{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,5]],"date-time":"2026-10-05T05:54:07Z","timestamp":1791179647619,"version":"4.1.0"},"reference-count":93,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,10,5]],"date-time":"2026-10-05T00:00:00Z","timestamp":1791158400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p>\n                    <jats:italic>Pantoea stewartii<\/jats:italic>\n                    subsp.\n                    <jats:italic>indologenes<\/jats:italic>\n                    is an emerging cereal phytopathogen with unclear virulence mechanisms. We sequenced a rice seed-borne strain, HR3-48, and classified it as\n                    <jats:italic>P. stewartii<\/jats:italic>\n                    subsp.\n                    <jats:italic>indologenes<\/jats:italic>\n                    (\n                    <jats:italic>Pnsi<\/jats:italic>\n                    ) through phylogeny of 92 housekeeping genes, ANI (&amp;gt; 99%), and dDDH (&amp;gt; 96%) comparisons. HR3-48 harbors a conserved plant-pathogenic PSI-1 type III secretion system (T3SS) and a single flagellar locus (\n                    <jats:italic>flag-1<\/jats:italic>\n                    ) with multiple\n                    <jats:italic>fliC<\/jats:italic>\n                    genes. The tandem\n                    <jats:italic>fliC456<\/jats:italic>\n                    cassette is functionally redundant for motility and flagellum assembly but contributes significantly to eliciting plant immune responses in\n                    <jats:italic>Nicotiana benthamiana<\/jats:italic>\n                    . The T3SS structural gene\n                    <jats:italic>hrcQ\u2013U<\/jats:italic>\n                    determines hypersensitive response (HR) induction. HR3-48 causes necrosis in maize and rice, a phenotype primarily reliant on T3SS. The flagellin-derived epitope flg22\n                    <jats:sup>PanM<\/jats:sup>\n                    , a key polymorphism of L19M, triggered robust reactive oxygen species (ROS) production and inhibited\n                    <jats:italic>Pst<\/jats:italic>\n                    DC3000-induced HR in\n                    <jats:italic>N. benthamiana<\/jats:italic>\n                    , whereas flg22\n                    <jats:sup>PanE<\/jats:sup>\n                    (L19E) showed weak or no activity in these early immune assays, indicating that the 19\n                    <jats:sup>th<\/jats:sup>\n                    residue dictates the specificity of plant immune recognition. Both peptides suppress Arabidopsis seedling growth. Collectively, our data indicate that PSI-1 T3SS in\n                    <jats:italic>Pnsi<\/jats:italic>\n                    HR3-48 is a major virulence determinant in cereal hosts, whereas polymorphic flagellins modulate MTI (MAMP-triggered immunity) outputs and motility of HR3-48, with the 19\n                    <jats:sup>th<\/jats:sup>\n                    residue of flg22 contributing to differential immune perception. It remains unclear how immune suppression is mediated by effectors.\n                  <\/jats:p>","DOI":"10.3389\/fmicb.2026.1969847","type":"journal-article","created":{"date-parts":[[2026,10,5]],"date-time":"2026-10-05T05:32:38Z","timestamp":1791178358000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Deciphering the genomic and functional basis of virulence and immune modulation in Pantoea stewartii"],"prefix":"10.3389","volume":"17","author":[{"given":"Jianying","family":"Liu","sequence":"first","affiliation":[{"name":"Key Laboratory of Microbial Resources Collection and Preservation, State Key Laboratory of Efficient Utilization of Arable Land in China, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences (CAAS)","place":["Beijing, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Na","family":"Peng","sequence":"additional","affiliation":[{"name":"Key Laboratory of Microbial Resources Collection and Preservation, State Key Laboratory of Efficient Utilization of Arable Land in China, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences (CAAS)","place":["Beijing, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoxia","family":"Zhang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Microbial Resources Collection and Preservation, State Key Laboratory