{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T02:55:05Z","timestamp":1790564105450,"version":"4.1.0"},"reference-count":70,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2026,7,3]],"date-time":"2026-07-03T00:00:00Z","timestamp":1783036800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T00:00:00Z","timestamp":1790553600000},"content-version":"vor","delay-in-days":87,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"funder":[{"name":"the Special Fund for Scientific and Technological Innovation Strategy of Guangdong Province","award":["pdjh2024a201"],"award-info":[{"award-number":["pdjh2024a201"]}]},{"name":"the grants from the Second-round Key Deployment of Rural Technology Commissioners under the \u201cHundred, Thousand, Ten-Thousand\u201d Project","award":["No. KTP20240299 and 2025A03011001"],"award-info":[{"award-number":["No. KTP20240299 and 2025A03011001"]}]},{"name":"Integrated Key Technology for Intensive Vegetable Seedling Cultivation and Demonstration Base","award":["No. 2024A0304009"],"award-info":[{"award-number":["No. 2024A0304009"]}]},{"name":"Research and Demonstration of Key Technologies for Agricultural Microbial Technology to Improve the Production Quality and Efficiency of Organic Vegetables and Fruits in South China","award":["No. 2023B0202010012"],"award-info":[{"award-number":["No. 2023B0202010012"]}]},{"name":"Research, Application and Demonstration of Key Simplified Green Prevention and Control Technologies for Banana Fusarium Wilt Based on Rhizosphere Immunity Regulation","award":["No. 202206010083"],"award-info":[{"award-number":["No. 202206010083"]}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Genomics"],"DOI":"10.1186\/s12864-026-13097-9","type":"journal-article","created":{"date-parts":[[2026,7,3]],"date-time":"2026-07-03T12:20:09Z","timestamp":1783081209000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Comparative genomic analysis of Herbaspirillum strains associated with banana sheath rot reveals potential virulence factors"],"prefix":"10.1186","volume":"27","author":[{"given":"Nianjia","family":"Li","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shuyin","family":"Luo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shijie","family":"You","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanhui","family":"Wu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yulan","family":"Ruan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sijia","family":"Luo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuefeng","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Huiwen","family":"Yang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yutao","family":"Huang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shurui","family":"Hu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guohui","family":"Yu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yunhao","family":"Sun","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,7,3]]},"reference":[{"issue":"4","key":"13097_CR1","first-page":"69","volume":"39","author":"K Chen","year":"2014","unstructured":"Chen K, Qing L, Yuan Y, et al. Pathogenicity differentiation and genetic diversity analysis of banana bacterial soft rot pathogens. J Southwest China Norm Univ (Nat Sci Ed). 2014;39(4):69\u201376.","journal-title":"J Southwest China Norm Univ (Nat Sci Ed)"},{"key":"13097_CR2","unstructured":"Wang F, Xie J. Review of Chinese Banana Industry during the 13th Five-Year Plan Period and Outlook of this Industry during the 14th Five-Year Plan Period. China Trop Agric. 2022;1(3):15\u201322."