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To gain insight into phylogenetic structure and mechanisms of pathogenicity for this bacterial species, we compared <jats:italic>M. ovipneumoniae<\/jats:italic> genomes for 99 samples from 6 countries (Australia, Bosnia and Herzegovina, Brazil, China, France and USA) and 4 host species (domestic sheep, domestic goats, bighorn sheep and caribou). Core genome sequences of <jats:italic>M. ovipneumoniae<\/jats:italic> assemblies from domestic sheep and goats fell into two well-supported phylogenetic clades that are divergent enough to be considered different bacterial species, consistent with each of these two clades having an evolutionary origin in separate host species. Genome assemblies from bighorn sheep and caribou also fell within these two clades, indicating multiple spillover events, most commonly from domestic sheep. Pangenome analysis indicated a high percentage (91.4\u200a%) of accessory genes (i.e. genes found only in a subset of assemblies) compared to core genes (i.e. genes found in all assemblies), potentially indicating a propensity for this pathogen to adapt to within-host conditions. In addition, many genes related to carbon metabolism, which is a virulence factor for Mycoplasmas, showed evidence for homologous recombination, a potential signature of adaptation. The presence or absence of annotated genes was very similar between sheep and goat clades, with only two annotated genes significantly clade-associated. However, three <jats:italic>M. ovipneumoniae<\/jats:italic> genome assemblies from asymptomatic caribou in Alaska formed a highly divergent subclade within the sheep clade that lacked 23 annotated genes compared to other assemblies, and many of these genes had functions related to carbon metabolism. Overall, our results suggest that adaptation of <jats:italic>M. ovipneumoniae<\/jats:italic> has involved evolution of carbon metabolism pathways and virulence mechanisms related to those pathways. The genes involved in these pathways, along with other genes identified as potentially involved in virulence in this study, are potential targets for future investigation into a possible genomic basis for the high variation observed in disease outcomes within and between wild and domestic host species.<\/jats:p>","DOI":"10.1099\/mgen.0.001279","type":"journal-article","created":{"date-parts":[[2024,8,30]],"date-time":"2024-08-30T16:16:51Z","timestamp":1725034611000},"source":"Crossref","is-referenced-by-count":3,"title":["Comparative genomic analysis identifies potential adaptive variation in Mycoplasma ovipneumoniae"],"prefix":"10.1099","volume":"10","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4721-1924","authenticated-orcid":false,"given":"Kimberly R.","family":"Andrews","sequence":"first","affiliation":[{"name":"Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID, USA"},{"name":"Present address: Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas E.","family":"Besser","sequence":"additional","affiliation":[{"name":"Department of Veterinary Microbiology and Pathology, Washington State University College of Veterinary Medicine, Pullman, WA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thibault","family":"Stalder","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of Idaho, Moscow, ID, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eva M.","family":"Top","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of Idaho, Moscow, ID, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katherine N.","family":"Baker","sequence":"additional","affiliation":[{"name":"Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew W.","family":"Fagnan","sequence":"additional","affiliation":[{"name":"Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel D.","family":"New","sequence":"additional","affiliation":[{"name":"Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"G. 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