of Efficient Utilization of Arable Land in China, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences (CAAS)","place":["Beijing, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hai-Lei","family":"Wei","sequence":"additional","affiliation":[{"name":"Key Laboratory of Microbial Resources Collection and Preservation, State Key Laboratory of Efficient Utilization of Arable Land in China, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences (CAAS)","place":["Beijing, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,10,5]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"1223","DOI":"10.1094\/MPMI.2001.14.10.1223","article-title":"Biological activity of harpin produced by Pantoea stewartii subsp. stewartii","volume":"14","author":"Ahmad","year":"2001","journal-title":"MPMI"},{"key":"ref2","doi-asserted-by":"publisher","first-page":"1407","DOI":"10.1094\/pdis-08-18-1403-pdn","article-title":"First report of Pantoea stewartii subsp. indologenes causing leaf blight on rice in Malaysia","volume":"103","author":"Azizi","year":"2019","journal-title":"Plant Dis."},{"key":"ref3","doi-asserted-by":"publisher","first-page":"e00418-19","DOI":"10.1128\/JB.00418-19","article-title":"Pseudomonas syringae AlgU downregulates flagellin gene expression, helping evade plant immunity","volume":"202","author":"Bao","year":"2020","journal-title":"J. Bacteriol."},{"key":"ref4","doi-asserted-by":"publisher","first-page":"e1002206","DOI":"10.1371\/journal.ppat.1002206","article-title":"Pseudomonas evades immune recognition of flagellin in both mammals and plants","volume":"7","author":"Bardoel","year":"2011","journal-title":"PLoS Pathog."},{"key":"ref5","doi-asserted-by":"publisher","first-page":"5000","DOI":"10.1128\/jb.177.17.5000-5008.1995","article-title":"Capsular polysaccharide biosynthesis and pathogenicity in Erwinia stewartii require induction by an N-acylhomoserine lactone autoinducer","volume":"177","author":"Beck Von Bodman","year":"1995","journal-title":"J. Bacteriol."},{"key":"ref6","doi-asserted-by":"publisher","first-page":"447","DOI":"10.1016\/j.tibs.2014.06.006","article-title":"The growth\u2013defense pivot: crisis management in plants mediated by LRR-RK surface receptors","volume":"39","author":"Belkhadir","year":"2014","journal-title":"Trends Biochem. Sci."},{"key":"ref7","doi-asserted-by":"publisher","first-page":"257","DOI":"10.1146\/annurev-phyto-080614-120106","article-title":"Function, discovery, and exploitation of plant pattern recognition receptors for broad-spectrum disease resistance","volume":"55","author":"Boutrot","year":"2017","journal-title":"Annu. Rev. Phytopathol."},{"key":"ref8","doi-asserted-by":"publisher","first-page":"eaav0748","DOI":"10.1126\/science.aav0748","article-title":"Glycosidase and glycan polymorphism control hydrolytic release of immunogenic flagellin peptides","volume":"364","author":"Buscaill","year":"2019","journal-title":"Science"},{"key":"ref9","doi-asserted-by":"publisher","first-page":"2116","DOI":"10.1093\/plcell\/koab109","article-title":"Defeated by the nines: nine extracellular strategies to avoid microbe-associated molecular patterns recognition in plants","volume":"33","author":"Buscaill","year":"2021","journal-title":"Plant Cell"},{"key":"ref10","doi-asserted-by":"publisher","first-page":"191","DOI":"10.1094\/MPMI-05-11-0138","article-title":"Flagella mediate endophytic competence rather than act as MAMPS in rice\u2013Azoarcus sp. strain BH72 interactions","volume":"25","author":"Buschart","year":"2012","journal-title":"MPMI"},{"key":"ref11","doi-asserted-by":"publisher","first-page":"262","DOI":"10.1128\/MMBR.05017-11","article-title":"Protein export according to schedule: architecture, assembly, regulation of type III secretion systems from plant- and animal-pathogenic bacteria","volume":"76","author":"B\u00fcttner","year":"2012","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"ref12","doi-asserted-by":"publisher","first-page":"221","DOI":"10.1111\/j.1574-6968.2006.00172.x","article-title":"The alternative \u03c3 factor HrpL negatively modulates the flagellar system in the phytopathogenic bacterium Erwinia amylovora under hrp-inducing conditions","volume":"257","author":"Cesbron","year":"2006","journal-title":"FEMS Microbiol. Lett."