},{"issue":"8","key":"13097_CR3","first-page":"1","volume":"107","author":"S Yunhao","year":"2023","unstructured":"Yunhao S, Chuanyuan Z, Jianuan Z, et al. Pathogen Profile of Klebsiella variicola, the Causative Agent of Banana Sheath Rot. Plant Dis. 2023;107(8):1\u20138.","journal-title":"Plant Dis"},{"issue":"1","key":"13097_CR4","first-page":"86","volume":"36","author":"JI Baldani","year":"1986","unstructured":"Baldani JI, Baldani VLD, Seldin L, et al. Characterization of Herbaspirillum seropedicae gen. nov., sp. nov., a root-associated nitrogen-fixing bacterium. Int J Syst Evol Microbiol. 1986;36(1):86\u201393.","journal-title":"Int J Syst Evol Microbiol"},{"issue":"1","key":"13097_CR5","doi-asserted-by":"publisher","first-page":"197","DOI":"10.1007\/BF00335935","volume":"21","author":"FL Olivares","year":"1996","unstructured":"Olivares FL, Baldani VLD, Reis VM, et al. Occurrence of endophytic diazotrophs Herbaspirillum spp. in roots, stems and leaves predominantly of Gramineae. Biol Fertil Soils. 1996;21(1):197\u2013200.","journal-title":"Biol Fertil Soils"},{"issue":"5","key":"13097_CR6","doi-asserted-by":"publisher","first-page":"2375","DOI":"10.1128\/AEM.67.5.2375-2379.2001","volume":"67","author":"L Magalhaes Cruz","year":"2001","unstructured":"Magalhaes Cruz L, de Souza EM, Weber OB, et al. 16S ribosomal DNA characterization of nitrogen-fixing bacteria isolated from banana (Musa spp.) and pineapple (Ananas comosus (L.) Merril). Appl Environ Microbiol. 2001;67(5):2375\u20139.","journal-title":"Appl Environ Microbiol"},{"issue":"1","key":"13097_CR7","doi-asserted-by":"publisher","first-page":"85","DOI":"10.1111\/j.1574-6941.2008.00582.x","volume":"66","author":"M Rothballer","year":"2008","unstructured":"Rothballer M, Eckert B, Schmid M, et al. Endophytic root colonization of gramineous plants by Herbaspirillum frisingense. FEMS Microbiol Ecol. 2008;66(1):85\u201395.","journal-title":"FEMS Microbiol Ecol"},{"issue":"6","key":"13097_CR8","doi-asserted-by":"publisher","first-page":"625","DOI":"10.1007\/s11103-017-0629-1","volume":"94","author":"G Valdameri","year":"2017","unstructured":"Valdameri G, Alberton D, Moure VR, et al. Herbaspirillum rubrisubalbicans, a mild pathogen impairs growth of rice by augmenting ethylene levels. Plant Mol Biol. 2017;94(6):625\u201340.","journal-title":"Plant Mol Biol"},{"key":"13097_CR9","doi-asserted-by":"publisher","first-page":"98","DOI":"10.1186\/1471-2180-12-98","volume":"12","author":"MA Schmidt","year":"2012","unstructured":"Schmidt MA, Balsanelli E, Faoro H, et al. The type III secretion system is necessary for the development of a pathogenic and endophytic interaction between Herbaspirillum rubrisubalbicans and Poaceae. BMC Microbiol. 2012;12:98.","journal-title":"BMC Microbiol"},{"issue":"3","key":"13097_CR10","doi-asserted-by":"publisher","first-page":"379","DOI":"10.1094\/PDIS-94-3-0379B","volume":"94","author":"ZQ Tan","year":"2010","unstructured":"Tan ZQ, Men R, Zhang RY, et al. First report of Herbaspirillum rubrisubalbicans causing mottled stripe disease on sugarcane in China. Plant Dis. 2010;94(3):379.","journal-title":"Plant Dis"},{"issue":"6","key":"13097_CR11","doi-asserted-by":"publisher","first-page":"2223","DOI":"10.1099\/ijs.0.02975-0","volume":"54","author":"L Ding","year":"2004","unstructured":"Ding L, Yokota A. Proposals of Curvibacter gracilis gen. nov., sp. nov. and Herbaspirillum putei sp. nov. for bacterial strains isolated from well water and reclassification of Pseudomonas huttiensis, Pseudomonas lanceolata, Aquaspirillum delicatum and Aquaspirillum autotrophicum as Herbaspirillum huttiense comb. nov., Curvibacter lanceolatus comb. nov., Curvibacter delicatus comb. nov. and Herbaspirillum autotrophicum comb. nov. Int J Syst Evol Microbiol. 