{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,22]],"date-time":"2026-07-22T16:06:20Z","timestamp":1784736380828,"version":"3.55.0"},"reference-count":158,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2026,7,10]],"date-time":"2026-07-10T00:00:00Z","timestamp":1783641600000},"content-version":"vor","delay-in-days":9,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"NSF-CAREER"},{"name":"U.S. National Science Foundation, Plant-Biotic Interactions Program","award":["1942956"],"award-info":[{"award-number":["1942956"]}]},{"name":"USDA-NIFA","award":["7005375"],"award-info":[{"award-number":["7005375"]}]},{"name":"Presidential Graduate"},{"DOI":"10.13039\/100007579","name":"Auburn University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100007579","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Bacterial plant pathogens have ravaged crops since the dawn of agriculture and continue to pose a serious threat today. Bacteria and their plant hosts have co-evolved in an evolutionary arms race, with artificial selection due to agriculture tipping the scale in favor of the pathogen. This review gives an overview of plant pathogenic bacterial diversity, showing that pathogenicity has independently evolved numerous times, and that there is not one unifying trait determining plant pathogenicity. Instead, these bacteria represent repeated, independent evolutionary transitions driven by life in complex ecological networks that include plant hosts, insect vectors, microbial competitors, and highly heterogeneous abiotic environments. Their genomes reflect this interplay through a dynamic balance of architecture and flux. These structural features, along with highly variable pangenomes, capture the balance between genome stability and flux imposed by ecological constraints and epidemiological dynamics. Horizontal gene transfer via conjugative plasmids, prophages, integrative and conjugative elements, transposons, and in some lineages, natural competence, remains the major source of adaptive novelty, enabling rapid remodeling of virulence repertoires, metabolic capabilities, and antibiotic or heavy metal resistance genes. These changes create distinct selective landscapes. Agricultural practices such as chemical use, host resistance deployment, or seed trade, can drive recurrent bottlenecks, expansions, and admixture events that leave strong genomic signatures in pathogens. Finally, this review explores the genomic differences enabling the divergence of lifestyles, while also acknowledging knowledge gaps and future directions of research on the evolution of bacterial plant pathogens.<\/jats:p>","DOI":"10.1093\/gbe\/evag174","type":"journal-article","created":{"date-parts":[[2026,7,10]],"date-time":"2026-07-10T06:29:44Z","timestamp":1783664984000},"source":"Crossref","is-referenced-by-count":0,"title":["Genome Evolution in Plant Pathogenic Bacteria"],"prefix":"10.1093","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0009-0003-6988-5273","authenticated-orcid":false,"given":"Kylie S","family":"Weis","sequence":"first","affiliation":[{"name":"Department of Entomology and Plant Pathology, Auburn University , Auburn, AL ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-9467-5424","authenticated-orcid":false,"given":"Amanpreet","family":"Kaur","sequence":"additional","affiliation":[{"name":"Department of Entomology and Plant Pathology, Auburn University , Auburn, AL ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-8146-2550","authenticated-orcid":false,"given":"Palash","family":"Ghosh","sequence":"additional","affiliation":[{"name":"Department of Entomology and Plant Pathology, Auburn University , Auburn, AL ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5418-5894","authenticated-orcid":false,"given":"Neha","family":"Potnis","sequence":"additional","affiliation":[{"name":"Department of Entomology and Plant Pathology, Auburn University , Auburn, AL ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,7,10]]},"reference":[{"key":"2026072211565317500_evag174-B1","doi-asserted-by":"publisher","first-page":"321","DOI":"10.3389\/fmicb.2014.00321","article-title":"The filamentous phage XacF1 causes loss of virulence in Xanthomonas axonopodis pv. citri, the causative agent of citrus canker disease","volume":"5","author":"Ahmad","year":"2014","journal-title":"Front Microbiol"},{"key":"2026072211565317500_evag174-B2","doi-asserted-by":"publisher","first-page":"eadx7408","DOI":"10.1126\/sciadv.adx7408","article-title":"Chromosome architecture affects virulence and competitiveness in Agrobacterium tumefaciens C58","volume":"11","author":"Aliu","year":"2025","journal-title":"Sci Adv"},{"key":"2026072211565317500_evag174-B3","doi-asserted-by":"publisher","first-page":"535","DOI":"10.1016\/j.tree.2004.07.021","article-title":"Emerging infectious diseases of plants: pathogen pollution, climate change and agrotechnology drivers","volume":"19","author":"Anderson","year":"2004","journal-title":"Trends Ecol Evol."},{"key":"2026072211565317500_evag174-B4","doi-asserted-by":"publisher","DOI":"10.1128\/mbio.00323-24","article-title":"A pangenomic atlas reveals eco-evolutionary dynamics that shape type VI secretion systems in plant-pathogenic Ralstonia","volume":"15","author":"Aoun","year":"2024","journal-title":"mBio"},{"key":"2026072211565317500_evag174-B5","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.02528-20","article-title":"A large Tn7-like transposon confers hyperresistance to copper in Pseudomonas syringae pv. syringae","volume":"87","author":"Aprile","year":"2021","journal-title":"Appl Environ Microbiol"},{"key":"2026072211565317500_evag174-B6","doi-asserted-by":"publisher","first-page":"251","DOI":"10.1099\/mic.0.000715","article-title":"Pseudomonas syringae: enterprising epiphyte and stealthy parasite: this article is part of the microbe profiles collection","volume":"165","author":"Arnold","year":"2019","journal-title":"Microbiology"},{"key":"2026072211565317500_evag174-B7","doi-asserted-by":"publisher","first-page":"1084","DOI":"10.1016\/j.tim.2024.04.001","article-title":"Tradeoffs and constraints on the evolution of tailocins","volume":"32","author":"Backman","year":"2024","journal-title":"Trends Microbiol."