{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,12]],"date-time":"2025-12-12T13:44:05Z","timestamp":1765547045097,"version":"3.37.3"},"reference-count":27,"publisher":"Wiley","issue":"6","license":[{"start":{"date-parts":[[2023,4,11]],"date-time":"2023-04-11T00:00:00Z","timestamp":1681171200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100009619","name":"Japan Agency for Medical Research and Development","doi-asserted-by":"publisher","award":["22fk0108614h0202"],"award-info":[{"award-number":["22fk0108614h0202"]}],"id":[{"id":"10.13039\/100009619","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Microbiology and Immunology"],"published-print":{"date-parts":[[2023,6]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Many <jats:italic>Rickettsia<\/jats:italic> species of the spotted fever group (SFG) cause tick\u2010borne diseases known as \u201cspotted fever.\u201d One of the candidate SFG <jats:italic>Rickettsia<\/jats:italic> species is \u201c<jats:italic>Candidatus Rickettsia kotlanii<\/jats:italic>,\u201d which was first detected in <jats:italic>Haemaphysalis concinna<\/jats:italic> in Hungary in 2006. However, its precise phylogenetic position in the SFG is not clear because only single\u2010gene sequence\u2013based phylogenetic analyses were performed using very limited genes. Here, we present the complete genome sequences of two Japanese \u201c<jats:italic>Ca<\/jats:italic>. <jats:italic>R. kotlanii<\/jats:italic>\u201d isolates, which differed only by a 135 bp insertion\/deletion (InDel). Using these genomes and publicly available whole genome sequences of other <jats:italic>Rickettsia<\/jats:italic> species, the precise phylogenetic position of \u201c<jats:italic>Ca<\/jats:italic>. <jats:italic>R. kotlanii<\/jats:italic>\u201d in <jats:italic>Rickettsia<\/jats:italic> was determined to be in a clade of the SFG. The phylogenetic relationships and average nucleotide identity of \u201c<jats:italic>Ca<\/jats:italic>. <jats:italic>R. kotlanii<\/jats:italic>\u201d relative to the other species indicated that \u201c<jats:italic>Ca<\/jats:italic>. <jats:italic>R. kotlanii<\/jats:italic>\u201d is an independent taxon in the SFG. Notably, although the genomes of the two isolates were almost identical, the isolates were obtained from different tick species in different regions and years, suggesting extremely low genomic diversity in \u201c<jats:italic>Ca<\/jats:italic>. <jats:italic>R. kotlanii<\/jats:italic>.\u201d While the genome of \u201c<jats:italic>Ca<\/jats:italic>. <jats:italic>R. kotlanii<\/jats:italic>\u201d is the smallest in the transitional group and SFG <jats:italic>Rickettsia<\/jats:italic> sequenced to date, we identified genes uniquely present or absent in \u201c<jats:italic>Ca<\/jats:italic>. <jats:italic>R. kotlanii<\/jats:italic>,\u201d but most were apparently degraded. Therefore, analyses of differences at the sequence (single nucleotide polymorphisms and small InDels) or gene expression level will be required to understand the functional or physiological features unique to \u201c<jats:italic>Ca<\/jats:italic>. <jats:italic>R. kotlanii<\/jats:italic>.\u201d<\/jats:p>","DOI":"10.1111\/1348-0421.13065","type":"journal-article","created":{"date-parts":[[2023,3,30]],"date-time":"2023-03-30T15:50:20Z","timestamp":1680191420000},"page":"275-280","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Phylogenic position and low genomic diversity of \u201c<i>Candidatus Rickettsia kotlanii<\/i>\u201d inferred by complete genome sequences of two Japanese isolates"],"prefix":"10.1111","volume":"67","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9716-2820","authenticated-orcid":false,"given":"Yasuhiro","family":"Gotoh","sequence":"first","affiliation":[{"name":"Department of Bacteriology, Faculty of Medical Sciences Kyushu University  Fukuoka Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5919-3738","authenticated-orcid":false,"given":"Ai","family":"Takano","sequence":"additional","affiliation":[{"name":"Department of Veterinary Medicine, Joint Faculty of Veterinary Medicine Yamaguchi University  Yamaguchi Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9704-6931","authenticated-orcid":false,"given":"Masako","family":"Andoh","sequence":"additional","affiliation":[{"name":"Department of Pathogenetic and Preventive Veterinary Science, Joint Faculty of Veterinary Medicine Kagoshima University  Kagoshima Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kentaro","family":"Kasama","sequence":"additional","affiliation":[{"name":"Department of Bacteriology, Faculty of Medical Sciences Kyushu University  Fukuoka Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Keiji","family":"Nakamura","sequence":"additional","affiliation":[{"name":"Department of Bacteriology, Faculty of Medical Sciences Kyushu University  Fukuoka Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shuji","family":"Ando","sequence":"additional","affiliation":[{"name":"Department of Virology\u20101 National Institute of Infectious Diseases  Shinjuku\u2010ku Tokyo Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tetsuya","family":"Hayashi","sequence":"additional","affiliation":[{"name":"Department of Bacteriology, Faculty of Medical Sciences Kyushu University  Fukuoka Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2023,4,11]]},"reference":[{"key":"e_1_2_10_2_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ttbdis.2018.11.007"},{"key":"e_1_2_10_3_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0000266"},{"key":"e_1_2_10_4_1","doi-asserted-by":"publisher","DOI":"10.1179\/136485906X91468"},{"key":"e_1_2_10_5_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.vetmic.2009.07.013"},{"key":"e_1_2_10_6_1","doi-asserted-by":"publisher","DOI":"10.1089\/vbz.2013.1483"},{"key":"e_1_2_10_7_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13071-022-05280-0"},{"key":"e_1_2_10_8_1","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2019.02787"},{"key":"e_1_2_10_9_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu170"},{"key":"e_1_2_10_10_1","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.1923"},{"key":"e_1_2_10_11_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkab831"},{"key":"e_1_2_10_12_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.186072.114"},{"key":"e_1_2_10_13_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btx713"},{"key":"e_1_2_10_14_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-017-1748-z"},{"key":"e_1_2_10_15_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv421"},{"key":"e_1_2_10_16_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu033"},{"key":"e_1_2_10_17_1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msz189"},{"key":"e_1_2_10_18_1","doi-asserted-by":"publisher","DOI":"10.1039\/C5AY02550H"},{"key":"e_1_2_10_19_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-015-0849-0"},{"volume-title":"R: 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