-by":"publisher","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res"},{"key":"2025111922042598800_B41","doi-asserted-by":"publisher","first-page":"D912","DOI":"10.1093\/nar\/gkab1107","article-title":"VFDB 2022: a general classification scheme for bacterial virulence factors","volume":"50","author":"Liu","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2025111922042598800_B42","doi-asserted-by":"publisher","first-page":"2196","DOI":"10.1111\/1462-2920.12794","article-title":"SecReT6: a web-based resource for type VI secretion systems found in bacteria","volume":"17","author":"Li","year":"2015","journal-title":"Environ Microbiol"},{"key":"2025111922042598800_B43","doi-asserted-by":"publisher","first-page":"12","DOI":"10.1101\/gr.086082.108","article-title":"Newly introduced genomic prophage islands are critical determinants of in vivo competitiveness in the Liverpool Epidemic Strain of Pseudomonas aeruginosa","volume":"19","author":"Winstanley","year":"2009","journal-title":"Genome Res"},{"key":"2025111922042598800_B44","doi-asserted-by":"publisher","first-page":"552","DOI":"10.1038\/nrmicro2382","article-title":"Integrative and conjugative elements: mosaic mobile genetic elements enabling dynamic lateral gene flow","volume":"8","author":"Wozniak","year":"2010","journal-title":"Nat Rev Micro"},{"key":"2025111922042598800_B45","doi-asserted-by":"publisher","first-page":"10868","DOI":"10.1093\/nar\/gkab883","article-title":"Identification and classification of antiviral defence systems in bacteria and archaea with PADLOC reveals new system types","volume":"49","author":"Payne","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2025111922042598800_B46","doi-asserted-by":"publisher","DOI":"10.1101\/2024.01.29.577857","article-title":"New antiviral defences are genetically embedded within prokaryotic immune systems","author":"Payne","year":"2024"},{"key":"2025111922042598800_B47","doi-asserted-by":"publisher","first-page":"12728","DOI":"10.1038\/s41598-021-91456-0","article-title":"AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence","volume":"11","author":"Feldgarden","year":"2021","journal-title":"Sci Rep"},{"key":"2025111922042598800_B48","doi-asserted-by":"publisher","first-page":"vbab016","DOI":"10.1093\/bioadv\/vbab016","article-title":"cblaster: a remote search tool for rapid identification and visualization of homologous gene clusters","volume":"1","author":"Gilchrist","year":"2021","journal-title":"Bioinform Adv"},{"key":"2025111922042598800_B49","doi-asserted-by":"publisher","first-page":"D732","DOI":"10.1093\/nar\/gkad935","article-title":"ICEberg 3.0: functional categorization and analysis of the integrative and conjugative elements in bacteria","volume":"52","author":"Wang","year":"2024","journal-title":"Nucleic Acids Res"},{"key":"2025111922042598800_B50","doi-asserted-by":"publisher","first-page":"6913","DOI":"10.1128\/JB.00824-08","article-title":"Integrative conjugative elements and related elements are major contributors to the genome diversity of Streptococcus agalactiae","volume":"190","author":"Brochet","year":"2008","journal-title":"J Bacteriol"},{"key":"2025111922042598800_B51","doi-asserted-by":"publisher","first-page":"86","DOI":"10.1186\/s12929-018-0489-2","article-title":"The role of integrating conjugative elements in Helicobacter pylori: a review","volume":"25","author":"Waskito","year":"2018","journal-title":"J Biomed Sci"},{"key":"2025111922042598800_B52","doi-asserted-by":"publisher","first-page":"11257","DOI":"10.1093\/nar\/gkab906","article-title":"The phage defence island of a multidrug resistant plasmid uses both BREX and type IV restriction for complementary protection from viruses","volume":"49","author":"Picton","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2025111922042598800_B53","doi-asserted-by":"publisher","first-page":"e00623","DOI":"10.1128\/aem.00623-23","article-title":"Diverse Durham collection phages demonstrate complex BREX defense responses","volume":"89","author":"Kelly","year":"2023","journal-title":"Appl Environ Microb"},{"key":"2025111922042598800_B54","doi-asserted-by":"publisher","first-page":"7236","DOI":"10.1038\/s41467-024-51629-7","article-title":"Structure and rational engineering of the PglX methyltransferase and specificity factor for BREX phage