},{"key":"2026072211565317500_evag174-B8","doi-asserted-by":"publisher","DOI":"10.1128\/aem.01102-24","article-title":"The vector regulation hypothesis: dynamic competition between pathogen and vector behaviors constrains Xylella fastidiosa biofilm development in sharpshooter foreguts","volume":"90","author":"Backus","year":"2024","journal-title":"Appl Environ Microbiol"},{"key":"2026072211565317500_evag174-B9","doi-asserted-by":"publisher","first-page":"237","DOI":"10.1038\/s41396-018-0261-3","article-title":"Localized recombination drives diversification of killing spectra for phage-derived syringacins","volume":"13","author":"Baltrus","year":"2019","journal-title":"ISME J"},{"key":"2026072211565317500_evag174-B10","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0025773","article-title":"Miniature transposable sequences are frequently mobilized in the bacterial plant pathogen Pseudomonas syringae pv. Phaseolicola","volume":"6","author":"Bardaji","year":"2011","journal-title":"PLoS One"},{"key":"2026072211565317500_evag174-B11","doi-asserted-by":"publisher","first-page":"161","DOI":"10.1007\/BF02373702","article-title":"Survival ofXanthomonas campestris pv.vesictoria in pepper seeds and roots in symptomless and dry leaves in non-host plants and in the soil","volume":"68","author":"Bashan","year":"1982","journal-title":"Plant Soil"},{"key":"2026072211565317500_evag174-B12","doi-asserted-by":"publisher","first-page":"884","DOI":"10.1016\/j.cell.2013.01.042","article-title":"Tit-for-tat: type VI secretion system counterattack during bacterial cell-cell interactions","volume":"152","author":"Basler","year":"2013","journal-title":"Cell"},{"key":"2026072211565317500_evag174-B13","doi-asserted-by":"publisher","first-page":"671","DOI":"10.1007\/s10658-016-1035-2","article-title":"Characterization of a unique copper resistance gene cluster in Xanthomonas campestris pv. campestris isolated in Trinidad, West Indies","volume":"147","author":"Behlau","year":"2017","journal-title":"Eur J Plant Pathol"},{"key":"2026072211565317500_evag174-B14","doi-asserted-by":"publisher","first-page":"170","DOI":"10.1128\/aem.56.1.170-175.1990","article-title":"Characterization of pXV10A, a copper resistance plasmid in Xanthomonas campestris pv. vesicatoria","volume":"56","author":"Bender","year":"1990","journal-title":"Appl Environ Microbiol"},{"key":"2026072211565317500_evag174-B15","doi-asserted-by":"publisher","first-page":"238","DOI":"10.1111\/mpp.12526","article-title":"The enemy within: phloem-limited pathogens","volume":"19","author":"Bendix","year":"2018","journal-title":"Mol Plant Pathol."},{"key":"2026072211565317500_evag174-B16","doi-asserted-by":"publisher","DOI":"10.1111\/mec.70033","article-title":"Interaction between climatic variation and pathogen diversity shape endemic disease dynamics in the agricultural settings","volume":"34","author":"Bhandari","year":"2025","journal-title":"Mol Ecol."},{"key":"2026072211565317500_evag174-B17","doi-asserted-by":"publisher","first-page":"24","DOI":"10.1038\/s43705-023-00232-w","article-title":"Xanthomonas infection and ozone stress distinctly influence the microbial community structure and interactions in the pepper phyllosphere","volume":"3","author":"Bhandari","year":"2023","journal-title":"ISME Commun"},{"key":"2026072211565317500_evag174-B18","doi-asserted-by":"publisher","first-page":"1394","DOI":"10.1094\/PHYTO-02-23-0077-SC","article-title":"A brief evaluation of a copper resistance Mobile genetic island in the bacterial leaf spot pathogen Xanthomonas euvesicatoria pv. perforans","volume":"113","author":"Bibi","year":"2023","journal-title":"Phytopathology"},{"key":"2026072211565317500_evag174-B19","doi-asserted-by":"publisher","first-page":"2466","DOI":"10.1093\/plcell\/koac076","article-title":"The multiple fates of gene duplications: deletion, hypofunctionalization, subfunctionalization, neofunctionalization, dosage balance constraints, and neutral variation","volume":"34","author":"Birchler","year":"2022","journal-title":"Plant Cell"},{"key":"2026072211565317500_evag174-B20","doi-asserted-by":"publisher","first-page":"3348","DOI":"10.1093\/nar\/gkac147","article-title":"A mobile restriction\u2013modification system provides phage defence and resolves an epigenetic conflict with an antagonistic endonuclease","volume":"50","author":"Birkholz","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"2026072211565317500_evag174-B21","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0000224","article-title":"Plant carbohydrate scavenging through TonB-dependent receptors: a feature shared by phytopathogenic and aquatic Bacteria","volume":"2","author":"Blanvillain","year":"2007","journal-title":"PLoS One"},{"key":"2026072211565317500_evag174-B22","doi-asserted-by":"publisher","first-page":"1307349","DOI":"10.3389\/fmicb.2023.1307349","article-title":"Soft rot pathogen Dickeya dadantii 3937 produces tailocins resembling the tails of Peduovirus P2","volume":"14","author":"Borowicz","year":"2023","journal-title":"Front Microbiol"},{"key":"2026072211565317500_evag174-B23","doi-asserted-by":"publisher","first-page":"ycag012","DOI":"10.1093\/ismeco\/ycag012","article-title":"Beyond kin killing: Dickeya-derived phage-tail-like bacteriocin P2D1 targets phylogenetically distant pseudomonas spp","volume":"6","author":"Borowicz","year":"2026","journal-title":"ISME Commun"},{"key":"2026072211565317500_evag174-B24","doi-asserted-by":"publisher","first-page":"fiv081","DOI":"10.1093\/femsec\/fiv081","article-title":"Assessment of the genetic and phenotypic diversity among rhizogenic Agrobacterium biovar 1 strains infecting solanaceous and cucurbit crops","volume":"91","author":"Bosmans","year":"2015","journal-title":"FEMS Microbiol Ecol."},{"key":"2026072211565317500_evag174-B25","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1002130","article-title":"The plant pathogen Pseudomonas syringae pv. Tomato is genetically monomorphic and under strong selection to evade tomato immunity","volume":"7","author":"Cai","year":"2011","journal-title":"PLoS Pathog."},{"key":"2026072211565317500_evag174-B26","doi-asserted-by":"publisher","first-page":"2289","DOI":"10.1038\/s41396-021-00921-1","article-title":"Systematic discovery of pseudomonad genetic factors involved in sensitivity to tailocins","volume":"15","author":"Carim","year":"2021","journal-title":"ISME J"},{"key":"2026072211565317500_evag174-B27","doi-asserted-by":"publisher","first-page":"7838","DOI":"10.1038\/s41467-023-43648-7","article-title":"The protein interactome of the citrus huanglongbing pathogen Candidatus Liberibacter asiaticus","volume":"14","author":"Carter","year":"2023","journal-title":"Nat Commun"},{"key":"2026072211565317500_evag174-B28","doi-asserted-by":"publisher","first-page":"935","DOI":"10.1111\/mpp.12579","article-title":"Pseudomonas syringae pv. Tomato DC3000 polymutants deploying coronatine and two type III effectors produce quantifiable chlorotic spots from individual bacterial colonies in Nicotiana benthamiana leaves","volume":"19","author":"Chakravarthy","year":"2018","journal-title":"Mol Plant Pathol."},{"key":"2026072211565317500_evag174-B29","doi-asserted-by":"publisher","DOI":"10.1128\/mbio.01648-22","article-title":"Single seed Microbiota: assembly and transmission from parent plant to seedling","volume":"13","author":"Chesneau","year":"2022","journal-title":"mBio"},{"key":"2026072211565317500_evag174-B30","doi-asserted-by":"publisher","first-page":"465","DOI":"10.1105\/tpc.105.036574","article-title":"The Arabidopsis receptor kinase FLS2 binds flg22 and determines the specificity of flagellin perception","volume":"18","author":"Chinchilla","year":"2006","journal-title":"Plant Cell"},{"key":"2026072211565317500_evag174-B31","doi-asserted-by":"publisher","first-page":"875","DOI":"10.1111\/mpp.12337","article-title":"Comparison of gene activation by two TAL effectors from X anthomonas axonopodis pv. manihotis reveals candidate host susceptibility genes in cassava","volume":"17","author":"Cohn","year":"2016","journal-title":"Mol Plant Pathol"},{"key":"2026072211565317500_evag174-B32","doi-asserted-by":"publisher","first-page":"819","DOI":"10.1111\/1462-2920.13662","article-title":"Evolution of copper resistance in the kiwifruit pathogen P seudomonas syringae pv. actinidiae through acquisition of integrative conjugative elements and plasmids","volume":"19","author":"Colombi","year":"2017","journal-title":"Environ Microbiol."