{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T19:07:42Z","timestamp":1792782462735,"version":"4.5.0"},"reference-count":93,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T00:00:00Z","timestamp":1792022400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T00:00:00Z","timestamp":1792022400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"funder":[{"name":"Science and Technology Program of Yunnan Province","award":["202402AE090018"],"award-info":[{"award-number":["202402AE090018"]}]},{"name":"China Agriculture Research System of MOF and MARA","award":["CARS-23-G56"],"award-info":[{"award-number":["CARS-23-G56"]}],"id":[{"id":"https:\/\/ror.org\/03p5eky76","id-type":"ROR","asserted-by":"crossref"}]},{"name":"Yunnan Academy of Agricultural Sciences Talent Introduction and Training Project","award":["2024RCYP-10"],"award-info":[{"award-number":["2024RCYP-10"]}],"id":[{"id":"https:\/\/ror.org\/02z2d6373","id-type":"ROR","asserted-by":"crossref"}]},{"name":"Yunnan Fundamental Research Project","award":["202501CF070036"],"award-info":[{"award-number":["202501CF070036"]}]},{"name":"Innovation Guidance and Technology Oriented Enterprise Cultivation Plan","award":["202404BI090009"],"award-info":[{"award-number":["202404BI090009"]}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Arch Microbiol"],"published-print":{"date-parts":[[2027,1]]},"DOI":"10.1007\/s00203-026-05256-z","type":"journal-article","created":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T20:51:39Z","timestamp":1792097499000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Comparative genomic analysis of Agrobacterium salinitolerans provides insights into genetic diversity and pathogenic potential"],"prefix":"10.1007","volume":"209","author":[{"given":"Lingling","family":"Xiong","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yinshan","family":"Cui","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ziming","family":"Shi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yingjie","family":"Yang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaolian","family":"Shen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanfei","family":"Cai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiuling","family":"Ji","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,10,15]]},"reference":[{"key":"5256_CR47","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/978-1-4939-7033-9_1","volume":"1615","author":"SS Abby","year":"2017","unstructured":"Abby SS, Rocha EPC (2017) Identification of protein secretion systems in bacterial genomes using MacSyFinder. Methods Mol Biol 1615:1\u201321. https:\/\/doi.org\/10.1007\/978-1-4939-7033-9_1","journal-title":"Methods Mol Biol"},{"issue":"10","key":"5256_CR46","doi-asserted-by":"publisher","first-page":"e110726","DOI":"10.1371\/journal.pone.0110726","volume":"9","author":"SS Abby","year":"2014","unstructured":"Abby SS, N\u00e9ron B, M\u00e9nager H, Touchon M, Rocha EP (2014) MacSyFinder: a program to mine genomes for molecular systems with an application to CRISPR-Cas systems. PLoS ONE 9(10):e110726. https:\/\/doi.org\/10.1371\/journal.pone.0110726","journal-title":"PLoS ONE"},{"key":"5256_CR74","doi-asserted-by":"publisher","first-page":"26","DOI":"10.1016\/j.nmni.2015.05.004","volume":"7","author":"C Al-Bayssari","year":"2015","unstructured":"Al-Bayssari C, Valentini C, Gomez C, Reynaud-Gaubert M, Rolain JM (2015) First detection of insertion sequence element ISPa1328 in the oprD porin gene of an imipenem-resistant Pseudomonas aeruginosa isolate from an idiopathic pulmonary fibrosis patient in Marseille, France. New Microbes New Infect 7:26\u201327. https:\/\/doi.org\/10.1016\/j.nmni.2015.05.004","journal-title":"New Microbes New Infect"},{"key":"5256_CR64","doi-asserted-by":"publisher","unstructured":"Amaro C, Sanju\u00e1n E, Fouz B, Pajuelo D, Lee C-T, Hor L-I et al (2015) The fish pathogen Vibrio vulnificus biotype 2: epidemiology, phylogeny, and virulence factors involved in warm-water vibriosis. Microbiol Spectr 3(3). https:\/\/doi.org\/10.1128\/microbiolspec","DOI":"10.1128\/microbiolspec"},{"issue":"5","key":"5256_CR16","doi-asserted-by":"publisher","first-page":"2159","DOI":"10.1093\/nar\/gky066","volume":"46","author":"S Ardui","year":"2018","unstructured":"Ardui S, Ameur A, Vermeesch JR, Hestand MS (2018) Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics. Nucleic Acids Res 46(5):2159\u20132168. https:\/\/doi.org\/10.1093\/nar\/gky066","journal-title":"Nucleic Acids Res"},{"issue":"W1","key":"5256_CR32","doi-asserted-by":"publisher","first-page":"W16","DOI":"10.1093\/nar\/gkw387","volume":"44","author":"D Arndt","year":"2016","unstructured":"Arndt D, Grant JR, Marcu A, Sajed T, Pon A, Liang Y et al (2016) PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res 44(W1):W16\u201321. https:\/\/doi.org\/10.1093\/nar\/gkw387","journal-title":"Nucleic Acids Res"},{"issue":"4","key":"5256_CR91","doi-asserted-by":"publisher","first-page":"206","DOI":"10.1038\/s41579-021-00650-4","volume":"20","author":"BJ Arnold","year":"2022","unstructured":"Arnold BJ, Huang I-T, Hanage WP (2022) Horizontal gene