},{"key":"ref13","doi-asserted-by":"publisher","first-page":"6421","DOI":"10.1099\/ijsem.0.006421","article-title":"EzBioCloud: a genome-driven database and platform for microbiome identification and discovery","volume":"74","author":"Chalita","year":"2024","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref14","doi-asserted-by":"publisher","first-page":"775","DOI":"10.1006\/jmbi.1998.2055","article-title":"Replication of R6K \u03b3 origin in vitro: discrete start sites for DNA synthesis dependent on \u03c0 and its copy-up variants","volume":"282","author":"Chen","year":"1998","journal-title":"J. Mol. Biol."},{"key":"ref15","doi-asserted-by":"publisher","first-page":"504","DOI":"10.1094\/MPMI-11-20-0314-SC","article-title":"Proteobacteria contain diverse flg22 epitopes that elicit varying immune responses in Arabidopsis thaliana","volume":"34","author":"Cheng","year":"2021","journal-title":"MPMI"},{"key":"ref16","doi-asserted-by":"publisher","first-page":"455","DOI":"10.1038\/nrmicro1887","article-title":"Coordinating assembly of a bacterial macromolecular machine","volume":"6","author":"Chevance","year":"2008","journal-title":"Nat. Rev. Microbiol."},{"key":"ref17","doi-asserted-by":"publisher","first-page":"497","DOI":"10.1038\/nature05999","article-title":"A flagellin-induced complex of the receptor FLS2 and BAK1 initiates plant defence","volume":"448","author":"Chinchilla","year":"2007","journal-title":"Nature"},{"key":"ref18","doi-asserted-by":"publisher","first-page":"847","DOI":"10.1111\/nph.12408","article-title":"Allelic variation in two distinct Pseudomonas syringae flagellin epitopes modulates the strength of plant immune responses but not bacterial motility","volume":"200","author":"Clarke","year":"2013","journal-title":"New Phytol."},{"key":"ref19","doi-asserted-by":"publisher","first-page":"635","DOI":"10.1016\/j.chom.2021.02.006","article-title":"A complex immune response to flagellin epitope variation in commensal communities","volume":"29","author":"Colaianni","year":"2021","journal-title":"Cell Host Microbe"},{"key":"ref20","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":"ref21","doi-asserted-by":"publisher","first-page":"1190","DOI":"10.1094\/PDIS-09-20-2015-PDN","article-title":"First report of Pantoea stewartii subsp. stewartii causing bacterial leaf wilt of sugarcane in China","volume":"105","author":"Cui","year":"2021","journal-title":"Plant Dis."},{"key":"ref22","doi-asserted-by":"publisher","first-page":"323","DOI":"10.1038\/nrmicro.2017.20","article-title":"Assembly, structure, function and regulation of type III secretion systems","volume":"15","author":"Deng","year":"2017","journal-title":"Nat. Rev. Microbiol."},{"key":"ref23","doi-asserted-by":"publisher","first-page":"e00435-17","DOI":"10.1128\/genomeA.00435-17","article-title":"Complete genome assembly of Pantoea stewartii subsp. stewartii DC283, a corn pathogen","volume":"5","author":"Duong","year":"2017","journal-title":"Genome Announc."},{"key":"ref24","doi-asserted-by":"publisher","first-page":"a000299","DOI":"10.1101\/cshperspect.a000299","article-title":"Bacterial nanomachines: the flagellum and type III injectisome","volume":"2","author":"Erhardt","year":"2010","journal-title":"Cold Spring Harb. Perspect. Biol."},{"key":"ref25","doi-asserted-by":"publisher","first-page":"2695","DOI":"10.1128\/JB.01172-10","article-title":"Flagellin redundancy in Caulobacter crescentus and its implications for flagellar filament assembly","volume":"193","author":"Faulds-Pain","year":"2011","journal-title":"J. Bacteriol."},{"key":"ref26","doi-asserted-by":"publisher","first-page":"265","DOI":"10.1046\/j.1365-313X.1999.00265.x","article-title":"Plants have a sensitive perception system for the most conserved domain of bacterial flagellin","volume":"18","author":"Felix","year":"1999","journal-title":"Plant J."