},{"key":"2026072211565317500_evag174-B33","doi-asserted-by":"publisher","first-page":"6327","DOI":"10.1128\/AEM.00892-12","article-title":"The bacterium Pantoea stewartii uses two different type III secretion systems to colonize its plant host and insect vector","volume":"78","author":"Correa","year":"2012","journal-title":"Appl Environ Microbiol"},{"key":"2026072211565317500_evag174-B34","doi-asserted-by":"publisher","first-page":"167","DOI":"10.1093\/molbev\/msn236","article-title":"Homologous recombination in Agrobacterium: potential implications for the genomic Species concept in Bacteria","volume":"26","author":"Costechareyre","year":"2009","journal-title":"Mol Biol Evol."},{"key":"2026072211565317500_evag174-B35","doi-asserted-by":"publisher","first-page":"14","DOI":"10.1111\/j.1574-6941.2008.00552.x","article-title":"Natural transformation in the Ralstonia solanacearum species complex: number and size of DNA that can be transferred","volume":"66","author":"Coupat","year":"2008","journal-title":"FEMS Microbiol Ecol."},{"key":"2026072211565317500_evag174-B36","doi-asserted-by":"publisher","first-page":"138","DOI":"10.3389\/fmicb.2019.00138","article-title":"May the phage be with you? Prophage-like elements in the genomes of soft rot Pectobacteriaceae: Pectobacterium spp. And Dickeya spp","volume":"10","author":"Czajkowski","year":"2019","journal-title":"Front Microbiol"},{"key":"2026072211565317500_evag174-B37","doi-asserted-by":"publisher","first-page":"3500","DOI":"10.1111\/pce.15037","article-title":"A stage-dependent seed defense response to explain efficient seed transmission of Xanthomonas citri pv. fuscans to common bean","volume":"49","author":"Darrasse","year":"2026","journal-title":"Plant Cell Environ."},{"key":"2026072211565317500_evag174-B38","doi-asserted-by":"publisher","first-page":"2669","DOI":"10.1128\/AEM.02906-07","article-title":"The type III secretion system of Xanthomonas fuscans subsp. fuscans is involved in the phyllosphere colonization process and in transmission to seeds of susceptible beans","volume":"74","author":"Darsonval","year":"2008","journal-title":"Appl Environ Microbiol"},{"key":"2026072211565317500_evag174-B39","doi-asserted-by":"publisher","first-page":"467","DOI":"10.1016\/S0968-4328(96)00028-5","article-title":"Bacteriocins: nature, function and structure","volume":"27","author":"Daw","year":"1996","journal-title":"Micron"},{"key":"2026072211565317500_evag174-B40","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1186\/s13100-022-00275-1","article-title":"Genomic analysis reveals the role of integrative and conjugative elements in plant pathogenic bacteria","volume":"13","author":"de Assis","year":"2022","journal-title":"Mob DNA"},{"key":"2026072211565317500_evag174-B41","doi-asserted-by":"publisher","first-page":"5985","DOI":"10.3390\/ijms22115985","article-title":"Gene transfer potential of outer membrane vesicles of gram-negative Bacteria","volume":"22","author":"Dell\u2019Annunziata","year":"2021","journal-title":"Int J Mol Sci"},{"key":"2026072211565317500_evag174-B42","doi-asserted-by":"publisher","first-page":"126","DOI":"10.1086\/717181","article-title":"Multiyear time-shift study of Bacteria and phage dynamics in the phyllosphere","volume":"199","author":"Dewald-Wang","year":"2022","journal-title":"Am Nat"},{"key":"2026072211565317500_evag174-B43","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2320170121","article-title":"Bacterial lifestyle shapes pangenomes","volume":"121","author":"Dewar","year":"2024","journal-title":"Proc Natl Acad Sci U S A."},{"key":"2026072211565317500_evag174-B44","doi-asserted-by":"publisher","first-page":"1325","DOI":"10.1038\/ismej.2011.202","article-title":"Pseudomonas syringae naturally lacking the canonical type III secretion system are ubiquitous in nonagricultural habitats, are phylogenetically diverse and can be pathogenic","volume":"6","author":"Diallo","year":"2012","journal-title":"ISME J"},{"key":"2026072211565317500_evag174-B45","doi-asserted-by":"publisher","first-page":"562","DOI":"10.1093\/molbev\/msy248","article-title":"Chromids aid genome expansion and functional diversification in the family Burkholderiaceae","volume":"36","author":"diCenzo","year":"2019","journal-title":"Mol Biol Evol."},{"key":"2026072211565317500_evag174-B46","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1186\/s13059-018-1606-y","article-title":"Recombination of ecologically and evolutionarily significant loci maintains genetic cohesion in the Pseudomonas syringae species complex","volume":"20","author":"Dillon","year":"2019","journal-title":"Genome Biol."},{"key":"2026072211565317500_evag174-B47","doi-asserted-by":"publisher","first-page":"145","DOI":"10.1016\/j.cub.2024.11.029","article-title":"Century-old herbarium specimen provides insights into Pierce's disease of grapevines emergence in the Americas","volume":"35","author":"Donegan","year":"2025","journal-title":"Curr Biol."},{"key":"2026072211565317500_evag174-B48","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.00706-17","article-title":"Pseudomonas chlororaphis produces two distinct R-tailocins that contribute to bacterial competition in biofilms and on roots","volume":"83","author":"Dorosky","year":"2017","journal-title":"Appl Environ Microbiol"},{"key":"2026072211565317500_evag174-B49","doi-asserted-by":"publisher","first-page":"330","DOI":"10.1094\/PHYTO-09-15-0232-R","article-title":"Embryo localization enhances the survival of Acidovorax citrulli in watermelon seeds","volume":"106","author":"Dutta","year":"2016","journal-title":"Phytopathology"},{"key":"2026072211565317500_evag174-B50","doi-asserted-by":"publisher","first-page":"7078","DOI":"10.1038\/s41467-025-62473-8","article-title":"The combination of active partitioning and toxin-antitoxin systems is most advantageous for low-copy plasmid fitness","volume":"16","author":"Effe","year":"2025","journal-title":"Nat Commun"},{"key":"2026072211565317500_evag174-B51","doi-asserted-by":"publisher","first-page":"785","DOI":"10.1111\/1758-2229.13103","article-title":"The plant host environment influences competitive interactions between bacterial pathogens","volume":"14","author":"Ehau-Taumaunu","year":"2022","journal-title":"Environ Microbiol Rep"},{"key":"2026072211565317500_evag174-B52","doi-asserted-by":"publisher","first-page":"1599","DOI":"10.1093\/gbe\/evx108","article-title":"Evolution of transcription activator-like effectors in Xanthomonas oryzae","volume":"9","author":"Erkes","year":"2017","journal-title":"Genome Biol Evol"},{"key":"2026072211565317500_evag174-B53","doi-asserted-by":"publisher","first-page":"ycaf099","DOI":"10.1093\/ismeco\/ycaf099","article-title":"Tailocin tail fiber diversity correlates with rfbD variation in the Pseudomonas syringae species complex","volume":"5","author":"Fautt","year":"2025","journal-title":"ISME Commun."