transfer and adaptive evolution in bacteria. Nat Rev Microbiol 20(4):206\u2013218","journal-title":"Nat Rev Microbiol"},{"issue":"2","key":"5256_CR68","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1016\/j.mib.2006.02.008","volume":"9","author":"S Backert","year":"2006","unstructured":"Backert S, Meyer TF (2006) Type IV secretion systems and their effectors in bacterial pathogenesis. Curr Opin Microbiol 9(2):207\u2013217. https:\/\/doi.org\/10.1016\/j.mib.2006.02.008","journal-title":"Curr Opin Microbiol"},{"key":"5256_CR76","doi-asserted-by":"publisher","unstructured":"Benson MA, Ohneck EA, Ryan C, Alonzo F 3rd, Smith H, Narechania A et al (2014) Evolution of hypervirulence by a MRSA clone through acquisition of a transposable element. Mol Microbiol 93(4):664\u2013681. https:\/\/doi.org\/10.1111\/mmi.12682","DOI":"10.1111\/mmi.12682"},{"issue":"W1","key":"5256_CR34","doi-asserted-by":"publisher","first-page":"W30","DOI":"10.1093\/nar\/gkx343","volume":"45","author":"C Bertelli","year":"2017","unstructured":"Bertelli C, Laird MR, Williams KP, Lau BY, Hoad G, Winsor GL et al (2017) IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets. Nucleic Acids Res 45(W1):W30\u2013w5. https:\/\/doi.org\/10.1093\/nar\/gkx343","journal-title":"Nucleic Acids Res"},{"key":"5256_CR84","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12862-018-1272-4","volume":"18","author":"L-M Bobay","year":"2018","unstructured":"Bobay L-M, Ochman H (2018) Factors driving effective population size and pan-genome evolution in bacteria. BMC Evol Biol 18:1\u201312","journal-title":"BMC Evol Biol"},{"issue":"1","key":"5256_CR75","doi-asserted-by":"publisher","first-page":"143","DOI":"10.1016\/S0378-1097(03)00882-6","volume":"230","author":"D Boutoille","year":"2004","unstructured":"Boutoille D, Corvec S, Caroff N, Giraudeau C, Espaze E, Caillon J et al (2004) Detection of an IS21 insertion sequence in the mexR gene of Pseudomonas aeruginosa increasing \u03b2-lactam resistance. FEMS Microbiol Lett 230(1):143\u2013146. https:\/\/doi.org\/10.1016\/S0378-1097(03)00882-6","journal-title":"FEMS Microbiol Lett"},{"issue":"20","key":"5256_CR92","doi-asserted-by":"publisher","first-page":"R1094","DOI":"10.1016\/j.cub.2019.08.012","volume":"29","author":"MA Brockhurst","year":"2019","unstructured":"Brockhurst MA, Harrison E, Hall JPJ, Richards T, McNally A, MacLean C (2019) The Ecology and Evolution of Pangenomes. Curr Biol 29(20):R1094\u2013r103. https:\/\/doi.org\/10.1016\/j.cub.2019.08.012","journal-title":"Curr Biol"},{"issue":"1","key":"5256_CR26","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1038\/nmeth.3176","volume":"12","author":"B Buchfink","year":"2015","unstructured":"Buchfink B, Xie C, Huson DH (2015) Fast and sensitive protein alignment using DIAMOND. Nat Methods 12(1):59\u201360. https:\/\/doi.org\/10.1038\/nmeth.3176","journal-title":"Nat Methods"},{"issue":"1","key":"5256_CR51","doi-asserted-by":"publisher","first-page":"81","DOI":"10.1111\/1574-6976.12085","volume":"39","author":"E Cabez\u00f3n","year":"2015","unstructured":"Cabez\u00f3n E, Ripoll-Rozada J, Pe\u00f1a A, de la Cruz F, Arechaga I (2015) Towards an integrated model of bacterial conjugation. FEMS Microbiol Rev 39(1):81\u201395. https:\/\/doi.org\/10.1111\/1574-6976.12085","journal-title":"FEMS Microbiol Rev"},{"key":"5256_CR62","doi-asserted-by":"publisher","first-page":"91","DOI":"10.1016\/j.semcdb.2015.10.032","volume":"46","author":"B Chaban","year":"2015","unstructured":"Chaban B, Hughes HV, Beeby M (2015) The flagellum in bacterial pathogens: for motility and a whole lot more. Semin Cell Dev Biol 46:91\u2013103. https:\/\/doi.org\/10.1016\/j.semcdb.2015.10.032","journal-title":"Semin Cell Dev Biol"},{"key":"5256_CR18","doi-asserted-by":"publisher","first-page":"238","DOI":"10.1186\/1471-2105-13-238","volume":"13","author":"MJ Chaisson","year":"2012","unstructured":"Chaisson MJ, Tesler G (2012) Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory. BMC Bioinformatics 13:238. https:\/\/doi.org\/10.1186\/1471-2105-13-238","journal-title":"BMC Bioinformatics"},{"issue":"16","key":"5256_CR20","doi-asserted-by":"publisher","first-page":"9077","DOI":"10.1093\/nar\/gkab688","volume":"49","author":"PP Chan","year":"2021","unstructured":"Chan PP, Lin BY, Mak AJ, Lowe TM (2021) tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes. Nucleic Acids Res 49(16):9077\u20139096. https:\/\/doi.org\/10.1093\/nar\/gkab688","journal-title":"Nucleic Acids Res"},{"issue":"30","key":"5256_CR83","doi-asserted-by":"publisher","first-page":"12412","DOI":"10.1073\/pnas.0906217106","volume":"106","author":"S Chattopadhyay","year":"2009","unstructured":"Chattopadhyay S, Weissman SJ, Minin VN, Russo TA, Dykhuizen DE, Sokurenko EV (2009) High frequency of hotspot mutations in core genes of Escherichia coli due to short-term positive selection. Proc Natl Acad Sci U S A 106(30):12412\u201312417. https:\/\/doi.org\/10.1073\/pnas.0906217106","journal-title":"Proc Natl Acad Sci U S A"},{"key":"5256_CR53","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1016\/j.micres.2015.01.004","volume":"172","author":"L