2004;54(6):2223\u201330.","journal-title":"Int J Syst Evol Microbiol"},{"issue":"12","key":"13097_CR12","first-page":"3762","volume":"107","author":"B Benitez","year":"2023","unstructured":"Benitez B, Poudel M, Jones JB, et al. First report of a Herbaspirillum sp. causing leaf spots on Boston Fern (Nephrolepis exaltata) in Florida. Plant Dis. 2023;107(12):3762.","journal-title":"Plant Dis"},{"issue":"1","key":"13097_CR13","doi-asserted-by":"publisher","first-page":"175","DOI":"10.1007\/s11104-012-1125-7","volume":"356","author":"RA Monteiro","year":"2012","unstructured":"Monteiro RA, Balsanelli E, Wassem R, et al. Herbaspirillum-plant interactions: microscopical, histological and molecular aspects. Plant Soil. 2012;356(1):175\u201396.","journal-title":"Plant Soil"},{"key":"13097_CR14","doi-asserted-by":"publisher","first-page":"882827","DOI":"10.3389\/fcimb.2022.882827","volume":"12","author":"X Li","year":"2022","unstructured":"Li X, Bao X, Qiao G, et al. First study of bacteremia caused by Herbaspirillum huttiense in China: a brief research report and literature review. Front Cell Infect Microbiol. 2022;12:882827.","journal-title":"Front Cell Infect Microbiol"},{"issue":"1","key":"13097_CR15","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1055\/a-2437-0367","volume":"229","author":"M Tas","year":"2025","unstructured":"Tas M, Turkyilmaz C, Bozdayi G, et al. Case Report: An Unexpected Herbaspirillum huttiense bacteremia in the Neonatal Intensive Care Unit. Z Geburtshilfe Neonatol. 2025;229(1):44\u20137.","journal-title":"Z Geburtshilfe Neonatol"},{"key":"13097_CR16","unstructured":"Oxford Nanopore Technologies. Dorado: High-speed nanopore basecaller [Software]. Available from: https:\/\/github.com\/nanoporetech\/dorado; 2023."},{"key":"13097_CR17","unstructured":"Wick RR. Porechop: Adapter trimmer for Oxford Nanopore reads [Software]. Available from: https:\/\/github.com\/rrwick\/Porechop; 2017."},{"issue":"17","key":"13097_CR18","doi-asserted-by":"publisher","first-page":"884","DOI":"10.1093\/bioinformatics\/bty560","volume":"34","author":"S Chen","year":"2018","unstructured":"Chen S, Zhou Y, Chen Y, et al. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018;34(17):884\u201390.","journal-title":"Bioinformatics"},{"issue":"5","key":"13097_CR19","doi-asserted-by":"publisher","first-page":"540","DOI":"10.1038\/s41587-019-0072-8","volume":"37","author":"M Kolmogorov","year":"2019","unstructured":"Kolmogorov M, Yuan J, Lin Y, et al. Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol. 2019;37(5):540\u20136.","journal-title":"Nat Biotechnol"},{"issue":"11","key":"13097_CR20","doi-asserted-by":"publisher","first-page":"e112963","DOI":"10.1371\/journal.pone.0112963","volume":"9","author":"BJ Walker","year":"2014","unstructured":"Walker BJ, Abeel T, Shea T, et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS ONE. 2014;9(11):e112963.","journal-title":"PLoS ONE"},{"key":"13097_CR21","unstructured":"Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv e-prints. 2013."},{"issue":"2","key":"13097_CR22","doi-asserted-by":"publisher","first-page":"8","DOI":"10.1093\/gigascience\/giab008","volume":"10","author":"P Danecek","year":"2021","unstructured":"Danecek P, Bonfield JK, Liddle J, et al. Twelve years of SAMtools and BCFtools. Gigascience. 2021;10(2):8.","journal-title":"Gigascience"},{"issue":"14","key":"13097_CR23","doi-asserted-by":"publisher","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","volume":"30","author":"T Seemann","year":"2014","unstructured":"Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30(14):2068\u20139.","journal-title":"Bioinformatics"},{"issue":"14","key":"13097_CR24","doi-asserted-by":"publisher","first-page":"6614","DOI":"10.1093\/nar\/gkw569","volume":"44","author":"T Tatusova","year":"2016","unstructured":"Tatusova T, DiCuccio M, Badretdin A, et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res. 2016;44(14):6614\u201324.","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"13097_CR25","doi-asserted-by":"publisher","first-page":"54","DOI":"10.1093\/nar\/gkw413","volume":"44","author":"TM Lowe","year":"2016","unstructured":"Lowe