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Reptile-associated (REP) <jats:italic>Borrelia<\/jats:italic>, once considered a peculiarity, are now recognised as a distinct and important evolutionary lineage, and are increasingly being discovered worldwide in association with novel hosts. Numerous novel <jats:italic>Borrelia<\/jats:italic> spp. associated with monitor lizards (<jats:italic>Varanus<\/jats:italic> spp.) have been recently identified throughout the Indo-Pacific region; however, there is a lack of genomic data on these <jats:italic>Borrelia<\/jats:italic>.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Methods<\/jats:title>\n                <jats:p>We used metagenomic techniques to sequence almost complete genomes of novel <jats:italic>Borrelia<\/jats:italic> spp. from <jats:italic>Varanus varius<\/jats:italic> and <jats:italic>Varanus giganteus<\/jats:italic> from Australia, and used long- and short-read technologies to sequence the complete genomes of two strains of a novel <jats:italic>Borrelia<\/jats:italic> sp. previously isolated from ticks infesting <jats:italic>Varanus salvator<\/jats:italic> from Indonesia. We investigated intra- and interspecies genomic diversity, including plasmid diversity and relatedness, among <jats:italic>Varanus<\/jats:italic>-associated <jats:italic>Borrelia<\/jats:italic> and other available REP <jats:italic>Borrelia<\/jats:italic> and, based on 712 whole genome orthologues, produced the most complete phylogenetic analysis, to the best of our knowledge, of REP <jats:italic>Borrelia<\/jats:italic> to date.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>The genomic architecture of <jats:italic>Varanus<\/jats:italic>-associated <jats:italic>Borrelia<\/jats:italic> spp. is similar to that of <jats:italic>Borrelia<\/jats:italic> spp. that cause relapsing fever (RF), and includes a highly conserved megaplasmid and numerous smaller linear and circular plasmids that lack structural consistency between species. Analysis of PF32 and PF57\/62 plasmid partitioning genes indicated that REP <jats:italic>Borrelia<\/jats:italic> plasmids fall into at least six distinct plasmid families, some of which are related to previously defined <jats:italic>Borrelia<\/jats:italic> plasmid families, whereas the others appear to be unique. REP <jats:italic>Borrelia<\/jats:italic> contain immunogenic variable major proteins that are homologous to those found in <jats:italic>Borrelia<\/jats:italic> spp. that cause RF, although they are limited in copy number and variability and have low sequence identities to RF variable major proteins. Phylogenetic analyses based on single marker genes and 712 single copy orthologs also definitively demonstrated the monophyly of REP <jats:italic>Borrelia<\/jats:italic> as a unique lineage.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>In this work we present four new genomes from three novel <jats:italic>Borrelia<\/jats:italic>, and thus double the number of REP <jats:italic>Borrelia<\/jats:italic> genomes publicly available. The genomic characterisation of these <jats:italic>Borrelia<\/jats:italic> clearly demonstrates their distinctiveness as species, and we propose the names <jats:italic>Borrelia salvatorii<\/jats:italic>, \u2018<jats:italic>Candidatus<\/jats:italic> Borrelia undatumii\u2019, and \u2018<jats:italic>Candidatus<\/jats:italic> Borrelia rubricentralis\u2019 for them.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Graphical Abstract<\/jats:title>\n                \n              <\/jats:sec>","DOI":"10.1186\/s13071-023-05937-4","type":"journal-article","created":{"date-parts":[[2023,9,5]],"date-time":"2023-09-05T14:02:53Z","timestamp":1693922573000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":11,"title":["Characterisation and comparative genomics of three new Varanus-associated Borrelia spp. from Indonesia and Australia"],"prefix":"10.1186","volume":"16","author":[{"given":"Alexander William","family":"Gofton","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Angel","family":"Popa-Baez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ai","family":"Takano","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kari","family":"Soennichsen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michelle","family":"Michie","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Makenna","family":"Short","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Supriyono","family":"Supriyono","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jack","family":"Pascoe","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sue","family":"Cusbert","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert","family":"Mulley","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2023,9,5]]},"reference":[{"key":"5937_CR1","doi-asserted-by":"crossref","first-page":"e0208432","DOI":"10.1371\/journal.pone.0208432","volume":"13","author":"G Margos","year":"2018","unstructured":"Margos G, Gofton A, Wibberg D, Dangel A, Marosevic D, Loh S-M, et al. 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