},{"key":"ref27","doi-asserted-by":"publisher","first-page":"1213","DOI":"10.1094\/MPMI.2001.14.10.1213","article-title":"Genetic organization of the Pantoea stewartii subsp. stewartii hrp gene cluster and sequence analysis of the hrpA, hrpC, hrpN, and wtsE operons","volume":"14","author":"Frederick","year":"2001","journal-title":"MPMI"},{"key":"ref28","doi-asserted-by":"publisher","first-page":"1322","DOI":"10.1126\/science.284.5418.1322","article-title":"Type III secretion machines: bacterial devices for protein delivery into host cells","volume":"284","author":"Gal\u00e1n","year":"1999","journal-title":"Science"},{"key":"ref29","doi-asserted-by":"publisher","first-page":"502","DOI":"10.1016\/j.chom.2022.03.017","article-title":"Dynamic nutrient acquisition from a hydrated apoplast supports biotrophic proliferation of a bacterial pathogen of maize","volume":"30","author":"Gentzel","year":"2022","journal-title":"Cell Host Microbe"},{"key":"ref30","doi-asserted-by":"publisher","first-page":"e02655-24","DOI":"10.1128\/spectrum.02655-24","article-title":"A novel transcriptional regulator, CdeR, modulates the type III secretion system via c-di-GMP signaling in Dickeya dadantii","volume":"13","author":"Ghasemi","year":"2025","journal-title":"Microbiol. Spectrum"},{"key":"ref31","doi-asserted-by":"publisher","first-page":"361","DOI":"10.1094\/MPMI-21-3-0361","article-title":"The Pseudomonas syringae type III effector HopAM1 enhances virulence on water-stressed plants","volume":"21","author":"Goel","year":"2008","journal-title":"MPMI"},{"key":"ref32","doi-asserted-by":"publisher","first-page":"277","DOI":"10.1046\/j.1365-313X.1999.00451.x","article-title":"A single locus determines sensitivity to bacterial flagellin in Arabidopsis thaliana","volume":"18","author":"G\u00f3mez-G\u00f3mez","year":"1999","journal-title":"Plant J."},{"key":"ref33","doi-asserted-by":"publisher","first-page":"2249","DOI":"10.1128\/JB.183.7.2249-2258.2001","article-title":"SirA orthologs affect both motility and virulence","volume":"183","author":"Goodier","year":"2001","journal-title":"J. Bacteriol."},{"key":"ref34","doi-asserted-by":"publisher","first-page":"649","DOI":"10.1094\/MPMI-09-10-0209","article-title":"HrpG and HrpX play global roles in coordinating different virulence traits of xanthomonas axonopodis pv. Citri","volume":"24","author":"Guo","year":"2011","journal-title":"MPMI"},{"key":"ref35","doi-asserted-by":"publisher","first-page":"1092","DOI":"10.1094\/MPMI-19-1092","article-title":"WtsE, an AvrE-family effector protein from Pantoea stewartii subsp. stewartii, causes disease-associated cell death in corn and requires a chaperone protein for stability","volume":"19","author":"Ham","year":"2006","journal-title":"MPMI"},{"key":"ref36","doi-asserted-by":"publisher","first-page":"633","DOI":"10.1111\/j.1364-3703.2008.00489.x","article-title":"WtsE, an AvrE-family type III effector protein of Pantoea stewartii subsp. stewartii, causes cell death in non-host plants","volume":"9","author":"Ham","year":"2008","journal-title":"Mol. Plant Pathol."},{"key":"ref37","doi-asserted-by":"publisher","first-page":"1359","DOI":"10.1094\/MPMI-21-10-1359","article-title":"Pantoea stewartii subsp. stewartii exhibits surface motility, which is a critical aspect of Stewart\u2019s wilt disease development on maize","volume":"21","author":"Herrera","year":"2008","journal-title":"MPMI"},{"key":"ref38","doi-asserted-by":"publisher","first-page":"e00705-19","DOI":"10.1128\/msystems.00705-19","article-title":"The remarkable dual-level diversity of prokaryotic flagellins","volume":"5","author":"Hu","year":"2020","journal-title":"mSystems"},{"key":"ref39","doi-asserted-by":"publisher","first-page":"5114","DOI":"10.1038\/s41467-018-07641-9","article-title":"High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries","volume":"9","author":"Jain","year":"2018","journal-title":"Nat. Commun."},{"key":"ref40","doi-asserted-by":"publisher","first-page":"5356","DOI":"10.2903\/j.efsa.2018.5356","article-title":"Pest categorisation of Pantoea stewartii subsp. stewartii","volume":"16","author":"Jeger","year":"2018","journal-title":"EFS2"},{"key":"ref41","doi-asserted-by":"publisher","first-page":"D591","DOI":"10.1093\/nar\/gkq1154","article-title":"Effective--a database of predicted secreted bacterial proteins","volume":"39","author":"Jehl","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"ref42","doi-asserted-by":"publisher","first-page":"e01793-19","DOI":"10.1128\/mBio.01793-19","article-title":"Role of flagellin-homologous proteins in biofilm formation by pathogenic Vibrio species","volume":"10","author":"Jung","year":"2019","journal-title":"MBio"},{"key":"ref43","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1016\/j.molcel.2014.02.021","article-title":"Direct regulation of the NADPH oxidase RBOHD by the PRR-associated kinase BIK1 during plant immunity","volume":"54","author":"Kadota","year":"2014","journal-title":"Mol. Cell"},{"key":"ref44","doi-asserted-by":"publisher","first-page":"e2568","DOI":"10.21769\/BioProtoc.2568","article-title":"Xanthomonas oryzae pv. Oryzae inoculation and growth rate on rice by leaf clipping method","volume":"7","author":"Ke","year":"2017","journal-title":"Bio-Protoc."