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We introduce here a method and a graphical user interface wrapper, called Annotator-RNAtor, for performing interspecies transcriptomic analysis and studying intragenus evolution. The pipeline uses third-party software to infer homologous genes in various species and highlight differences in the expression of the core-genes. To illustrate the methodology and demonstrate its usefulness, we focus on the emergence of the highly virulent Leptospira subclade known as P1+, which includes the causative agents of leptospirosis. Here, we expand on the genomic study through the comparison of transcriptomes between species from P1+ and their related P1- counterparts (low-virulent pathogens). In doing so, we shed light on differentially expressed pathways and focused on describing a specific example of adaptation based on a differential expression of PerRA-controlled genes. We showed that P1+ species exhibit higher expression of the katE gene, a well-known virulence determinant in pathogenic Leptospira species correlated with greater tolerance to peroxide. Switching PerRA alleles between P1+ and P1- species demonstrated that the lower repression of katE and greater tolerance to peroxide in P1+ species was solely controlled by PerRA and partly caused by a PerRA amino-acid permutation. Overall, these results demonstrate the strategic fit of the methodology and its ability to decipher adaptive transcriptomic changes, not observable by comparative genome analysis, that may have been implicated in the emergence of these pathogens.<\/jats:p>","DOI":"10.1093\/molbev\/msae066","type":"journal-article","created":{"date-parts":[[2024,4,4]],"date-time":"2024-04-04T00:03:48Z","timestamp":1712189028000},"source":"Crossref","is-referenced-by-count":24,"title":["Inter-species Transcriptomic Analysis Reveals a Constitutive Adaptation Against Oxidative Stress for the Highly Virulent <i>Leptospira<\/i> Species"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0984-5977","authenticated-orcid":false,"given":"Alexandre","family":"Giraud-Gatineau","sequence":"first","affiliation":[{"name":"Microbiology Department, Institut Pasteur, Universit\u00e9 Paris Cit\u00e9, Biology of Spirochetes Unit , Paris , France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6776-1435","authenticated-orcid":false,"given":"Garima","family":"Ayachit","sequence":"additional","affiliation":[{"name":"INRS-Centre Armand-Frappier Sant\u00e9 Biotechnologie, Bacterial Symbionts Evolution , Laval, Quebec H7V 1B7 , Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7324-1663","authenticated-orcid":false,"given":"Cecilia","family":"Nieves","sequence":"additional","affiliation":[{"name":"INRS-Centre Armand-Frappier Sant\u00e9 Biotechnologie, Bacterial Symbionts Evolution , Laval, Quebec H7V 1B7 , Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-9709-9076","authenticated-orcid":false,"given":"Kouessi C","family":"Dagbo","sequence":"additional","affiliation":[{"name":"INRS-Centre Armand-Frappier Sant\u00e9 Biotechnologie, Bacterial Symbionts Evolution , Laval, Quebec H7V 1B7 , Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Konogan","family":"Bourhy","sequence":"additional","affiliation":[{"name":"INRS-Centre Armand-Frappier Sant\u00e9 Biotechnologie, Bacterial Symbionts Evolution , Laval, Quebec H7V 1B7 , Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-4923-1879","authenticated-orcid":false,"given":"Francisco","family":"Pulido","sequence":"additional","affiliation":[{"name":"INRS-Centre Armand-Frappier Sant\u00e9 Biotechnologie, Bacterial Symbionts Evolution , Laval, Quebec H7V 1B7 , Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3029-0753","authenticated-orcid":false,"given":"Samuel G","family":"Huete","sequence":"additional","affiliation":[{"name":"Microbiology Department, Institut Pasteur, Universit\u00e9 Paris Cit\u00e9, Biology of Spirochetes Unit , Paris , France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6475-0041","authenticated-orcid":false,"given":"Nadia","family":"Benaroudj","sequence":"additional","affiliation":[{"name":"Microbiology Department, Institut Pasteur, Universit\u00e9 Paris Cit\u00e9, Biology of Spirochetes Unit , Paris , France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5338-5579","authenticated-orcid":false,"given":"Mathieu","family":"Picardeau","sequence":"additional","affiliation":[{"name":"Microbiology Department, Institut Pasteur, Universit\u00e9 Paris Cit\u00e9, Biology of Spirochetes Unit , Paris , France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8574-0547","authenticated-orcid":false,"given":"Fr\u00e9d\u00e9ric J","family":"Veyrier","sequence":"additional","affiliation":[{"name":"INRS-Centre Armand-Frappier Sant\u00e9 Biotechnologie, Bacterial Symbionts 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