TM, Chan PP. tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes. Nucleic Acids Res. 2016;44(1):54\u20137.","journal-title":"Nucleic Acids Res"},{"issue":"9","key":"13097_CR26","doi-asserted-by":"publisher","first-page":"3100","DOI":"10.1093\/nar\/gkm160","volume":"35","author":"K Lagesen","year":"2007","unstructured":"Lagesen K, Hallin P, R\u00f8dland EA, et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 2007;35(9):3100\u20138.","journal-title":"Nucleic Acids Res"},{"issue":"22","key":"13097_CR27","doi-asserted-by":"publisher","first-page":"2933","DOI":"10.1093\/bioinformatics\/btt509","volume":"29","author":"EP Nawrocki","year":"2013","unstructured":"Nawrocki EP, Eddy SR. Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics. 2013;29(22):2933\u20135.","journal-title":"Bioinformatics"},{"issue":"2","key":"13097_CR28","doi-asserted-by":"publisher","first-page":"52","DOI":"10.1093\/nar\/gkm360","volume":"35","author":"I Grissa","year":"2007","unstructured":"Grissa I, Vergnaud G, Pourcel C. CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res. 2007;35(2):52\u20137.","journal-title":"Nucleic Acids Res"},{"issue":"13","key":"13097_CR29","doi-asserted-by":"publisher","first-page":"2161","DOI":"10.1093\/bioinformatics\/bty095","volume":"34","author":"C Bertelli","year":"2018","unstructured":"Bertelli C, Brinkman FSL. Improved genomic island predictions with IslandPath-DIMOB. Bioinformatics. 2018;34(13):2161\u20137.","journal-title":"Bioinformatics"},{"issue":"20","key":"13097_CR30","doi-asserted-by":"publisher","first-page":"5839","DOI":"10.1093\/nar\/gkl732","volume":"34","author":"DE Fouts","year":"2006","unstructured":"Fouts DE. Phage_Finder: automated identification and classification of prophage regions in complete bacterial genome sequences. Nucleic Acids Res. 2006;34(20):5839\u201351.","journal-title":"Nucleic Acids Res"},{"key":"13097_CR31","volume-title":"TransposonPSI: an application of PSI-Blast to mine (retro-)transposon ORF homologies","author":"B Haas","year":"2007","unstructured":"Haas B. TransposonPSI: an application of PSI-Blast to mine (retro-)transposon ORF homologies. Cambridge, MA, USA: Broad Institute; 2007."},{"issue":"2","key":"13097_CR32","doi-asserted-by":"publisher","first-page":"573","DOI":"10.1093\/nar\/27.2.573","volume":"27","author":"G Benson","year":"1999","unstructured":"Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999;27(2):573\u201380.","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"13097_CR33","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1002\/0471250953.bi0410s25","volume":"25","author":"M Tarailo-Graovac","year":"2009","unstructured":"Tarailo-Graovac M, Chen N. Using RepeatMasker to identify repetitive elements in genomic sequences. Curr Protoc Bioinf. 2009;25(1):1\u201314.","journal-title":"Curr Protoc Bioinf"},{"issue":"11","key":"13097_CR34","doi-asserted-by":"publisher","first-page":"108141","DOI":"10.1016\/j.isci.2023.108141","volume":"26","author":"Y Mao","year":"2023","unstructured":"Mao Y, Liu X, Zhang N, Wang Z, Han M. NCRD: A non-redundant comprehensive database for detecting antibiotic resistance genes. iScience. 2023;26(11):108141.","journal-title":"iScience"},{"issue":"3","key":"13097_CR35","first-page":"47","volume":"3","author":"E Gasteiger","year":"2001","unstructured":"Gasteiger E, Jung E, Bairoch A. SWISS-PROT: connecting biomolecular knowledge via a protein database. Curr Issues Mol Biol. 2001;3(3):47\u201355.","journal-title":"Curr Issues Mol Biol"},{"issue":"Database issue","key":"13097_CR36","first-page":"D258","volume":"32","author":"MA Harris","year":"2004","unstructured":"Harris MA, Clark J, Ireland A, et al. Gene Ontology Consortium. The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res. 2004;32(Database issue):D258\u201361.","journal-title":"Nucleic Acids Res"},{"key":"13097_CR37","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1186\/1471-2105-4-41","volume":"4","author":"RL Tatusov","year":"2003","unstructured":"Tatusov RL, Fedorova ND, Jackson JD, et al. The COG database: an updated version includes eukaryotes. BMC Bioinform. 