Chen","year":"2015","unstructured":"Chen L, Zou Y, She P, Wu Y (2015) Composition, function, and regulation of T6SS in Pseudomonas aeruginosa. Microbiol Res 172:19\u201325. https:\/\/doi.org\/10.1016\/j.micres.2015.01.004","journal-title":"Microbiol Res"},{"issue":"3","key":"5256_CR67","doi-asserted-by":"publisher","first-page":"579","DOI":"10.1046\/j.1365-2958.1997.d01-1875.x","volume":"23","author":"O Chesnokova","year":"1997","unstructured":"Chesnokova O, Coutinho JB, Khan IH, Mikhail MS, Kado CI (1997) Characterization of flagella genes of Agrobacterium tumefaciens, and the effect of a bald strain on virulence. Mol Microbiol 23(3):579\u2013590. https:\/\/doi.org\/10.1046\/j.1365-2958.1997.d01-1875.x","journal-title":"Mol Microbiol"},{"issue":"1","key":"5256_CR1","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1111\/j.1462-5822.2006.00830.x","volume":"9","author":"V Citovsky","year":"2007","unstructured":"Citovsky V, Kozlovsky SV, Lacroix B, Zaltsman A, Dafny-Yelin M, Vyas S et al (2007) Biological systems of the host cell involved in Agrobacterium infection. Cell Microbiol 9(1):9\u201320. https:\/\/doi.org\/10.1111\/j.1462-5822.2006.00830.x","journal-title":"Cell Microbiol"},{"issue":"6","key":"5256_CR52","doi-asserted-by":"publisher","first-page":"343","DOI":"10.1038\/nrmicro3456","volume":"13","author":"TR Costa","year":"2015","unstructured":"Costa TR, Felisberto-Rodrigues C, Meir A, Prevost MS, Redzej A, Trokter M et al (2015) Secretion systems in Gram-negative bacteria: structural and mechanistic insights. Nat Rev Microbiol 13(6):343\u2013359. https:\/\/doi.org\/10.1038\/nrmicro3456","journal-title":"Nat Rev Microbiol"},{"key":"5256_CR89","doi-asserted-by":"publisher","first-page":"73","DOI":"10.1016\/j.mib.2022.01.005","volume":"66","author":"EA Cummins","year":"2022","unstructured":"Cummins EA, Hall RJ, McInerney JO, McNally A (2022) Prokaryote pangenomes are dynamic entities. Curr Opin Microbiol 66:73\u201378. https:\/\/doi.org\/10.1016\/j.mib.2022.01.005","journal-title":"Curr Opin Microbiol"},{"key":"5256_CR2","doi-asserted-by":"publisher","first-page":"107677","DOI":"10.1016\/j.biotechadv.2020.107677","volume":"53","author":"J De Saeger","year":"2021","unstructured":"De Saeger J, Park J, Chung HS, Hernalsteens jp, van lijsebettens m, inz\u00e9 d et al (2021) agrobacterium strains and strain improvement: present and outlook. Biotechnol Adv 53:107677. https:\/\/doi.org\/10.1016\/j.biotechadv.2020.107677","journal-title":"Biotechnol Adv"},{"issue":"6","key":"5256_CR19","doi-asserted-by":"publisher","first-page":"673","DOI":"10.1093\/bioinformatics\/btm009","volume":"23","author":"AL Delcher","year":"2007","unstructured":"Delcher AL, Bratke KA, Powers EC, Salzberg SL (2007) Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23(6):673\u2013679. https:\/\/doi.org\/10.1093\/bioinformatics\/btm009","journal-title":"Bioinformatics"},{"issue":"1","key":"5256_CR82","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/s00248-012-0017-y","volume":"64","author":"F Dini-Andreote","year":"2012","unstructured":"Dini-Andreote F, Andreote FD, Ara\u00fajo WL, Trevors JT, van Elsas JD (2012) Bacterial genomes: habitat specificity and uncharted organisms. Microb Ecol 64(1):1\u20137. https:\/\/doi.org\/10.1007\/s00248-012-0017-y","journal-title":"Microb Ecol"},{"issue":"2","key":"5256_CR40","doi-asserted-by":"publisher","first-page":"e02924","DOI":"10.1128\/spectrum.02924-22","volume":"11","author":"Y Du","year":"2023","unstructured":"Du Y, Zou J, Yin Z, Chen T (2023) Pan-chromosome and comparative analysis of agrobacterium fabrum reveal important traits concerning the genetic diversity, evolutionary dynamics, and niche adaptation of the species. Microbiol Spectr 11(2):e02924\u2013e02922","journal-title":"Microbiol Spectr"},{"key":"5256_CR90","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1007\/BF02703681","volume":"27","author":"C Dutta","year":"2002","unstructured":"Dutta C, Pan A (2002) Horizontal gene transfer and bacterial diversity. J Biosci 27:27\u201333","journal-title":"J Biosci"},{"issue":"1","key":"5256_CR25","doi-asserted-by":"publisher","first-page":"157","DOI":"10.1186\/s13059-015-0721-2","volume":"16","author":"DM Emms","year":"2015","unstructured":"Emms DM, Kelly S (2015) OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biol 16(1):157. https:\/\/doi.org\/10.1186\/s13059-015-0721-2","journal-title":"Genome Biol"},{"key":"5256_CR57","doi-asserted-by":"publisher","unstructured":"Fan E, Chauhan N, Udatha D, Leo JC, Linke D (2016) Type V Secretion Systems in Bacteria. Microbiol Spectr. https:\/\/doi.org\/10.1128\/microbiolspec.VMBF-0009-2015","DOI":"10.1128\/microbiolspec.VMBF-0009-2015"},{"issue":"Database issue","key":"5256_CR30","doi-asserted-by":"publisher","first-page":"D261","DOI":"10.1093\/nar\/gku1223","volume":"43","author":"MY Galperin","year":"2015","unstructured":"Galperin MY, Makarova KS, Wolf YI, Koonin EV (2015) Expanded microbial genome coverage and improved protein family annotation in the COG database. Nucleic Acids Res 43(Database issue):D261\u2013D269. https:\/\/doi.org\/10.1093\/nar\/gku1223","journal-title":"Nucleic Acids Res"},{"key":"5256_CR50","doi-asserted-by":"publisher","unstructured":"Gavande PV, Goyal A, Fontes CM (2023) Carbohydrates and carbohydrate-active enZymes (CAZyme): an overview. Glycoside Hydrolases. 