defence","volume":"15","author":"Went","year":"2024","journal-title":"Nat Commun"},{"key":"2025111922042598800_B55","doi-asserted-by":"publisher","first-page":"e37459","DOI":"10.1371\/journal.pone.0037459","article-title":"Genetic and phenotypic characterization of a Pseudomonas aeruginosa population with high frequency of genomic islands","volume":"7","author":"Morales-Espinosa","year":"2012","journal-title":"PLoS One"},{"key":"2025111922042598800_B56","doi-asserted-by":"publisher","first-page":"20240076","DOI":"10.1098\/rstb.2024.0076","article-title":"Lineage-specific defence systems of pandemic Vibrio cholerae","volume":"380","author":"Blokesch","year":"2025","journal-title":"Phil. Trans. R. Soc. B"},{"key":"2025111922042598800_B57","doi-asserted-by":"publisher","first-page":"4385","DOI":"10.1093\/nar\/gkad282","article-title":"Defense systems are pervasive across chromosomally integrated mobile genetic elements and are inversely correlated to virulence and antimicrobial resistance","volume":"51","author":"Botelho","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2025111922042598800_B58","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/nar\/gkab006","article-title":"Mobile element warfare via CRISPR and anti-CRISPR in Pseudomonas aeruginosa","volume":"49","author":"Le\u00f3n","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2025111922042598800_B59","doi-asserted-by":"publisher","first-page":"e1010065","DOI":"10.1371\/journal.pgen.1010065","article-title":"Interactions between mobile genetic elements: an anti-phage gene in an integrative and conjugative element protects host cells from predation by a temperate bacteriophage","volume":"18","author":"Johnson","year":"2022","journal-title":"PLoS Genet"},{"key":"2025111922042598800_B60","first-page":"000729","article-title":"A Campylobacter integrative and conjugative element with a CRISPR-Cas9 system targeting competing plasmids: a history of plasmid warfare?","volume":"7","author":"van\u00a0Vliet","year":"2021","journal-title":"Microb Genom"},{"key":"2025111922042598800_B61","doi-asserted-by":"publisher","first-page":"603","DOI":"10.1146\/annurev-micro-032521-022006","article-title":"Mobile genetic element flexibility as an underlying principle to bacterial evolution","volume":"77","author":"Weisberg","year":"2023","journal-title":"Annu. Rev. Microbiol"},{"key":"2025111922042598800_B62","doi-asserted-by":"publisher","first-page":"620","DOI":"10.1038\/s41564-020-0692-2","article-title":"Broad-spectrum anti-CRISPR proteins facilitate horizontal gene transfer","volume":"5","author":"Mahendra","year":"2020","journal-title":"Nat Microbiol"},{"key":"2025111922042598800_B63","doi-asserted-by":"publisher","first-page":"323","DOI":"10.1038\/s41586-022-04546-y","article-title":"Two defence systems eliminate plasmids from 7th pandemic Vibrio cholerae","volume":"604","author":"Jask\u00f3lska","year":"2022","journal-title":"Nature"},{"key":"2025111922042598800_B64","doi-asserted-by":"publisher","DOI":"10.1101\/2025.01.08.631726","article-title":"DefensePredictor: a machine learning model to discover novel prokaryotic immune systems","author":"DeWeirdt","year":"2025"},{"key":"2025111922042598800_B65","doi-asserted-by":"publisher","DOI":"10.1101\/2025.01.08.631966","article-title":"Protein and genomic language models chart a vast landscape of antiphage defenses","author":"Mordret","year":"2025"},{"key":"2025111922042598800_B66","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1038\/s42003-025-07459-4","article-title":"In silico characterization of defense system hotspots in Acinetobacter spp","volume":"8","author":"Yi","year":"2025","journal-title":"Commun Biol"},{"key":"2025111922042598800_B67","doi-asserted-by":"publisher","first-page":"90","DOI":"10.1109\/MCSE.2007.55","article-title":"Matplotlib: a 2D graphics environment","volume":"9","author":"Hunter","year":"2007","journal-title":"Comput. Sci. Eng"},{"key":"2025111922042598800_B68","author":"McKinney","year":"2011"},{"key":"2025111922042598800_B69","doi-asserted-by":"publisher","first-page":"2473","DOI":"10.1093\/bioinformatics\/btab007","article-title":"clinker & clustermap.Js: automatic generation of gene cluster comparison figures","volume":"37","author":"Gilchrist","year":"2021","journal-title":"Bioinformatics"},{"key":"2025111922042598800_B70","doi-asserted-by":"publisher","first-page":"2561","DOI":"10.1038\/s41467-022-30269-9","article-title":"Systematic