},{"key":"2026072211565317500_evag174-B54","doi-asserted-by":"publisher","first-page":"001219","DOI":"10.1099\/mgen.0.001219","article-title":"Investigating the impact of insertion sequences and transposons in the genomes of the most significant phytopathogenic bacteria","volume":"10","author":"Fernandes","year":"2024","journal-title":"Microb Genom."},{"key":"2026072211565317500_evag174-B55","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.02505-14","article-title":"A TALE of transposition: Tn3-like transposons play a major role in the spread of pathogenicity determinants of Xanthomonas citri and other xanthomonads","volume":"6","author":"Ferreira","year":"2015","journal-title":"mBio"},{"key":"2026072211565317500_evag174-B56","doi-asserted-by":"publisher","first-page":"275","DOI":"10.1146\/annurev.py.09.090171.001423","article-title":"Current Status of the gene-for-gene concept","volume":"9","author":"Flor","year":"1971","journal-title":"Annu Rev Phytopathol."},{"key":"2026072211565317500_evag174-B57","doi-asserted-by":"publisher","first-page":"fuab033","DOI":"10.1093\/femsre\/fuab033","article-title":"The ecological impact of a bacterial weapon: microbial interactions and the type VI secretion system","volume":"45","author":"Gallegos-Monterrosa","year":"2021","journal-title":"FEMS Microbiol Rev."},{"key":"2026072211565317500_evag174-B58","doi-asserted-by":"publisher","first-page":"7053","DOI":"10.1128\/JB.182.24.7053-7059.2000","article-title":"Molecular evolution of virulence in natural field strains of Xanthomonas campestris pv. vesicatoria","volume":"182","author":"Gassmann","year":"2000","journal-title":"J Bacteriol"},{"key":"2026072211565317500_evag174-B59","doi-asserted-by":"publisher","DOI":"10.1128\/msystems.01140-25","article-title":"Dormancy and reactivation of the seed and its microbiome: a holobiont perspective","volume":"11","author":"Gerna","year":"2026","journal-title":"mSystems"},{"key":"2026072211565317500_evag174-B60","doi-asserted-by":"publisher","DOI":"10.1002\/pro.5083","article-title":"A new lysine biosynthetic enzyme from a bacterial endosymbiont shaped by genetic drift and genome reduction","volume":"33","author":"Gilkes","year":"2024","journal-title":"Protein Sci"},{"key":"2026072211565317500_evag174-B61","doi-asserted-by":"publisher","first-page":"eabc4516","DOI":"10.1126\/sciadv.abc4516","article-title":"Repeated gain and loss of a single gene modulates the evolution of vascular plant pathogen lifestyles","volume":"6","author":"Gluck-Thaler","year":"2020","journal-title":"Sci Adv"},{"key":"2026072211565317500_evag174-B62","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1002010","article-title":"The stealth episome: suppression of gene expression on the excised genomic island PPHGI-1 from Pseudomonas syringae pv. Phaseolicola","volume":"7","author":"Godfrey","year":"2011","journal-title":"PLoS Pathog."},{"key":"2026072211565317500_evag174-B63","doi-asserted-by":"publisher","first-page":"689","DOI":"10.1186\/s12864-022-08909-7","article-title":"Global diversity and distribution of prophages are lineage-specific within the Ralstonia solanacearum species complex","volume":"23","author":"Greenrod","year":"2022","journal-title":"BMC Genomics"},{"key":"2026072211565317500_evag174-B64","doi-asserted-by":"publisher","first-page":"103507","DOI":"10.1016\/j.isci.2021.103507","article-title":"The cost of bacterial predation via type VI secretion system leads to predator extinction under environmental stress","volume":"24","author":"Gupta","year":"2021","journal-title":"iScience"},{"key":"2026072211565317500_evag174-B65","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0006632","article-title":"A \u2018repertoire for repertoire\u2019 hypothesis: repertoires of type three effectors are candidate determinants of host specificity in Xanthomonas","volume":"4","author":"Hajri","year":"2009","journal-title":"PLoS One"},{"key":"2026072211565317500_evag174-B66","doi-asserted-by":"publisher","first-page":"3581","DOI":"10.1128\/AEM.71.7.3581-3588.2005","article-title":"Relative importance of bacteriocin-like genes in antagonism of Xanthomonas perforans tomato race 3 to Xanthomonas euvesicatoria tomato race 1 strains","volume":"71","author":"Hert","year":"2005","journal-title":"Appl Environ Microbiol"},{"key":"2026072211565317500_evag174-B67","doi-asserted-by":"publisher","first-page":"2744","DOI":"10.1074\/jbc.RA117.001611","article-title":"CRISPR RNA and anti-CRISPR protein binding to the Xanthomonas albilineans Csy1-csy2 heterodimer in the type I-F CRISPR-cas system","volume":"293","author":"Hong","year":"2018","journal-title":"J Biol Chem."},{"key":"2026072211565317500_evag174-B68","doi-asserted-by":"publisher","first-page":"2146","DOI":"10.1128\/AEM.03504-15","article-title":"Genome content and phylogenomics reveal both ancestral and lateral evolutionary pathways in plant-pathogenic Streptomyces Species","volume":"82","author":"Huguet-Tapia","year":"2016","journal-title":"Appl Environ Microbiol"},{"key":"2026072211565317500_evag174-B69","doi-asserted-by":"publisher","first-page":"959","DOI":"10.1111\/nph.18573","article-title":"Genomic and functional analysis of phage-mediated horizontal gene transfer in Pseudomonas syringae on the plant surface","volume":"237","author":"Hulin","year":"2023","journal-title":"New Phytol"},{"key":"2026072211565317500_evag174-B70","doi-asserted-by":"publisher","first-page":"431","DOI":"10.3389\/fpls.2015.00431","article-title":"Comparative genomics of a cannabis pathogen","volume":"6","author":"Jacobs","year":"2015","journal-title":"Front Plant Sci."},{"key":"2026072211565317500_evag174-B71","doi-asserted-by":"publisher","first-page":"163","DOI":"10.1146\/annurev-phyto-080615-100147","article-title":"Using ecology, physiology, and genomics to understand host specificity in Xanthomonas","volume":"54","author":"Jacques","year":"2016","journal-title":"Annu Rev Phytopathol."},{"key":"2026072211565317500_evag174-B72","doi-asserted-by":"publisher","first-page":"257","DOI":"10.1094\/MPMI-09-21-0230-R","article-title":"Candidatus Liberibacter asiaticus\u2019-encoded BCP peroxiredoxin suppresses lipopolysaccharide-mediated defense signaling and nitrosative stress in planta","volume":"35","author":"Jain","year":"2022","journal-title":"Mol Plant Microbe Interact."},{"key":"2026072211565317500_evag174-B73","doi-asserted-by":"publisher","first-page":"100087","DOI":"10.1016\/j.xplc.2020.100087","article-title":"Xa1 allelic R genes activate rice blight resistance suppressed by interfering TAL effectors","volume":"1","author":"Ji","year":"2020","journal-title":"Plant Commun."