1\u201323. https:\/\/doi.org\/10.1016\/B978-0-323-91805-3.00012-5","DOI":"10.1016\/B978-0-323-91805-3.00012-5"},{"key":"5256_CR3","doi-asserted-by":"publisher","first-page":"195","DOI":"10.1146\/annurev-genet-120215-035320","volume":"51","author":"SB Gelvin","year":"2017","unstructured":"Gelvin SB (2017) Integration of Agrobacterium T-DNA into the plant genome. Annu Rev Genet 51:195\u2013217. https:\/\/doi.org\/10.1146\/annurev-genet-120215-035320","journal-title":"Annu Rev Genet"},{"key":"5256_CR28","doi-asserted-by":"crossref","unstructured":"Gmiter D, Nawrot S, Pacak I, Zegad\u0142o K, Kaca W (2021) Towards a better understanding of the bacterial pan-genome.","DOI":"10.18778\/1730-2366.16.19"},{"key":"5256_CR5","doi-asserted-by":"crossref","unstructured":"Gosal SS, Wani SH (2018) Plant genetic transformation and transgenic crops: methods and applications. Biotechnol Crop Improv Transgenic Approaches. 2:1\u201323","DOI":"10.1007\/978-3-319-90650-8_1"},{"issue":"10","key":"5256_CR88","doi-asserted-by":"publisher","first-page":"e1007763","DOI":"10.1371\/journal.pgen.1007763","volume":"14","author":"A Goyal","year":"2018","unstructured":"Goyal A (2018) Metabolic adaptations underlying genome flexibility in prokaryotes. PLoS Genet 14(10):e1007763. https:\/\/doi.org\/10.1371\/journal.pgen.1007763","journal-title":"PLoS Genet"},{"key":"5256_CR63","doi-asserted-by":"publisher","unstructured":"Halte M, Erhardt M (2021) Protein export via the type III secretion system of the bacterial flagellum. Biomolecules 11(2). https:\/\/doi.org\/10.3390\/biom11020186","DOI":"10.3390\/biom11020186"},{"issue":"12","key":"5256_CR15","doi-asserted-by":"publisher","first-page":"1458","DOI":"10.1094\/mpmi-06-21-0154-a","volume":"34","author":"H Hao","year":"2021","unstructured":"Hao H, Wang Z, Gou C, Sha S, Yan C, Niu D et al (2021) Genome sequence of the Agrobacterium salinitolerans DG3-1 isolated from cotton roots. Mol Plant Microbe Interact 34(12):1458\u20131460. https:\/\/doi.org\/10.1094\/mpmi-06-21-0154-a","journal-title":"Mol Plant Microbe Interact"},{"key":"5256_CR80","doi-asserted-by":"publisher","unstructured":"Harmer CJ, Hall RM (2016) IS26-Mediated Formation of Transposons Carrying Antibiotic Resistance Genes. mSphere 1(2). https:\/\/doi.org\/10.1128\/mSphere.00038-16","DOI":"10.1128\/mSphere.00038-16"},{"issue":"3","key":"5256_CR58","doi-asserted-by":"publisher","first-page":"1231","DOI":"10.1128\/iai.69.3.1231-1243.2001","volume":"69","author":"IR Henderson","year":"2001","unstructured":"Henderson IR, Nataro JP (2001) Virulence functions of autotransporter proteins. Infect Immun 69(3):1231\u20131243. https:\/\/doi.org\/10.1128\/iai.69.3.1231-1243.2001","journal-title":"Infect Immun"},{"issue":"4","key":"5256_CR8","doi-asserted-by":"publisher","first-page":"594","DOI":"10.1094\/phyto-11-22-0432-ia","volume":"113","author":"PJJ Hooykaas","year":"2023","unstructured":"Hooykaas PJJ (2023) The Ti plasmid, driver of agrobacterium pathogenesis. Phytopathology 113(4):594\u2013604. https:\/\/doi.org\/10.1094\/phyto-11-22-0432-ia","journal-title":"Phytopathology"},{"issue":"8","key":"5256_CR31","doi-asserted-by":"publisher","first-page":"2115","DOI":"10.1093\/molbev\/msx148","volume":"34","author":"J Huerta-Cepas","year":"2017","unstructured":"Huerta-Cepas J, Forslund K, Coelho LP, Szklarczyk D, Jensen LJ, von Mering C et al (2017) Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper. Mol Biol Evol 34(8):2115\u20132122. https:\/\/doi.org\/10.1093\/molbev\/msx148","journal-title":"Mol Biol Evol"},{"issue":"1\u20133","key":"5256_CR59","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1016\/j.bbamcr.2004.03.008","volume":"1694","author":"F Jacob-Dubuisson","year":"2004","unstructured":"Jacob-Dubuisson F, Fernandez R, Coutte L (2004) Protein secretion through autotransporter and two-partner pathways. Biochim Biophys Acta 1694(1\u20133):235\u2013257. https:\/\/doi.org\/10.1016\/j.bbamcr.2004.03.008","journal-title":"Biochim Biophys Acta"},{"issue":"1","key":"5256_CR23","doi-asserted-by":"publisher","first-page":"5114","DOI":"10.1038\/s41467-018-07641-9","volume":"9","author":"C Jain","year":"2018","unstructured":"Jain C, Rodriguez RL, Phillippy AM, Konstantinidis KT, Aluru S (2018) High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun 9(1):5114. https:\/\/doi.org\/10.1038\/s41467-018-07641-9","journal-title":"Nat Commun"},{"issue":"D1","key":"5256_CR45","doi-asserted-by":"publisher","first-page":"D566","DOI":"10.1093\/nar\/gkw1004","volume":"45","author":"B Jia","year":"2017","unstructured":"Jia B, Raphenya AR, Alcock B, Waglechner N, Guo P, Tsang KK et al (2017) CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database. Nucleic Acids Res 45(D1):D566\u2013d73. https:\/\/doi.org\/10.1093\/nar\/gkw1004","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"5256_CR29","doi-asserted-by":"publisher","first-page":"989","DOI":"10.1038\/s41467-020-14779-y","volume":"11","author":"W-B