},{"key":"ref45","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. Gen. Genomics."},{"key":"ref46","doi-asserted-by":"publisher","first-page":"1509","DOI":"10.1094\/PHYTO-11-20-0508-R","article-title":"Identification of two novel pathovars of Pantoea stewartii subsp. indologenes affecting Allium sp. and millets","volume":"111","author":"Koirala","year":"2021","journal-title":"Phytopathology"},{"key":"ref47","doi-asserted-by":"publisher","first-page":"e1000388","DOI":"10.1371\/journal.ppat.1000388","article-title":"Deletions in the repertoire of Pseudomonas syringae pv. Tomato DC3000 type III secretion effector genes reveal functional overlap among effectors","volume":"5","author":"Kvitko","year":"2009","journal-title":"PLoS Pathog."},{"key":"ref48","doi-asserted-by":"publisher","first-page":"W78","DOI":"10.1093\/nar\/gkae268","article-title":"Interactive tree of life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool","volume":"52","author":"Letunic","year":"2024","journal-title":"Nucleic Acids Res."},{"key":"ref49","doi-asserted-by":"publisher","first-page":"958","DOI":"10.1038\/s41564-025-01966-0","article-title":"Pseudomonas syringae subpopulations cooperate by coordinating flagellar and type III secretion spatiotemporal dynamics to facilitate plant infection","volume":"10","author":"L\u00f3pez-Pag\u00e1n","year":"2025","journal-title":"Nat. Microbiol."},{"key":"ref50","doi-asserted-by":"publisher","first-page":"270","DOI":"10.3389\/fcimb.2019.00270","article-title":"Salmonella pathogenicity island 1 (SPI-1) and its complex regulatory network","volume":"9","author":"Lou","year":"2019","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"ref51","doi-asserted-by":"publisher","first-page":"e03621","DOI":"10.1128\/spectrum.03621-22","article-title":"Duplicated flagellins in Pseudomonas divergently contribute to motility and plant immune elicitation","volume":"11","author":"Luo","year":"2023","journal-title":"Microbiol. Spectrum"},{"key":"ref52","doi-asserted-by":"publisher","first-page":"106836","DOI":"10.1016\/j.cropro.2024.106836","article-title":"First report of maize leaf blight disease caused by Pantoea stewartii subsp indologenes in Kerman Province, Iran","volume":"184","author":"Mangeli","year":"2024","journal-title":"Crop Prot."},{"key":"ref53","doi-asserted-by":"publisher","first-page":"162","DOI":"10.1099\/00207713-43-1-162","article-title":"Transfer of Erwinia ananas (synonym, Erwinia uredovora) and Erwinia stewartii to the genus Pantoea emend. As Pantoea ananas (serrano 1928) comb. nov. and Pantoea stewartii (Smith 1898) comb. nov., respectively, and description of Pantoea stewartii subsp. indologenes subsp. nov","volume":"43","author":"Mergaert","year":"1993","journal-title":"Int. J. Syst. Bacteriol."},{"key":"ref54","doi-asserted-by":"publisher","first-page":"223","DOI":"10.1094\/PDIS.2003.87.3.223","article-title":"Relationships between reactions of sweet corn hybrids to Stewart\u2019s wilt and incidence of systemic infection by Erwinia stewartii","volume":"87","author":"Michener","year":"2003","journal-title":"Plant Dis."},{"key":"ref55","doi-asserted-by":"publisher","first-page":"1209","DOI":"10.1111\/mpp.13105","article-title":"Synergistic interaction between the type III secretion system of the endophytic bacterium Pantoea agglomerans DAPP-PG 734 and the virulence of the causal agent of olive knot Pseudomonas savastanoi pv. Savastanoi DAPP-PG 722","volume":"22","author":"Moretti","year":"2021","journal-title":"Mol. Plant Pathol."},{"key":"ref56","doi-asserted-by":"publisher","first-page":"210","DOI":"10.1016\/j.jssas.2015.06.006","article-title":"Study of southern corn leaf blight (SCLB) on maize genotypes and its effect on yield","volume":"16","author":"Mubeen","year":"2017","journal-title":"J. Saudi Soc. Agric. Sci."