},{"key":"2026072211565317500_evag174-B74","doi-asserted-by":"publisher","DOI":"10.1128\/JB.00142-20","article-title":"Pseudomonas can survive tailocin killing via persistence-like and heterogenous resistance mechanisms","volume":"202","author":"Kandel","year":"2020","journal-title":"J Bacteriol"},{"key":"2026072211565317500_evag174-B75","doi-asserted-by":"publisher","DOI":"10.1111\/eva.70069","article-title":"Navigating host immunity and concurrent ozone stress: strain-resolved metagenomics reveals maintenance of intraspecific diversity and genetic variation in Xanthomonas on pepper","volume":"18","author":"Kaur","year":"2025","journal-title":"Evol Appl."},{"key":"2026072211565317500_evag174-B76","doi-asserted-by":"publisher","DOI":"10.1128\/aem.02070-24","article-title":"Pseudogenes and host specialization in the emergent bacterial plant pathogen Xylella fastidiosa","volume":"91","author":"Kaur","year":"2025","journal-title":"Appl Environ Microbiol"},{"key":"2026072211565317500_evag174-B77","doi-asserted-by":"crossref","first-page":"385","DOI":"10.1038\/346385a0","article-title":"Widespread distribution and fitness contribution of Xanthomonas campestris avirulence gene Avrbs2","volume":"346","author":"Kearney","year":"1990","journal-title":"Nature"},{"key":"2026072211565317500_evag174-B78","doi-asserted-by":"publisher","first-page":"416","DOI":"10.1094\/MPMI.1997.10.3.416","article-title":"Comparison of avrD alleles from Pseudomonas syringae pv. glycinea","volume":"10","author":"Keith","year":"1997","journal-title":"Mol Plant Microbe Interact."},{"key":"2026072211565317500_evag174-B79","doi-asserted-by":"publisher","first-page":"420","DOI":"10.1128\/AEM.03156-13","article-title":"Factors affecting the initial adhesion and retention of the plant pathogen Xylella fastidiosa in the foregut of an insect vector","volume":"80","author":"Killiny","year":"2014","journal-title":"Appl Environ Microbiol"},{"key":"2026072211565317500_evag174-B80","doi-asserted-by":"publisher","first-page":"1044","DOI":"10.1094\/MPMI-09-12-0211-R","article-title":"The exopolysaccharide of Xylella fastidiosa is essential for biofilm formation, plant virulence, and vector transmission","volume":"26","author":"Killiny","year":"2013","journal-title":"Mol Plant Microbe Interact."},{"key":"2026072211565317500_evag174-B81","doi-asserted-by":"publisher","first-page":"2075","DOI":"10.1007\/s00438-015-1062-2","article-title":"Inheritance of Pantoea type III secretion systems through both vertical and horizontal transfer","volume":"290","author":"Kirzinger","year":"2015","journal-title":"Mol Genet Genomics"},{"key":"2026072211565317500_evag174-B82","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1016\/j.mib.2017.05.008","article-title":"Diversity, classification and evolution of CRISPR-cas systems","volume":"37","author":"Koonin","year":"2017","journal-title":"Curr Opin Microbiol"},{"key":"2026072211565317500_evag174-B83","doi-asserted-by":"publisher","first-page":"313","DOI":"10.1111\/mpp.12345","article-title":"Gram-negative phytopathogenic bacteria, all hemibiotrophs after all?","volume":"17","author":"Kraepiel","year":"2016","journal-title":"Mol Plant Pathol"},{"key":"2026072211565317500_evag174-B84","doi-asserted-by":"publisher","first-page":"415","DOI":"10.1094\/MPMI-23-4-0415","article-title":"Molecular and evolutionary analyses of Pseudomonas syringae pv. Tomato race 1","volume":"23","author":"Kunkeaw","year":"2010","journal-title":"Mol Plant Microbe Interact."},{"key":"2026072211565317500_evag174-B85","doi-asserted-by":"publisher","first-page":"355","DOI":"10.1111\/j.1364-3703.2006.00343.x","article-title":"Different versions of Pseudomonas syringae pv. Tomato DC3000 exist due to the activity of an effector transposon","volume":"7","author":"Landgraf","year":"2006","journal-title":"Mol Plant Pathol."},{"key":"2026072211565317500_evag174-B86","doi-asserted-by":"publisher","first-page":"363","DOI":"10.1146\/annurev.py.21.090183.002051","article-title":"The role of bacterial ICE nucleation in frost injury to plants","volume":"21","author":"Lindow","year":"1983","journal-title":"Annu Rev Phytopathol"},{"key":"2026072211565317500_evag174-B87","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1000093","article-title":"Quorum sensing coordinates brute force and stealth modes of infection in the plant pathogen Pectobacterium atrosepticum","volume":"4","author":"Liu","year":"2008","journal-title":"PLoS Pathog"},{"key":"2026072211565317500_evag174-B88","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1013757","article-title":"Natural competence in the bacterial pathogen Xylella fastidiosa varies across genotypes and is associated with adhesins","volume":"21","author":"Liu","year":"2025","journal-title":"PLoS Pathog."},{"key":"2026072211565317500_evag174-B89","doi-asserted-by":"publisher","first-page":"752","DOI":"10.1094\/PHYTO-02-21-0069-R","article-title":"Mutation of a single core gene, tssM, of type VI secretion system of Xanthomonas perforans influences virulence, epiphytic survival, and transmission during pathogenesis on tomato","volume":"112","author":"Liyanapathiranage","year":"2022","journal-title":"Phytopathology"},{"key":"2026072211565317500_evag174-B90","doi-asserted-by":"publisher","first-page":"1586","DOI":"10.1016\/j.cub.2009.08.018","article-title":"Bacterial evolution by genomic island transfer occurs via DNA transformation in planta","volume":"19","author":"Lovell","year":"2009","journal-title":"Curr Biol."},{"key":"2026072211565317500_evag174-B91","doi-asserted-by":"publisher","first-page":"1849","DOI":"10.1094\/PHYTO-05-19-0152-R","article-title":"Variation in streptomycin resistance mechanisms in Clavibacter michiganensis","volume":"109","author":"Lyu","year":"2019","journal-title":"Phytopathology"},{"key":"2026072211565317500_evag174-B92","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.0020209","article-title":"Type III effector diversification via both pathoadaptation and horizontal transfer in response to a coevolutionary arms race","volume":"2","author":"Ma","year":"2006","journal-title":"PLoS Genet."},{"key":"2026072211565317500_evag174-B93","doi-asserted-by":"publisher","first-page":"157","DOI":"10.1094\/MPMI-08-21-0211-R","article-title":"Influence of flagellin polymorphisms, gene regulation, and responsive memory on the motility of Xanthomonas Species that cause bacterial spot disease of Solanaceous plants","volume":"35","author":"Malvino","year":"2022","journal-title":"Mol Plant Microbe Interact."},{"key":"2026072211565317500_evag174-B94","doi-asserted-by":"publisher","first-page":"307","DOI":"10.1046\/j.1364-3703.2003.00178.x","article-title":"Pantoea agglomerans pvs. Gypsophilae and betae, recently evolved pathogens?","volume":"4","author":"Manulis","year":"2003","journal-title":"Mol Plant Pathol."},{"key":"2026072211565317500_evag174-B95","doi-asserted-by":"publisher","first-page":"evag002","DOI":"10.1093\/gbe\/evag002","article-title":"Prevalence and evolutionary implications of genome rearrangements in Bacteria","volume":"18","author":"Martinez-Gutierrez","year":"2026","journal-title":"Genome Biol Evol."