Jiao","year":"2020","unstructured":"Jiao W-B, Schneeberger K (2020) Chromosome-level assemblies of multiple Arabidopsis genomes reveal hotspots of rearrangements with altered evolutionary dynamics. Nat Commun 11(1):989. https:\/\/doi.org\/10.1038\/s41467-020-14779-y","journal-title":"Nat Commun"},{"issue":"1","key":"5256_CR86","doi-asserted-by":"publisher","first-page":"989","DOI":"10.1038\/s41467-020-14779-y","volume":"11","author":"WB Jiao","year":"2020","unstructured":"Jiao WB, Schneeberger K (2020) Chromosome-level assemblies of multiple Arabidopsis genomes reveal hotspots of rearrangements with altered evolutionary dynamics. Nat Commun 11(1):989. https:\/\/doi.org\/10.1038\/s41467-020-14779-y","journal-title":"Nat Commun"},{"issue":"3","key":"5256_CR72","doi-asserted-by":"publisher","first-page":"1673","DOI":"10.1093\/nar\/gkac004","volume":"50","author":"Y Kanai","year":"2022","unstructured":"Kanai Y, Tsuru S, Furusawa C (2022) Experimental demonstration of operon formation catalyzed by insertion sequence. Nucleic Acids Res 50(3):1673\u20131686. https:\/\/doi.org\/10.1093\/nar\/gkac004","journal-title":"Nucleic Acids Res"},{"issue":"6","key":"5256_CR54","doi-asserted-by":"publisher","first-page":"596","DOI":"10.1016\/j.resmic.2013.03.011","volume":"164","author":"K Kanonenberg","year":"2013","unstructured":"Kanonenberg K, Schwarz CK, Schmitt L (2013) Type I secretion systems\u2014a story of appendices. Res Microbiol 164(6):596\u2013604. https:\/\/doi.org\/10.1016\/j.resmic.2013.03.011","journal-title":"Res Microbiol"},{"issue":"4","key":"5256_CR36","doi-asserted-by":"publisher","first-page":"772","DOI":"10.1093\/molbev\/mst010","volume":"30","author":"K Katoh","year":"2013","unstructured":"Katoh K, Standley DM (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30(4):772\u2013780. https:\/\/doi.org\/10.1093\/molbev\/mst010","journal-title":"Mol Biol Evol"},{"issue":"9","key":"5256_CR10","doi-asserted-by":"publisher","first-page":"251","DOI":"10.1007\/s00284-022-02948-9","volume":"79","author":"SK Keleshyan","year":"2022","unstructured":"Keleshyan SK, Karapetyan ZV, Toplaghaltsyan AG, Avetisova GY, Melkonyan LH, Vardanyan AA et al (2022) Obtaining osmo-resistant mutants in nitrogen-fixing bacteria isolated from saline soils. Curr Microbiol 79(9):251. https:\/\/doi.org\/10.1007\/s00284-022-02948-9","journal-title":"Curr Microbiol"},{"issue":"5","key":"5256_CR73","doi-asserted-by":"publisher","first-page":"739","DOI":"10.1016\/j.chom.2024.03.005","volume":"32","author":"JM Kirsch","year":"2024","unstructured":"Kirsch JM, Hryckowian AJ, Duerkop BA (2024) A metagenomics pipeline reveals insertion sequence-driven evolution of the microbiota. Cell Host Microbe 32(5):739\u201354e4. https:\/\/doi.org\/10.1016\/j.chom.2024.03.005","journal-title":"Cell Host Microbe"},{"issue":"5","key":"5256_CR17","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, Pevzner PA (2019) Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol 37(5):540\u2013546. https:\/\/doi.org\/10.1038\/s41587-019-0072-8","journal-title":"Nat Biotechnol"},{"issue":"6\u20138","key":"5256_CR9","doi-asserted-by":"publisher","first-page":"467","DOI":"10.1387\/ijdb.130199bl","volume":"57","author":"B Lacroix","year":"2013","unstructured":"Lacroix B, Citovsky V (2013) The roles of bacterial and host plant factors in Agrobacterium-mediated genetic transformation. Int J Dev Biol 57(6\u20138):467","journal-title":"Int J Dev Biol"},{"issue":"9","key":"5256_CR21","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, Staerfeldt HH, Rognes T, Ussery DW (2007) RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 35(9):3100\u20133108. https:\/\/doi.org\/10.1093\/nar\/gkm160","journal-title":"Nucleic Acids Res"},{"key":"5256_CR33","doi-asserted-by":"publisher","first-page":"329","DOI":"10.1186\/1471-2105-9-329","volume":"9","author":"MG Langille","year":"2008","unstructured":"Langille MG, Hsiao WW, Brinkman FS (2008) Evaluation of genomic island predictors using a comparative genomics approach. BMC Bioinformatics 9:329. https:\/\/doi.org\/10.1186\/1471-2105-9-329","journal-title":"BMC Bioinformatics"},{"issue":"W1","key":"5256_CR38","doi-asserted-by":"publisher","first-page":"W293","DOI":"10.1093\/nar\/gkab301","volume":"49","author":"I Letunic","year":"2021","unstructured":"Letunic I, Bork P (2021) Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res 49(W1):W293\u2013w6. https:\/\/doi.org\/10.1093\/nar\/gkab301","journal-title":"Nucleic Acids Res"},{"issue":"2","key":"5256_CR55","doi-asserted-by":"publisher","first-page":"195","DOI":"10.3390\/antibiotics12020195","volume":"12","author":"P Li","year":"2023","unstructured":"Li P, Zhang S, Wang J, Al-Shamiri MM, Han B, Chen Y et al (2023) Uncovering the secretion systems of Acinetobacter baumannii: Structures and functions in pathogenicity and antibiotic resistance. Antibiotics 12(2):195","journal-title":"Antibiotics"},{"key":"5256_CR85","doi-asserted-by":"publisher","unstructured":"Lian Q, Huettel B, Walkemeier B, Mayjonade B, Lopez-Roques C, Gil L et al (2024) A pan-genome of 69 Arabidopsis