and quantitative view of the antiviral arsenal of prokaryotes","volume":"13","author":"Tesson","year":"2022","journal-title":"Nat Commun"},{"key":"2025111922042598800_B71","article-title":"A general introduction to the E-utilities","volume-title":"Entrez Programming Utilities Help [Internet]","author":"Sayers","year":"2022"},{"key":"2025111922042598800_B72","volume-title":"Efficient \u2018Pythonic\u2019 access to FASTA Files Using pyfaidx PeerJ Inc","author":"Shirley","year":"2015"},{"key":"2025111922042598800_B73","doi-asserted-by":"publisher","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"BEDTools: a flexible suite of utilities for comparing genomic features","volume":"26","author":"Quinlan","year":"2010","journal-title":"Bioinformatics"},{"key":"2025111922042598800_B74","doi-asserted-by":"publisher","first-page":"1422","DOI":"10.1093\/bioinformatics\/btp163","article-title":"Biopython: freely available Python tools for computational molecular biology and bioinformatics","volume":"25","author":"Cock","year":"2009","journal-title":"Bioinformatics"},{"key":"2025111922042598800_B75","doi-asserted-by":"publisher","first-page":"1026","DOI":"10.1038\/nbt.3988","article-title":"MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets","volume":"35","author":"Steinegger","year":"2017","journal-title":"Nat Biotechnol"},{"key":"2025111922042598800_B76","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1186\/1471-2105-5-113","article-title":"MUSCLE: a multiple sequence alignment method with reduced time and space complexity","volume":"5","author":"Edgar","year":"2004","journal-title":"BMC Bioinf"},{"key":"2025111922042598800_B77","doi-asserted-by":"publisher","first-page":"e1002195","DOI":"10.1371\/journal.pcbi.1002195","article-title":"Accelerated profile HMM searches","volume":"7","author":"Eddy","year":"2011","journal-title":"PLoS Comput Biol"},{"key":"2025111922042598800_B78","doi-asserted-by":"publisher","first-page":"D412","DOI":"10.1093\/nar\/gkaa913","article-title":"Pfam: the protein families database in 2021","volume":"49","author":"Mistry","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2025111922042598800_B79","doi-asserted-by":"publisher","first-page":"1762","DOI":"10.21105\/joss.01762","article-title":"Mashtree: a rapid comparison of whole genome sequence files","volume":"4","author":"Katz","year":"2019","journal-title":"JOSS"},{"key":"2025111922042598800_B80","author":"Wickham","year":"2016"},{"key":"2025111922042598800_B81","doi-asserted-by":"publisher","first-page":"28","DOI":"10.1111\/2041-210X.12628","article-title":"ggtree: an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data","volume":"8","author":"Yu","year":"2017","journal-title":"Methods Ecol Evol"},{"key":"2025111922042598800_B82","doi-asserted-by":"publisher","first-page":"309","DOI":"10.1111\/j.1469-1809.1955.tb01285.x","article-title":"The estimation and significance of the logarithm of a ratio of frequencies","volume":"20","author":"Haldane","year":"1956","journal-title":"Ann Hum Genet"},{"key":"2025111922042598800_B83","doi-asserted-by":"publisher","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the false discovery rate: a practical and powerful approach to multiple testing","volume":"57","author":"Benjamini","year":"1995","journal-title":"J R Stat Soc Series B Stat Methodol"}],"container-title":["NAR Genomics and Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/nargab\/article-pdf\/7\/4\/lqaf148\/65397838\/lqaf148.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/nargab\/article-pdf\/7\/4\/lqaf148\/65397838\/lqaf148.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,11,20]],"date-time":"2025-11-20T03:04:39Z","timestamp":1763607879000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nargab\/article\/doi\/10.1093\/nargab\/lqaf148\/8328389"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,10,7]]},"references-count":83,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2025,10,7]]}},"URL":"https:\/\/doi.org\/10.1093\/nargab\/lqaf148","relation":{},"ISSN":["2631-9268"],"issn-type":[{"value":"2631-9268","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2025,12]]},"published":{"date-parts":[[2025,10,7]]},"article-number":"lqaf148"}}