},{"key":"2026072211565317500_evag174-B96","doi-asserted-by":"publisher","first-page":"572","DOI":"10.1111\/1758-2229.12397","article-title":"Recombination-prone bacterial strains form a reservoir from which epidemic clones emerge in agroecosystems","volume":"8","author":"Merda","year":"2016","journal-title":"Environ Microbiol Rep."},{"key":"2026072211565317500_evag174-B97","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1011154","article-title":"Complete functional analysis of type IV pilus components of a reemergent plant pathogen reveals neofunctionalization of paralog genes","volume":"19","author":"Merfa","year":"2023","journal-title":"PLoS Pathog."},{"key":"2026072211565317500_evag174-B98","doi-asserted-by":"publisher","DOI":"10.1111\/mpp.70067","article-title":"Pthxo2b orthologue Tal7 of Xanthomonas oryzae pv. oryzae strain IX-221 acts as a Major virulence factor in Indica rice without activating a clade III SWEET gene","volume":"26","author":"Mishra","year":"2025","journal-title":"Mol Plant Pathol."},{"key":"2026072211565317500_evag174-B99","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1000693","article-title":"Expanding the paradigms of plant pathogen life history and evolution of parasitic fitness beyond agricultural boundaries","volume":"5","author":"Morris","year":"2009","journal-title":"PLoS Pathog"},{"key":"2026072211565317500_evag174-B100","doi-asserted-by":"publisher","first-page":"1462","DOI":"10.1094\/PHYTO-01-24-0010-SC","article-title":"CRISPRals: a web database for assessing the CRISPR defense system in the Ralstonia solanacearum Species Complex to avoid phage resistance","volume":"114","author":"Motoche-Monar","year":"2024","journal-title":"Phytopathology"},{"key":"2026072211565317500_evag174-B101","doi-asserted-by":"publisher","first-page":"804","DOI":"10.1094\/PHYTO-02-17-0047-RVW","article-title":"Rathayibacter toxicus, other Rathayibacter Species inducing bacterial head blight of grasses, and the potential for livestock poisonings","volume":"107","author":"Murray","year":"2017","journal-title":"Phytopathology"},{"key":"2026072211565317500_evag174-B102","doi-asserted-by":"publisher","first-page":"444","DOI":"10.1111\/mmi.14111","article-title":"Supercoiling of an excised genomic island represses effector gene expression to prevent activation of host resistance","volume":"110","author":"Neale","year":"2018","journal-title":"Mol Microbiol"},{"key":"2026072211565317500_evag174-B103","doi-asserted-by":"publisher","first-page":"270","DOI":"10.3389\/fmicb.2019.00270","article-title":"Inference of convergent gene acquisition among Pseudomonas syringae strains isolated from watermelon, cantaloupe, and squash","volume":"10","author":"Newberry","year":"2019","journal-title":"Front Microbiol."},{"key":"2026072211565317500_evag174-B104","doi-asserted-by":"publisher","first-page":"400","DOI":"10.1094\/PHYTO-08-22-0294-R","article-title":"Genome-wide association to study the host-specificity determinants of Xanthomonas perforans","volume":"113","author":"Newberry","year":"2023","journal-title":"Phytopathology"},{"key":"2026072211565317500_evag174-B105","doi-asserted-by":"publisher","first-page":"1737","DOI":"10.1073\/pnas.0308399100","article-title":"Cell-cell signaling controls Xylella fastidiosa interactions with both insects and plants","volume":"101","author":"Newman","year":"2004","journal-title":"Proc Natl Acad Sci U S A."},{"key":"2026072211565317500_evag174-B106","doi-asserted-by":"publisher","DOI":"10.1111\/mpp.70228","article-title":"Virulence regulation and lifestyle transitions: the role of c-di-GMP and two-component systems in Erwinia amylovora and their evolutionary context within enterobacterales","volume":"27","author":"Niroula","year":"2026","journal-title":"Mol Plant Pathol"},{"key":"2026072211565317500_evag174-B107","doi-asserted-by":"publisher","first-page":"383","DOI":"10.1146\/annurev-micro-051524-032254","article-title":"Evolution and ecology of Streptomyces","volume":"79","author":"Norte","year":"2025","journal-title":"Annu Rev Microbiol."},{"key":"2026072211565317500_evag174-B108","doi-asserted-by":"publisher","DOI":"10.1128\/aem.01873-22","article-title":"Natural recombination among type I restriction-modification systems creates diverse genomic methylation patterns among Xylella fastidiosa strains","volume":"89","author":"O\u2019Leary","year":"2023","journal-title":"Appl Environ Microbiol"},{"key":"2026072211565317500_evag174-B109","doi-asserted-by":"publisher","first-page":"954","DOI":"10.1016\/j.cub.2025.01.003","article-title":"Evolution of a vascular plant pathogen is associated with the loss of CRISPR-cas and an increase in genome plasticity and virulence genes","volume":"35","author":"Paauw","year":"2025","journal-title":"Curr Biol."},{"key":"2026072211565317500_evag174-B110","doi-asserted-by":"publisher","first-page":"1393","DOI":"10.1038\/s41559-025-02773-w","article-title":"Functional replacement of ancestral antibacterial secretion system in a bacterial plant pathogen","volume":"9","author":"Peduzzi","year":"2025","journal-title":"Nat Ecol Evol"},{"key":"2026072211565317500_evag174-B111","doi-asserted-by":"publisher","first-page":"evae074","DOI":"10.1093\/gbe\/evae074","article-title":"Genetic and functional diversity help explain pathogenic, weakly pathogenic, and commensal lifestyles in the genus Xanthomonas","volume":"16","author":"Pena Michelle","year":"2024","journal-title":"Genome Biol Evol."},{"key":"2026072211565317500_evag174-B112","doi-asserted-by":"publisher","first-page":"102351","DOI":"10.1016\/j.pbi.2023.102351","article-title":"Plant-microbiome crosstalk and disease development","volume":"72","author":"Pereira","year":"2023","journal-title":"Curr Opin Plant Biol."},{"key":"2026072211565317500_evag174-B113","doi-asserted-by":"publisher","first-page":"1163","DOI":"10.3389\/fpls.2016.01163","article-title":"Vector-borne bacterial plant pathogens: interactions with hemipteran insects and plants","volume":"7","author":"Perilla-Henao","year":"2016","journal-title":"Front Plant Sci"},{"key":"2026072211565317500_evag174-B114","doi-asserted-by":"publisher","first-page":"136","DOI":"10.1038\/s41564-023-01555-z","article-title":"Leaf microbiome dysbiosis triggered by T2SS-dependent enzyme secretion from opportunistic Xanthomonas pathogens","volume":"9","author":"Pfeilmeier","year":"2024","journal-title":"Nat Microbiol"},{"key":"2026072211565317500_evag174-B115","doi-asserted-by":"publisher","first-page":"4486","DOI":"10.1128\/AEM.70.8.4486-4490.2004","article-title":"Bactericidal activity of glycinecin A, a bacteriocin derived from Xanthomonas campestris pv. glycines, on phytopathogenic Xanthomonas campestris pv. vesicatoria cells","volume":"70","author":"Pham","year":"2004","journal-title":"Appl Environ Microbiol"},{"key":"2026072211565317500_evag174-B116","doi-asserted-by":"publisher","author":"Picazo","DOI":"10.1101\/2024.10.17.618910"},{"key":"2026072211565317500_evag174-B117","doi-asserted-by":"publisher","first-page":"289","DOI":"10.3389\/fpls.2015.00289","article-title":"What makes Xanthomonas albilineans unique amongst xanthomonads?","volume":"6","author":"Pieretti","year":"2015","journal-title":"Front Plant Sci"},{"key":"2026072211565317500_evag174-B118","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000461","article-title":"Host adaptation and microbial competition drive Ralstonia solanacearum phylotype I evolution in the Republic of Korea","volume":"6","author":"Prokchorchik","year":"2020","journal-title":"Microb Genom."