2003;4:41.","journal-title":"BMC Bioinform"},{"issue":"D1","key":"13097_CR38","doi-asserted-by":"publisher","first-page":"D587","DOI":"10.1093\/nar\/gkac963","volume":"51","author":"M Kanehisa","year":"2023","unstructured":"Kanehisa M, Furumichi M, Sato Y, et al. KEGG for taxonomy-based analysis of pathways and genomes. Nucleic Acids Res. 2023;51(D1):D587\u201392.","journal-title":"Nucleic Acids Res"},{"key":"13097_CR39","unstructured":"Sayols S. rrvgo: a Bioconductor package for interpreting lists of Gene Ontology terms. microPublication Biol. 2023."},{"issue":"D1","key":"13097_CR40","doi-asserted-by":"publisher","first-page":"D222","DOI":"10.1093\/nar\/gkt1223","volume":"42","author":"RD Finn","year":"2014","unstructured":"Finn RD, Bateman A, Clements J, et al. Pfam: the protein families database. Nucleic Acids Res. 2014;42(D1):D222\u201330.","journal-title":"Nucleic Acids Res"},{"issue":"D1","key":"13097_CR41","first-page":"D613","volume":"48","author":"M Urban","year":"2020","unstructured":"Urban M, Cuzick A, Seager J, Wood V, Rutherford K, Venkatesh SY, et al. PHI-base: the pathogen-host interactions database. Nucleic Acids Res. 2020;48(D1):D613\u201320.","journal-title":"Nucleic Acids Res"},{"issue":"D1","key":"13097_CR42","first-page":"D517","volume":"48","author":"BP Alcock","year":"2020","unstructured":"Alcock BP, Raphenya AR, Lau TTY, et al. CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Res. 2020;48(D1):D517\u201325.","journal-title":"Nucleic Acids Res"},{"issue":"Database issue","key":"13097_CR43","doi-asserted-by":"publisher","first-page":"D490","DOI":"10.1093\/nar\/gkt1178","volume":"42","author":"V Lombard","year":"2014","unstructured":"Lombard V, Golaconda Ramulu H, Drula E, et al. The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res. 2014;42(Database issue):D490\u20135.","journal-title":"Nucleic Acids Res"},{"issue":"10","key":"13097_CR44","doi-asserted-by":"publisher","first-page":"785","DOI":"10.1038\/nmeth.1701","volume":"8","author":"TN Petersen","year":"2011","unstructured":"Petersen TN, Brunak S, von Heijne G, et al. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods. 2011;8(10):785\u20136.","journal-title":"Nat Methods"},{"issue":"3","key":"13097_CR45","doi-asserted-by":"publisher","first-page":"567","DOI":"10.1006\/jmbi.2000.4315","volume":"305","author":"A Krogh","year":"2001","unstructured":"Krogh A, Larsson B, von Heijne G, et al. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol. 2001;305(3):567\u201380.","journal-title":"J Mol Biol"},{"key":"13097_CR46","doi-asserted-by":"crossref","unstructured":"Arnold R, Brandmaier S, Kleine F et al. Sequence-based prediction of type III secreted proteins. PLoS Pathog. 2009;5(4):e1000376. https:\/\/doi.org\/10.1371\/journal.ppat.1000376.","DOI":"10.1371\/journal.ppat.1000376"},{"issue":"1","key":"13097_CR47","doi-asserted-by":"publisher","first-page":"36","DOI":"10.1093\/nar\/gkx319","volume":"45","author":"K Blin","year":"2017","unstructured":"Blin K, Wolf T, Chevrette MG, et al. antiSMASH 4.0\u2014improvements in chemistry prediction and gene cluster boundary identification. Nucleic Acids Res. 2017;45(1):36\u201341.","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"13097_CR48","doi-asserted-by":"publisher","first-page":"30","DOI":"10.1093\/nar\/gkx343","volume":"45","author":"C Bertelli","year":"2017","unstructured":"Bertelli C, Laird MR, Williams KP, et al. IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets. Nucleic Acids Res. 2017;45(1):30\u20135.","journal-title":"Nucleic Acids Res"},{"issue":"7","key":"13097_CR49","doi-asserted-by":"publisher","first-page":"1043","DOI":"10.1101\/gr.186072.114","volume":"25","author":"DH Parks","year":"2015","unstructured":"Parks DH, Imelfort M, Skennerton CT, et al. