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The taxonomy of rhizogenic agrobacteria has undergone several changes in the past and is still somewhat controversial. While the classification of\n                    <jats:italic>Agrobacterium<\/jats:italic>\n                    strains was initially mainly based on phenotypic properties and the symptoms they induced on plants, more and more genetic information has been used along the years to infer\n                    <jats:italic>Agrobacterium<\/jats:italic>\n                    taxonomy. This has led to the definition of the so-called\n                    <jats:italic>Agrobacterium tumefaciens<\/jats:italic>\n                    species complex (Atsc), which comprises several genomospecies. Interestingly, the rhizogenic\n                    <jats:italic>Agrobacterium<\/jats:italic>\n                    strains are found in several of these genomospecies. Nevertheless, even up until today\n                    <jats:italic>Agrobacterium<\/jats:italic>\n                    strains, and in particular rhizogenic agrobacteria, are prone to misclassification and considerable confusion in literature. In this study, we evaluated different phylogenetic analysis approaches for their use to improve\n                    <jats:italic>Agrobacterium<\/jats:italic>\n                    taxonomy and tried to gain more insight in the classification of strains into this complex genus, with a particular focus on rhizogenic agrobacteria. The genome sequence analysis of 580 assemblies, comprising\n                    <jats:italic>Agrobacterium<\/jats:italic>\n                    ,\n                    <jats:italic>Allorhizobium<\/jats:italic>\n                    and\n                    <jats:italic>Rhizobium<\/jats:italic>\n                    strains demonstrated that phylogenies based on single marker genes, such as the commonly used 16S rRNA and\n                    <jats:italic>recA<\/jats:italic>\n                    gene, do not provide sufficient resolution for proper delineation of the different genomospecies within the Atsc. Our results revealed that (in silico) multi-locus sequences analysis (MLSA) in combination with average nucleotide identity (ANIb) at a 94.0% threshold delineates genomospecies accurately and efficiently. Additionally, this latter approach permitted the identification of two new candidate genomospecies.\n                  <\/jats:p>","DOI":"10.1371\/journal.pone.0302954","type":"journal-article","created":{"date-parts":[[2024,11,19]],"date-time":"2024-11-19T16:01:22Z","timestamp":1732032082000},"page":"e0302954","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":5,"title":["Evaluation of sequence-based tools to gather more insight into the positioning of rhizogenic agrobacteria within the Agrobacterium tumefaciens species complex"],"prefix":"10.1371","volume":"19","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0435-284X","authenticated-orcid":true,"given":"Pablo Roberto","family":"Vargas Ribera","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nuri","family":"Kim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marc","family":"Venbrux","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6587-8995","authenticated-orcid":true,"given":"Sergio","family":"\u00c1lvarez-P\u00e9rez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hans","family":"Rediers","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2024,11,19]]},"reference":[{"key":"pone.0302954.ref001","doi-asserted-by":"crossref","first-page":"126046","DOI":"10.1016\/j.syapm.2019.126046","volume":"43","author":"JD Flores-F\u00e9lix","year":"2020","journal-title":"Systematic and Applied Microbiology"},{"key":"pone.0302954.ref002","first-page":"1","author":"JM Young","year":"2015","journal-title":"Bergey\u2019s Manual of Systematics of Archaea and Bacteria"},{"key":"pone.0302954.ref003","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1007\/82_2018_83","volume-title":"Agrobacterium Biology, from basic science to biotechnology.","author":"Y Dessaux","year":"2018"},{"key":"pone.0302954.ref004","doi-asserted-by":"crossref","first-page":"805","DOI":"10.1007\/s00203-015-1118-z","volume":"197","author":"S-A Chihaoui","year":"2015","journal-title":"Archives of Microbiology"},{"key":"pone.0302954.ref005","doi-asserted-by":"crossref","first-page":"1043","DOI":"10.1111\/ppa.12687","volume":"66","author":"L Bosmans","year":"2017","journal-title":"Plant Pathology"},{"key":"pone.0302954.ref006","doi-asserted-by":"crossref","first-page":"817","DOI":"10.3390\/agronomy11050817","volume":"11","author":"P Vargas","year":"2021","journal-title":"Agronomy."},{"key":"pone.0302954.ref007","doi-asserted-by":"crossref","first-page":"37","DOI":"10.17660\/ActaHortic.2016.1149.7","author":"J. 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