},{"key":"2026072211565317500_evag174-B119","doi-asserted-by":"publisher","first-page":"244","DOI":"10.1016\/j.cropro.2005.04.013","article-title":"Assessments of farm yield and district production loss from bacterial leaf blight epidemics in rice","volume":"25","author":"Rajarajeswari","year":"2006","journal-title":"Crop Protection"},{"key":"2026072211565317500_evag174-B120","doi-asserted-by":"publisher","first-page":"255","DOI":"10.1146\/annurev.genet.32.1.255","article-title":"Molecular mechanisms of bacteriocin evolution","volume":"32","author":"Riley","year":"1998","journal-title":"Annu Rev Genet"},{"key":"2026072211565317500_evag174-B121","doi-asserted-by":"publisher","first-page":"3778","DOI":"10.1128\/AEM.71.7.3778-3785.2005","article-title":"Changes in race-specific virulence in Pseudomonas syringae pv. Phaseolicola are associated with a chimeric transposable element and rare deletion events in a plasmid-borne pathogenicity island","volume":"71","author":"Rivas","year":"2005","journal-title":"Appl Environ Microbiol."},{"key":"2026072211565317500_evag174-B122","doi-asserted-by":"publisher","first-page":"1376","DOI":"10.1094\/MPMI.2004.17.12.1376","article-title":"Relationship between avirulence gene (avrA) diversity in Ralstonia solanacearum and bacterial wilt incidence","volume":"17","author":"Robertson","year":"2004","journal-title":"Mol Plant Microbe Interact."},{"key":"2026072211565317500_evag174-B123","doi-asserted-by":"publisher","first-page":"17","DOI":"10.1093\/aob\/mcx125","article-title":"Molecular mimicry modulates plant host responses to pathogens","volume":"121","author":"Ronald","year":"2018","journal-title":"Ann Bot"},{"key":"2026072211565317500_evag174-B124","doi-asserted-by":"publisher","first-page":"497","DOI":"10.1038\/415497a","article-title":"Genome sequence of the plant pathogen Ralstonia solanacearum","volume":"415","author":"Salanoubat","year":"2002","journal-title":"Nature"},{"key":"2026072211565317500_evag174-B125","doi-asserted-by":"publisher","first-page":"204","DOI":"10.1186\/1471-2164-9-204","article-title":"Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A","volume":"9","author":"Salzberg","year":"2008","journal-title":"BMC Genomics"},{"key":"2026072211565317500_evag174-B126","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.01301-23","article-title":"The plant pathogenic bacterium Candidatus Liberibacter solanacearum induces calcium-regulated autophagy in midgut cells of its insect vector Bactericera trigonica","volume":"11","author":"Sarkar","year":"2023","journal-title":"Microbiol Spectr"},{"key":"2026072211565317500_evag174-B127","doi-asserted-by":"publisher","first-page":"8491","DOI":"10.1128\/AEM.71.12.8491-8499.2005","article-title":"Multilocus sequence type system for the plant pathogen Xylella fastidiosa and relative contributions of recombination and point mutation to clonal diversity","volume":"71","author":"Scally","year":"2005","journal-title":"Appl Environ Microbiol"},{"key":"2026072211565317500_evag174-B128","doi-asserted-by":"publisher","first-page":"649","DOI":"10.1093\/gbe\/evw016","article-title":"Horizontal gene acquisitions, Mobile element proliferation, and genome decay in the host-restricted plant pathogen Erwinia Tracheiphila","volume":"8","author":"Shapiro","year":"2016","journal-title":"Genome Biol Evol"},{"key":"2026072211565317500_evag174-B129","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.01307-18","article-title":"An introduced crop plant is driving diversification of the virulent bacterial pathogen Erwinia tracheiphila","volume":"9","author":"Shapiro","year":"2018","journal-title":"mBio"},{"key":"2026072211565317500_evag174-B130","doi-asserted-by":"publisher","first-page":"wraf019","DOI":"10.1093\/ismejo\/wraf019","article-title":"Plasmids encode and can mobilize onion pathogenicity in Pantoea agglomerans","volume":"19","author":"Shin","year":"2025","journal-title":"ISME J."},{"key":"2026072211565317500_evag174-B131","doi-asserted-by":"publisher","first-page":"6155","DOI":"10.1038\/s41467-022-33871-z","article-title":"Structural insight into Tn3 family transposition mechanism","volume":"13","author":"Shkumatov","year":"2022","journal-title":"Nat Commun"},{"key":"2026072211565317500_evag174-B132","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1093\/jipm\/pmz037","article-title":"The economic challenges of dealing with Citrus greening: the case of Florida","volume":"11","author":"Singerman","year":"2020","journal-title":"J Integr Pest Manag."},{"key":"2026072211565317500_evag174-B133","doi-asserted-by":"publisher","first-page":"2501","DOI":"10.1128\/JB.01779-08","article-title":"Genome sequences of three Agrobacterium Biovars help elucidate the evolution of multichromosome genomes in Bacteria","volume":"191","author":"Slater","year":"2009","journal-title":"J Bacteriol"},{"key":"2026072211565317500_evag174-B134","doi-asserted-by":"publisher","first-page":"285","DOI":"10.1111\/j.1462-5822.2007.01078.x","article-title":"Host\u2013pathogen interplay and the evolution of bacterial effectors","volume":"10","author":"Stavrinides","year":"2008","journal-title":"Cell Microbiol."},{"key":"2026072211565317500_evag174-B135","doi-asserted-by":"publisher","first-page":"165","DOI":"10.1046\/j.1365-2958.1998.00918.x","article-title":"Sequence variations in alleles of the avirulence gene avrPphE. R2 from Pseudomonas syringae pv. Phaseolicola lead to loss of recognition of the AvrPphE protein within bean cells and a gain in cultivar-specific virulence","volume":"29","author":"Stevens","year":"1998","journal-title":"Mol Microbiol"},{"key":"2026072211565317500_evag174-B136","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2319499121","article-title":"Natural variation of immune epitopes reveals intrabacterial antagonism","volume":"121","author":"Stevens","year":"2024","journal-title":"Proc Natl Acad Sci U S A."},{"key":"2026072211565317500_evag174-B137","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1094\/PHYTO-09-20-0412-RVW","article-title":"Population genomics of bacterial plant pathogens","volume":"111","author":"Straub","year":"2021","journal-title":"Phytopathology"},{"key":"2026072211565317500_evag174-B138","doi-asserted-by":"publisher","first-page":"161","DOI":"10.1146\/annurev-phyto-080417-045946","article-title":"Antibiotic resistance in plant-pathogenic Bacteria","volume":"56","author":"Sundin","year":"2018","journal-title":"Annu Rev Phytopathol"},{"key":"2026072211565317500_evag174-B139","doi-asserted-by":"publisher","first-page":"4661","DOI":"10.1128\/jb.178.15.4661-4669.1996","article-title":"Spontaneous and induced mutations in a single open Reading frame alter both virulence and avirulence in Xanthomonas campestris pv. vesicatoria avrBs2","volume":"178","author":"Swords","year":"1996","journal-title":"J Bacteriol."