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25(7):1043\u201355.","journal-title":"Genome Res"},{"issue":"2","key":"13097_CR50","doi-asserted-by":"publisher","first-page":"12","DOI":"10.1186\/gb-2004-5-2-r12","volume":"5","author":"S Kurtz","year":"2004","unstructured":"Kurtz S, Phillippy A, Delcher AL, et al. Versatile and open software for comparing large genomes. Genome Biol. 2004;5(2):12.","journal-title":"Genome Biol"},{"issue":"4","key":"13097_CR51","doi-asserted-by":"publisher","first-page":"366","DOI":"10.1038\/s41592-021-01101-x","volume":"18","author":"B Buchfink","year":"2021","unstructured":"Buchfink B, Reuter K, Drost HG. Sensitive protein alignments at tree-of-life scale using DIAMOND. Nat Methods. 2021;18(4):366\u20138.","journal-title":"Nat Methods"},{"issue":"9","key":"13097_CR52","doi-asserted-by":"publisher","first-page":"2178","DOI":"10.1101\/gr.1224503","volume":"13","author":"L Li","year":"2003","unstructured":"Li L, Stoeckert CJ Jr, Roos DS. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 2003;13(9):2178\u201389.","journal-title":"Genome Res"},{"issue":"1","key":"13097_CR53","doi-asserted-by":"publisher","first-page":"12","DOI":"10.1039\/C5AY02550H","volume":"8","author":"L Pritchard","year":"2016","unstructured":"Pritchard L, Glover RH, Humphris S, et al. Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens. Anal Methods. 2016;8(1):12\u201324.","journal-title":"Anal Methods"},{"key":"13097_CR54","unstructured":"Parks DH. CompareM: a comparative genomics toolbox [Computer software]. Version 0.1.2. GitHub; 2021. Available from: https:\/\/github.com\/dparks1134\/CompareM"},{"issue":"22","key":"13097_CR55","doi-asserted-by":"publisher","first-page":"3691","DOI":"10.1093\/bioinformatics\/btv421","volume":"31","author":"AJ Page","year":"2015","unstructured":"Page AJ, Cummins CA, Hunt M, et al. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics. 2015;31(22):3691\u20133.","journal-title":"Bioinformatics"},{"key":"13097_CR56","doi-asserted-by":"crossref","unstructured":"Edgar RC. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics. 2004;5:113.","DOI":"10.1186\/1471-2105-5-113"},{"key":"13097_CR57","unstructured":"Edgar RC. MUSCLE v5 enables improved estimates of phylogenetic tree confidence by ensemble bootstrapping. Nat Biotechnol. 2021;39:1563\u20135."},{"key":"13097_CR58","doi-asserted-by":"crossref","unstructured":"Castresana J. Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis. Mol Biol Evol. 2000;17(4):540\u201352.","DOI":"10.1093\/oxfordjournals.molbev.a026334"},{"key":"13097_CR59","doi-asserted-by":"crossref","unstructured":"Nguyen LT, Schmidt HA, von Haeseler A, et al. IQ-TREE: A fast and effective stochastic algorithm for estimating maximum likelihood phylogenies. Mol Biol Evol. 2015;32(1):268\u201374.","DOI":"10.1093\/molbev\/msu300"},{"key":"13097_CR60","doi-asserted-by":"crossref","unstructured":"Jain C, Rodriguez-R LM, Phillippy AM, et al. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun. 2018;9(1):5114.","DOI":"10.1038\/s41467-018-07641-9"},{"key":"13097_CR61","doi-asserted-by":"crossref","unstructured":"Poudel M, Sharma A, Minsavage GV, et al. Genomic insights into two new subspecies of Herbaspirillum huttiense strains isolated from diseased foliage in Florida. Int J Syst Evol Microbiol. 2024;74(12):1\u201311.","DOI":"10.1099\/ijsem.0.006597"},{"key":"13097_CR62","doi-asserted-by":"crossref","unstructured":"Augusta MS, Eduardo B, Hellison F, et al. The type III secretion system is necessary for the development of a pathogenic and endophytic interaction between Herbaspirillum rubrisubalbicans and Poaceae. BMC Microbiol. 