thaliana accessions reveals a conserved genome structure throughout the global species range. Nat Genet 1\u201310. https:\/\/doi.org\/10.1038\/s41588-024-01715-9","DOI":"10.1038\/s41588-024-01715-9"},{"issue":"2","key":"5256_CR12","doi-asserted-by":"publisher","first-page":"220","DOI":"10.5423\/ppj.Oa.07.2022.0095","volume":"39","author":"S Lim","year":"2023","unstructured":"Lim S, Chun SC, Kim JW (2023) Cultivar resistance of Korean breeding cut-rose against crown gall by agrobacterium tumefaciens evaluated by an in vitro inoculation. Plant Pathol J 39(2):220\u2013227. https:\/\/doi.org\/10.5423\/ppj.Oa.07.2022.0095","journal-title":"Plant Pathol J"},{"issue":"D1","key":"5256_CR44","doi-asserted-by":"publisher","first-page":"D687","DOI":"10.1093\/nar\/gky1080","volume":"47","author":"B Liu","year":"2019","unstructured":"Liu B, Zheng D, Jin Q, Chen L, Yang J (2019) VFDB 2019: a comparative pathogenomic platform with an interactive web interface. Nucleic Acids Res 47(D1):D687\u2013d92. https:\/\/doi.org\/10.1093\/nar\/gky1080","journal-title":"Nucleic Acids Res"},{"key":"5256_CR56","doi-asserted-by":"publisher","unstructured":"Lukaszczyk M, Pradhan B, Remaut H (2019) The biosynthesis and structures of bacterial pili. Bacterial Cell Walls Membr 369\u2013413. https:\/\/doi.org\/10.1007\/978-3-030-18768-2_12","DOI":"10.1007\/978-3-030-18768-2_12"},{"key":"5256_CR11","doi-asserted-by":"publisher","first-page":"212","DOI":"10.1186\/s40168-021-01164-0","volume":"9","author":"Z Luo","year":"2021","unstructured":"Luo Z, Zhong Q, Han X et al (2021) Depth-dependent variability of biological nitrogen fixation and diazotrophic communities in mangrove sediments. Microbiome 9:212. https:\/\/doi.org\/10.1186\/s40168-021-01164-0","journal-title":"Microbiome"},{"key":"5256_CR27","doi-asserted-by":"publisher","unstructured":"Mainguy J, Lemane T, Bazin A, Arnoux J, Gautreau G, M\u00e9digue C, Calteau A, Vallenet D (2026) PanGBank: a large-scale resource of precomputed microbial pangenomes built with PPanGGOLiN. Nucleic Acids Res gkag948. https:\/\/doi.org\/10.1093\/nar\/gkag948","DOI":"10.1093\/nar\/gkag948"},{"key":"5256_CR49","doi-asserted-by":"publisher","first-page":"60","DOI":"10.1186\/1471-2105-14-60","volume":"14","author":"JP Meier-Kolthoff","year":"2013","unstructured":"Meier-Kolthoff JP, Auch AF, Klenk HP, G\u00f6ker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 14:60. https:\/\/doi.org\/10.1186\/1471-2105-14-60","journal-title":"BMC Bioinformatics"},{"issue":"D1","key":"5256_CR24","doi-asserted-by":"publisher","first-page":"D801","DOI":"10.1093\/nar\/gkab902","volume":"50","author":"JP Meier-Kolthoff","year":"2022","unstructured":"Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, G\u00f6ker M (2022) TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res 50(D1):D801\u2013d7. https:\/\/doi.org\/10.1093\/nar\/gkab902","journal-title":"Nucleic Acids Res"},{"issue":"5","key":"5256_CR37","doi-asserted-by":"publisher","first-page":"1530","DOI":"10.1093\/molbev\/msaa015","volume":"37","author":"BQ Minh","year":"2020","unstructured":"Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD, von Haeseler A et al (2020) IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol 37(5):1530\u20131534. https:\/\/doi.org\/10.1093\/molbev\/msaa015","journal-title":"Mol Biol Evol"},{"issue":"5","key":"5256_CR78","doi-asserted-by":"publisher","first-page":"387","DOI":"10.1016\/j.resmic.2004.01.008","volume":"155","author":"Z Nagy","year":"2004","unstructured":"Nagy Z, Chandler M (2004) Regulation of transposition in bacteria. Res Microbiol 155(5):387\u2013398. https:\/\/doi.org\/10.1016\/j.resmic.2004.01.008","journal-title":"Res Microbiol"},{"issue":"8","key":"5256_CR66","doi-asserted-by":"publisher","first-page":"2020","DOI":"10.1111\/j.1462-2920.2008.01618.x","volume":"10","author":"I Oberpichler","year":"2008","unstructured":"Oberpichler I, Rosen R, Rasouly A, Vugman M, Ron EZ, Lamparter T (2008) Light affects motility and infectivity of Agrobacterium tumefaciens. Environ Microbiol 10(8):2020\u20132029. https:\/\/doi.org\/10.1111\/j.1462-2920.2008.01618.x","journal-title":"Environ Microbiol"},{"issue":"6784","key":"5256_CR93","doi-asserted-by":"publisher","first-page":"299","DOI":"10.1038\/35012500","volume":"405","author":"H Ochman","year":"2000","unstructured":"Ochman H, Lawrence JG, Groisman EA (2000) Lateral gene transfer and the nature of bacterial innovation. Nature 405(6784):299\u2013304. https:\/\/doi.org\/10.1038\/35012500","journal-title":"Nature"},{"key":"5256_CR13","doi-asserted-by":"publisher","unstructured":"Oksel C, Liyanapathiranage P, Parajuli M, Avin FA, Jennings C, Simmons T et al (2024) Evaluation of chemical and biological products for control of crown gall on rose. Pathogens 13(8). https:\/\/doi.org\/10.3390\/pathogens13080708","DOI":"10.3390\/pathogens13080708"},{"issue":"Pt12","key":"5256_CR60","doi-asserted-by":"publisher","first-page":"2328","DOI":"10.1099\/mic.0.000197","volume":"161","author":"J Park","year":"2015","unstructured":"Park J, Zhang Y, Chen C, Dudley EG, Harvill ET (2015) Diversity of secretion systems associated with