},{"key":"ref57","doi-asserted-by":"publisher","first-page":"2213","DOI":"10.1105\/tpc.112.096073","article-title":"Chimeric FLS2 receptors reveal the basis for differential flagellin perception in Arabidopsis and tomato","volume":"24","author":"Mueller","year":"2012","journal-title":"Plant Cell"},{"key":"ref58","doi-asserted-by":"publisher","first-page":"629","DOI":"10.1021\/acs.analchem.5b03884","article-title":"Interfacing microfluidics with negative stain transmission electron microscopy","volume":"88","author":"Mukhitov","year":"2016","journal-title":"Anal. Chem."},{"key":"ref59","doi-asserted-by":"publisher","first-page":"280","DOI":"10.1007\/s12275-018-8014-6","article-title":"UBCG: up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction","volume":"56","author":"Na","year":"2018","journal-title":"J. Microbiol."},{"key":"ref60","doi-asserted-by":"publisher","first-page":"1165","DOI":"10.1094\/MPMI-21-9-1165","article-title":"Amino acid sequence of bacterial microbe-associated molecular pattern flg22 is required for virulence","volume":"21","author":"Naito","year":"2008","journal-title":"MPMI"},{"key":"ref61","doi-asserted-by":"publisher","first-page":"7521","DOI":"10.3390\/ijms22147521","article-title":"Bacterial flagellar filament: a supramolecular multifunctional nanostructure","volume":"22","author":"Nedeljkovi\u0107","year":"2021","journal-title":"IJMS"},{"key":"ref62","doi-asserted-by":"publisher","first-page":"1582","DOI":"10.1111\/mpp.12860","article-title":"Two Pantoea agglomerans type III effectors can transform nonpathogenic and phytopathogenic bacteria into host-specific gall-forming pathogens","volume":"20","author":"Nissan","year":"2019","journal-title":"Mol. Plant Pathol."},{"key":"ref63","doi-asserted-by":"publisher","first-page":"e3237","DOI":"10.7717\/peerj.3237","article-title":"Analysis of the in planta transcriptome expressed by the corn pathogen Pantoea stewartii subsp. stewartii via RNA-seq","volume":"5","author":"Packard","year":"2017","journal-title":"PeerJ"},{"key":"ref64","doi-asserted-by":"publisher","first-page":"620","DOI":"10.1016\/j.chom.2021.02.008","article-title":"Signatures of antagonistic pleiotropy in a bacterial flagellin epitope","volume":"29","author":"Parys","year":"2021","journal-title":"Cell Host Microbe"},{"key":"ref65","doi-asserted-by":"publisher","first-page":"603","DOI":"10.1094\/MPMI-02-14-0032-R","article-title":"Pseudomonas syringae evades host immunity by degrading flagellin monomers with alkaline protease AprA","volume":"27","author":"Pel","year":"2014","journal-title":"MPMI"},{"key":"ref66","doi-asserted-by":"publisher","first-page":"W200","DOI":"10.1093\/nar\/gky448","article-title":"HMMER web server: 2018 update","volume":"46","author":"Potter","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"ref67","doi-asserted-by":"publisher","first-page":"e9490","DOI":"10.1371\/journal.pone.0009490","article-title":"FastTree 2 \u2013 approximately maximum-likelihood trees for large alignments","volume":"5","author":"Price","year":"2010","journal-title":"PLoS One"},{"key":"ref68","doi-asserted-by":"publisher","first-page":"19126","DOI":"10.1073\/pnas.0906412106","article-title":"Shifting the genomic gold standard for the prokaryotic species definition","volume":"106","author":"Richter","year":"2009","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref69","doi-asserted-by":"publisher","first-page":"6300","DOI":"10.1099\/ijsem.0.006300","article-title":"Update on the proposed minimal standards for the use of genome data for the taxonomy of prokaryotes","volume":"74","author":"Riesco","year":"2024","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref70","doi-asserted-by":"publisher","first-page":"1729","DOI":"10.3390\/microorganisms11071729","article-title":"Complete genome sequence of Pantoea stewartii RON18713 from Brazil nut tree phyllosphere reveals genes involved in plant growth promotion","volume":"11","author":"Rocha","year":"2023","journal-title":"Microorganisms"},{"key":"ref71","doi-asserted-by":"publisher","first-page":"628","DOI":"10.1111\/j.1364-3703.2010.00698.x","article-title":"Pantoea stewartii subsp. stewartii: lessons learned from a xylem-dwelling pathogen of sweet corn","volume":"12","author":"Roper","year":"2011","journal-title":"Mol. 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