2012;12(1):98.","DOI":"10.1186\/1471-2180-12-98"},{"key":"13097_CR63","doi-asserted-by":"crossref","unstructured":"Gupta G, Chauhan PS, Jha PN, et al. Secretory molecules from secretion systems fine-tune the host-beneficial bacteria (PGPRs) interaction. Front Microbiol. 2024;15:1355750.","DOI":"10.3389\/fmicb.2024.1355750"},{"key":"13097_CR64","doi-asserted-by":"crossref","unstructured":"Salinero-Lanzarote A, Pacheco-Moreno A, Domingo-Serrano L, et al. The Type VI secretion system of Rhizobium etli Mim1 has a positive effect in symbiosis. FEMS Microbiol Ecol. 2019;95(5):54.","DOI":"10.1093\/femsec\/fiz054"},{"key":"13097_CR65","doi-asserted-by":"crossref","unstructured":"Montgomery AP, Xiao K, Wang X, et al. Computational glycobiology: mechanistic studies of carbohydrate-active enzymes and implication for inhibitor design. Adv Protein Chem Struct Biol. 2017;109:25\u201376.","DOI":"10.1016\/bs.apcsb.2017.04.003"},{"key":"13097_CR66","doi-asserted-by":"crossref","unstructured":"Alcock BP, Huynh W, Chalil R, et al. CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database. Nucleic Acids Res. 2023;51(1):690\u20139.","DOI":"10.1093\/nar\/gkac920"},{"key":"13097_CR67","doi-asserted-by":"publisher","unstructured":"Pedrosa FO, Monteiro RA, Wassem R et al. Genome of Herbaspirillum seropedicae strain SmR1, a specialized diazotrophic endophyte of tropical grasses. PLoS Genet. 2011;7(5):e1002064.\u00a0https:\/\/doi.org\/10.1371\/journal.pgen.1002064.","DOI":"10.1371\/journal.pgen.1002064"},{"key":"13097_CR68","doi-asserted-by":"crossref","unstructured":"Peeters N, Carr\u00e8re S, Anisimova M, et al. Repertoire, unified nomenclature and evolution of the Type III effector gene set in the Ralstonia solanacearum species complex. BMC Genomics. 2013;14:859.","DOI":"10.1186\/1471-2164-14-859"},{"key":"13097_CR69","doi-asserted-by":"crossref","unstructured":"Yang L, Xu B, He W, et al. The HrpW protein of Lonsdalea quercina N-5-1 has pectate lyase activity and is required for full bacterial virulence. J Basic Microbiol. 2014;54(10):1126\u201335","DOI":"10.1002\/jobm.201300342"},{"key":"13097_CR70","doi-asserted-by":"crossref","unstructured":"Dong Z, Wang Z. Isolation and Heterologous Expression of a Polygalacturonase Produced by Fusarium oxysporum f. sp. cubense Race 1 and 4. Int J Mol Sci. 2015;16(4):7595\u2013607.","DOI":"10.3390\/ijms16047595"}],"container-title":["BMC Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12864-026-13097-9","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12864-026-13097-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12864-026-13097-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T02:02:11Z","timestamp":1790560931000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1186\/s12864-026-13097-9"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,7,3]]},"references-count":70,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,12]]}},"alternative-id":["13097"],"URL":"https:\/\/doi.org\/10.1186\/s12864-026-13097-9","relation":{},"ISSN":["1471-2164"],"issn-type":[{"value":"1471-2164","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,7,3]]},"assertion":[{"value":"28 November 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"16 June 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"3 July 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Not applicable.","order":1,"name":"Ethics","label":"Ethics approval and consent to participate","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not applicable.","order":2,"name":"Ethics","label":"Consent for publication","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The authors declare no competing interests.","order":3,"name":"Ethics","label":"Competing interests","group":{"name":"EthicsHeading","label":"Declarations"}}],"article-number":"792"}}