},{"key":"2026072211565317500_evag174-B140","doi-asserted-by":"publisher","first-page":"651","DOI":"10.1094\/PHYTO-10-22-0365-KD","article-title":"The dynamic transcription activator-like effector family of Xanthomonas","volume":"113","author":"Teper","year":"2023","journal-title":"Phytopathology"},{"key":"2026072211565317500_evag174-B141","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.00654-17","article-title":"Horizontal gene transfer of functional type VI killing genes by natural transformation","volume":"8","author":"Thomas","year":"2017","journal-title":"mBio"},{"key":"2026072211565317500_evag174-B142","doi-asserted-by":"publisher","first-page":"466","DOI":"10.1016\/j.mib.2005.06.003","article-title":"The biology of restriction and anti-restriction","volume":"8","author":"Tock","year":"2005","journal-title":"Curr Opin Microbiol."},{"key":"2026072211565317500_evag174-B143","doi-asserted-by":"publisher","first-page":"dsaf009","DOI":"10.1093\/dnares\/dsaf009","article-title":"Comparative genomics of native plasmids from plant pathogenic Gammaproteobacteria","volume":"32","author":"Urriza","year":"2025","journal-title":"DNA Res."},{"key":"2026072211565317500_evag174-B144","doi-asserted-by":"publisher","first-page":"1358","DOI":"10.1094\/PHYTO.2000.90.12.1358","article-title":"Survival of Ralstonia solanacearum biovar 2, the causative agent of potato brown rot, in field and microcosm soils in temperate climates","volume":"90","author":"van Elsas","year":"2000","journal-title":"Phytopathology"},{"key":"2026072211565317500_evag174-B145","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.02972-18","article-title":"Genomic diversity and recombination among Xylella fastidiosa subspecies","volume":"85","author":"Vanhove","year":"2019","journal-title":"Appl Environ Microbiol"},{"key":"2026072211565317500_evag174-B146","doi-asserted-by":"publisher","first-page":"429","DOI":"10.1146\/annurev-phyto-081211-173010","article-title":"The role of prophage in plant-pathogenic Bacteria","volume":"51","author":"Varani","year":"2013","journal-title":"Annu Rev Phytopathol"},{"key":"2026072211565317500_evag174-B147","doi-asserted-by":"publisher","author":"Verma","DOI":"10.1101\/2025.10.05.680514"},{"key":"2026072211565317500_evag174-B148","doi-asserted-by":"publisher","first-page":"253","DOI":"10.1093\/evlett\/qrad056","article-title":"Phage selection drives resistance\u2013virulence trade-offs in Ralstonia solanacearum plant-pathogenic bacterium irrespective of the growth temperature","volume":"8","author":"Wang","year":"2024","journal-title":"Evol Lett."},{"key":"2026072211565317500_evag174-B149","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1146\/annurev-phyto-021622-125009","article-title":"Virulence and ecology of agrobacteria in the context of evolutionary genomics","volume":"61","author":"Weisberg","year":"2023","journal-title":"Annu Rev Phytopathol"},{"key":"2026072211565317500_evag174-B150","doi-asserted-by":"publisher","first-page":"3078","DOI":"10.3389\/fmicb.2019.03078","article-title":"CRISPR-Cas Systems and the paradox of self-targeting spacers","volume":"10","author":"Wimmer","year":"2019","journal-title":"Front Microbiol"},{"key":"2026072211565317500_evag174-B151","doi-asserted-by":"publisher","first-page":"2317","DOI":"10.1126\/science.1066804","article-title":"The genome of the natural genetic engineer Agrobacterium tumefaciens C58","volume":"294","author":"Wood","year":"2001","journal-title":"Science"},{"key":"2026072211565317500_evag174-B152","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0055962","article-title":"Identification and characterization of integron-mediated antibiotic resistance in the phytopathogen Xanthomonas oryzae pv. oryzae","volume":"8","author":"Xu","year":"2013","journal-title":"PLoS One"},{"key":"2026072211565317500_evag174-B153","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1013598","article-title":"A broad-spectrum anti-fungal effector dictates bacterial-fungal interkingdom interactions","volume":"21","author":"Yan","year":"2025","journal-title":"PLoS Pathog"},{"key":"2026072211565317500_evag174-B154","doi-asserted-by":"publisher","first-page":"142","DOI":"10.1094\/MPMI-18-0142","article-title":"Avoidance of host recognition by alterations in the repetitive and C-terminal regions of AvrXa7, a type III effector of Xanthomonas oryzae pv. oryzae","volume":"18","author":"Yang","year":"2005","journal-title":"Mol Plant Microbe Interact."},{"key":"2026072211565317500_evag174-B155","doi-asserted-by":"publisher","first-page":"2174","DOI":"10.1094\/PHYTO-01-23-0004-SA","article-title":"Examination of large chromosomal inversions in the genome of Erwinia amylovora strains reveals worldwide distribution and North America-specific types","volume":"113","author":"Yang","year":"2023","journal-title":"Phytopathology"},{"key":"2026072211565317500_evag174-B156","doi-asserted-by":"publisher","first-page":"291","DOI":"10.1111\/j.1574-6976.1998.tb00355.x","article-title":"Control of genes for conjugative transfer of plasmids and other mobile elements","volume":"21","author":"Zatyka","year":"1998","journal-title":"FEMS Microbiol Rev"},{"key":"2026072211565317500_evag174-B157","doi-asserted-by":"publisher","DOI":"10.1002\/ece3.11081","article-title":"Constitutive expression of the type VI secretion system carries no measurable fitness cost in Vibrio cholerae","volume":"14","author":"Zhang","year":"2024","journal-title":"Ecol Evol."},{"key":"2026072211565317500_evag174-B158","doi-asserted-by":"publisher","first-page":"454","DOI":"10.1094\/PHYTO-08-17-0282-R","article-title":"A type 3 prophage of \u2018Candidatus Liberibacter asiaticus\u2019 carrying a restriction-modification system","volume":"108","author":"Zheng","year":"2018","journal-title":"Phytopathology"}],"container-title":["Genome Biology and Evolution"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/gbe\/advance-article-pdf\/doi\/10.1093\/gbe\/evag174\/68742348\/evag174.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/gbe\/article-pdf\/18\/7\/evag174\/68742348\/evag174.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/gbe\/article-pdf\/18\/7\/evag174\/68742348\/evag174.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,22]],"date-time":"2026-07-22T15:57:01Z","timestamp":1784735821000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/gbe\/article\/doi\/10.1093\/gbe\/evag174\/8729594"}},"subtitle":[],"editor":[{"given":"Chuan","family":"Ku","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,7,1]]},"references-count":158,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2026,7,1]]}},"URL":"https:\/\/doi.org\/10.1093\/gbe\/evag174","relation":{},"ISSN":["1759-6653"],"issn-type":[{"value":"1759-6653","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,7]]},"published":{"date-parts":[[2026,7,1]]},"article-number":"evag174"}}