virulence characteristics of the classical bordetellae. Microbiology 161(Pt12):2328\u20132340","journal-title":"Microbiology"},{"issue":"7","key":"5256_CR22","doi-asserted-by":"publisher","first-page":"1043","DOI":"10.1101\/gr.186072.114","volume":"25","author":"DH Parks","year":"2015","unstructured":"Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW (2015) CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 25(7):1043\u20131055. https:\/\/doi.org\/10.1101\/gr.186072.114","journal-title":"Genome Res"},{"issue":"4","key":"5256_CR4","doi-asserted-by":"publisher","first-page":"239","DOI":"10.1007\/s13205-017-0870-y","volume":"7","author":"N Parmar","year":"2017","unstructured":"Parmar N, Singh KH, Sharma D, Singh L, Kumar P, Nanjundan J et al (2017) Genetic engineering strategies for biotic and abiotic stress tolerance and quality enhancement in horticultural crops: a comprehensive review. 3 Biotech 7(4):239. https:\/\/doi.org\/10.1007\/s13205-017-0870-y","journal-title":"3 Biotech"},{"issue":"1","key":"5256_CR70","doi-asserted-by":"publisher","first-page":"199","DOI":"10.1038\/s41392-022-01056-1","volume":"7","author":"S Qin","year":"2022","unstructured":"Qin S, Xiao W, Zhou C, Pu Q, Deng X, Lan L et al (2022) Pseudomonas aeruginosa: pathogenesis, virulence factors, antibiotic resistance, interaction with host, technology advances and emerging therapeutics. Signal Transduct Target therapy 7(1):199","journal-title":"Signal Transduct Target therapy"},{"key":"5256_CR65","doi-asserted-by":"publisher","first-page":"1547","DOI":"10.1007\/s43630-021-00124-9","volume":"20","author":"C Ramesh","year":"2021","unstructured":"Ramesh C, Bessho-Uehara M (2021) Acquisition of bioluminescent trait by non-luminous organisms from luminous organisms through various origins. Photochem Photobiol Sci 20:1547\u20131562. https:\/\/doi.org\/10.1007\/s43630-021-00124-9","journal-title":"Photochem Photobiol Sci"},{"key":"5256_CR87","doi-asserted-by":"publisher","first-page":"55","DOI":"10.1016\/j.meegid.2018.07.009","volume":"65","author":"J-P Rasigade","year":"2018","unstructured":"Rasigade J-P, Hollandt F, Wirth T (2018) Genes under positive selection in the core genome of pathogenic Bacillus cereus group members. Infect Genet Evol 65:55\u201364","journal-title":"Infect Genet Evol"},{"issue":"45","key":"5256_CR48","doi-asserted-by":"publisher","first-page":"19126","DOI":"10.1073\/pnas.0906412106","volume":"106","author":"M Richter","year":"2009","unstructured":"Richter M, Rossell\u00f3-M\u00f3ra R (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 106(45):19126\u201319131. https:\/\/doi.org\/10.1073\/pnas.0906412106","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"2","key":"5256_CR61","doi-asserted-by":"publisher","first-page":"227","DOI":"10.1016\/j.chom.2014.07.007","volume":"16","author":"AB Russell","year":"2014","unstructured":"Russell AB, Wexler AG, Harding BN, Whitney JC, Bohn AJ, Goo YA et al (2014) A type VI secretion-related pathway in Bacteroidetes mediates interbacterial antagonism. Cell Host Microbe 16(2):227\u2013236","journal-title":"Cell Host Microbe"},{"issue":"5","key":"5256_CR71","doi-asserted-by":"publisher","first-page":"865","DOI":"10.1111\/1574-6976.12067","volume":"38","author":"P Siguier","year":"2014","unstructured":"Siguier P, Gourbeyre E, Chandler M (2014) Bacterial insertion sequences: their genomic impact and diversity. FEMS Microbiol Rev 38(5):865\u2013891. https:\/\/doi.org\/10.1111\/1574-6976.12067","journal-title":"FEMS Microbiol Rev"},{"key":"5256_CR6","doi-asserted-by":"publisher","first-page":"765943","DOI":"10.3389\/fmicb.2021.765943","volume":"12","author":"NK Singh","year":"2021","unstructured":"Singh NK, Lavire C, Nesme J, Vial L, Nesme X, Mason CE et al (2021) Comparative Genomics of Novel Agrobacterium G3 Strains Isolated From the International Space Station and Description of Agrobacterium tomkonis sp. nov. Front Microbiol 12:765943. https:\/\/doi.org\/10.3389\/fmicb.2021.765943","journal-title":"Front Microbiol"},{"issue":"1","key":"5256_CR81","doi-asserted-by":"publisher","first-page":"2335","DOI":"10.1038\/s41467-023-38071-x","volume":"14","author":"M Sp\u00ednola-Amilibia","year":"2023","unstructured":"Sp\u00ednola-Amilibia M, Ara\u00fajo-Baz\u00e1n L, de la G\u00e1ndara \u00c1, Berger JM, Arias-Palomo E (2023) IS21 family transposase cleaved donor complex traps two right-handed superhelical crossings. Nat Commun 14(1):2335. https:\/\/doi.org\/10.1038\/s41467-023-38071-x","journal-title":"Nat Commun"},{"key":"5256_CR69","doi-asserted-by":"crossref","unstructured":"Thakur A, Mikkelsen H, Jungersen G (2019) Intracellular pathogens: host immunity and microbial persistence strategies. J Immunol Res.","DOI":"10.1155\/2019\/1356540"},{"issue":"21","key":"5256_CR79","doi-asserted-by":"publisher","first-page":"5410","DOI":"10.1002\/j.1460-2075.1995.tb00225.x","volume":"14","author":"C Turlan","year":"1995","unstructured":"Turlan C, Chandler M (1995) IS1-mediated intramolecular rearrangements: formation of excised transposon circles and replicative deletions. Embo j 