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In this work, we present the genome sequences of<jats:italic>M. flocculare<\/jats:italic>and<jats:italic>M. hyopneumoniae<\/jats:italic>strain 7422, and we compare these genomes with the genomes of other<jats:italic>M. hyoponeumoniae<\/jats:italic>strain and to the a<jats:italic>M. hyorhinis<\/jats:italic>genome. These analyses were performed to identify possible characteristics that may help to explain the different behaviors of these species in swine respiratory tracts.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>The overall genome organization of three species was analyzed, revealing that the ORF clusters (OCs) differ considerably and that inversions and rearrangements are common. Although<jats:italic>M. flocculare<\/jats:italic>and<jats:italic>M. hyopneumoniae<\/jats:italic>display a high degree of similarity with respect to the gene content, only some genomic regions display considerable synteny. Genes encoding proteins that may be involved in host-cell adhesion in<jats:italic>M. hyopneumoniae<\/jats:italic>and<jats:italic>M. flocculare<\/jats:italic>display differences in genomic structure and organization. Some genes encoding adhesins of the P97 family are absent in<jats:italic>M. flocculare<\/jats:italic>and some contain sequence differences or lack of domains that are considered to be important for adhesion to host cells. The phylogenetic relationship of the three species was confirmed by a phylogenomic approach. The set of genes involved in metabolism, especially in the uptake of precursors for nucleic acids synthesis and nucleotide metabolism, display some differences in copy number and the presence\/absence in the three species.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>The comparative analyses of three mycoplasma species that inhabit the swine respiratory tract facilitated the identification of some characteristics that may be related to their different behaviors.<jats:italic>M. hyopneumoniae<\/jats:italic>and<jats:italic>M. flocculare<\/jats:italic>display many differences that may help to explain why one species is pathogenic and the other is considered to be commensal. However, it was not possible to identify specific virulence determinant factors that could explain the differences in the pathogenicity of the analyzed species. The<jats:italic>M. hyorhinis<\/jats:italic>genome contains differences in some components involved in metabolism and evasion of the host\u2019s immune system that may contribute to its growth aggressiveness. Several horizontal gene transfer events were identified. The phylogenomic analysis places<jats:italic>M. hyopneumoniae, M. flocculare<\/jats:italic>and<jats:italic>M. hyorhinis<\/jats:italic>in the hyopneumoniae clade.<\/jats:p><\/jats:sec>","DOI":"10.1186\/1471-2164-14-175","type":"journal-article","created":{"date-parts":[[2013,3,15]],"date-time":"2013-03-15T00:21:36Z","timestamp":1363306896000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":66,"title":["New insights on the biology of swine respiratory tract mycoplasmas from a comparative genome analysis"],"prefix":"10.1186","volume":"14","author":[{"given":"Franciele Maboni","family":"Siqueira","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Claudia Elizabeth","family":"Thompson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Veridiana Gomes","family":"Virginio","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Taylor","family":"Gonchoroski","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luciano","family":"Reolon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luiz Gonzaga","family":"Almeida","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marbella Maria","family":"da Fons\u00eaca","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rangel","family":"de Souza","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Francisco","family":"Prosdocimi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Irene Silveira","family":"Schrank","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Henrique Bunselmeyer","family":"Ferreira","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ana Tereza Ribeiro","family":"de Vasconcelos","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arnaldo","family":"Zaha","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2013,3,14]]},"reference":[{"key":"4857_CR1","doi-asserted-by":"crossref","first-page":"1094","DOI":"10.1128\/MMBR.62.4.1094-1156.1998","volume":"62","author":"S Razin","year":"1998","unstructured":"Razin S, Yogev D, Naot Y: Molecular biology and pathogenicity of mycoplasmas. 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