14(21):5410\u20135421. https:\/\/doi.org\/10.1002\/j.1460-2075.1995.tb00225.x","journal-title":"Embo j"},{"issue":"6","key":"5256_CR77","doi-asserted-by":"publisher","first-page":"709","DOI":"10.1080\/1040841x.2017.1303661","volume":"43","author":"J Vandecraen","year":"2017","unstructured":"Vandecraen J, Chandler M, Aertsen A, Van Houdt R (2017) The impact of insertion sequences on bacterial genome plasticity and adaptability. Crit Rev Microbiol 43(6):709\u2013730. https:\/\/doi.org\/10.1080\/1040841x.2017.1303661","journal-title":"Crit Rev Microbiol"},{"key":"5256_CR7","doi-asserted-by":"publisher","unstructured":"Weisberg AJ, Davis EW 2nd, Tabima J, Belcher MS, Miller M, Kuo CH et al (2020) Unexpected conservation and global transmission of agrobacterial virulence plasmids. Science 368(6495). https:\/\/doi.org\/10.1126\/science.aba5256","DOI":"10.1126\/science.aba5256"},{"issue":"6","key":"5256_CR14","doi-asserted-by":"publisher","first-page":"1906","DOI":"10.1099\/ijsem.0.001885","volume":"67","author":"J Yan","year":"2017","unstructured":"Yan J, Li Y, Yan H, Chen WF, Zhang X, Wang ET et al (2017) Agrobacterium salinitolerans sp. nov., a saline-alkaline-tolerant bacterium isolated from root nodule of Sesbania cannabina. Int J Syst Evol Microbiol 67(6):1906\u20131911. https:\/\/doi.org\/10.1099\/ijsem.0.001885","journal-title":"Int J Syst Evol Microbiol"},{"issue":"2","key":"5256_CR41","doi-asserted-by":"publisher","first-page":"e0207221","DOI":"10.1128\/spectrum.02072-21","volume":"10","author":"Z Yin","year":"2022","unstructured":"Yin Z, Liu X, Qian C, Sun L, Pang S, Liu J et al (2022) Pan-genome analysis of delftia tsuruhatensis reveals important traits concerning the genetic diversity, pathogenicity, and biotechnological properties of the species. Microbiol Spectr 10(2):e0207221. https:\/\/doi.org\/10.1128\/spectrum.02072-21","journal-title":"Microbiol Spectr"},{"issue":"3","key":"5256_CR43","doi-asserted-by":"publisher","first-page":"536","DOI":"10.1016\/j.gpb.2021.12.002","volume":"20","author":"Z Zhang","year":"2022","unstructured":"Zhang Z (2022) KaKs_calculator 3.0: calculating selective pressure on coding and non-coding sequences. Genomics Proteom Bioinf 20(3):536\u2013540. https:\/\/doi.org\/10.1016\/j.gpb.2021.12.002","journal-title":"Genomics Proteom Bioinf"},{"issue":"4","key":"5256_CR42","doi-asserted-by":"publisher","first-page":"779","DOI":"10.1016\/j.bbrc.2012.02.101","volume":"419","author":"Z Zhang","year":"2012","unstructured":"Zhang Z, Xiao J, Wu J, Zhang H, Liu G, Wang X et al (2012) ParaAT: a parallel tool for constructing multiple protein-coding DNA alignments. Biochem Biophys Res Commun 419(4):779\u2013781. https:\/\/doi.org\/10.1016\/j.bbrc.2012.02.101","journal-title":"Biochem Biophys Res Commun"},{"issue":"W1","key":"5256_CR35","doi-asserted-by":"publisher","first-page":"W95","DOI":"10.1093\/nar\/gky418","volume":"46","author":"H Zhang","year":"2018","unstructured":"Zhang H, Yohe T, Huang L, Entwistle S, Wu P, Yang Z et al (2018) dbCAN2: a meta server for automated carbohydrate-active enzyme annotation. Nucleic Acids Res 46(W1):W95\u2013w101. https:\/\/doi.org\/10.1093\/nar\/gky418","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"5256_CR39","doi-asserted-by":"publisher","first-page":"717","DOI":"10.1186\/1471-2164-15-717","volume":"15","author":"Q Zhu","year":"2014","unstructured":"Zhu Q, Kosoy M, Dittmar K (2014) HGTector: an automated method facilitating genome-wide discovery of putative horizontal gene transfers. BMC Genomics 15(1):717. https:\/\/doi.org\/10.1186\/1471-2164-15-717","journal-title":"BMC Genomics"}],"container-title":["Archives of Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s00203-026-05256-z.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s00203-026-05256-z","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s00203-026-05256-z.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T20:51:40Z","timestamp":1792097500000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s00203-026-05256-z"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,10,15]]},"references-count":93,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2027,1]]}},"alternative-id":["5256"],"URL":"https:\/\/doi.org\/10.1007\/s00203-026-05256-z","relation":{},"ISSN":["0302-8933","1432-072X"],"issn-type":[{"value":"0302-8933","type":"print"},{"value":"1432-072X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,10,15]]},"assertion":[{"value":"27 July 2026","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"23 September 2026","order":2,"name":"revised","label":"Revised","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"1 October 2026","order":3,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"15 October 2026","order":4,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","label":"Conflict of interest","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"No ethical approval was required for this study, as it did not involve human participants, animals, or any procedures requiring institutional oversight.","order":2,"name":"Ethics","label":"Ethical approval","group":{"name":"EthicsHeading","label":"Declarations"}}],"article-number":"24"}}