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There are two genotypes of <jats:italic>M. bovoculi<\/jats:italic> (genotypes 1 and 2) that differ in their gene content and potential virulence factors, although neither have been experimentally shown to cause IBK. <jats:italic>M. bovis<\/jats:italic> is a causative IBK agent, however, not all strains carry a complete assortment of known virulence factors. The goals of this study were to determine the population structure and depth of <jats:italic>M. bovis<\/jats:italic> genomic diversity, and to compare core and accessory genes and predicted outer membrane protein profiles both within and between <jats:italic>M. bovis<\/jats:italic> and <jats:italic>M. bovoculi<\/jats:italic>.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>Phylogenetic trees and bioinformatic analyses of 36\u2009<jats:italic>M. bovis<\/jats:italic> chromosomes sequenced in this study and additional available chromosomes of <jats:italic>M. bovis<\/jats:italic> and both genotype 1 and 2\u2009<jats:italic>M. bovoculi,<\/jats:italic> showed there are two genotypes (1 and 2) of <jats:italic>M. bovis.<\/jats:italic> The two <jats:italic>M. bovis<\/jats:italic> genotypes share a core of 2015 genes, with 121 and 186 genes specific to genotype 1 and 2, respectively. The two genotypes differ by their chromosome size and prophage content, encoded protein variants of the virulence factor hemolysin, and by their affiliation with different plasmids. Eight plasmid types were identified in this study, with types 1 and 6 observed in 88 and 56% of genotype 2 strains, respectively, and absent from genotype 1 strains. Only type 1 plasmids contained one or two gene copies encoding filamentous haemagglutinin-like proteins potentially involved with adhesion. A core of 1403 genes was shared between the genotype 1 and 2 strains of both <jats:italic>M. bovis<\/jats:italic> and <jats:italic>M. bovoculi<\/jats:italic>, which encoded a total of nine predicted outer membrane proteins.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>There are two genotypes of <jats:italic>M. bovis<\/jats:italic> that differ in both chromosome content and plasmid profiles and thus may not equally associate with IBK. Immunological reagents specifically targeting select genotypes of <jats:italic>M. bovis<\/jats:italic>, or all genotypes of <jats:italic>M. bovis<\/jats:italic> and <jats:italic>M. bovoculi<\/jats:italic> together could be designed from the outer membrane proteins identified in this study.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12866-022-02670-3","type":"journal-article","created":{"date-parts":[[2022,10,21]],"date-time":"2022-10-21T06:05:45Z","timestamp":1666332345000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":20,"title":["Whole genome sequencing of Moraxella bovis strains from North America reveals two genotypes with different genetic determinants"],"prefix":"10.1186","volume":"22","author":[{"given":"Emily L.","family":"Wynn","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew M.","family":"Hille","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John Dustin","family":"Loy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gennie","family":"Schuller","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kristen L.","family":"Kuhn","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aaron M.","family":"Dickey","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James L.","family":"Bono","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael L.","family":"Clawson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2022,10,21]]},"reference":[{"issue":"2","key":"2670_CR1","doi-asserted-by":"publisher","first-page":"355","DOI":"10.1016\/j.cvfa.2021.03.010","volume":"37","author":"EJ Dennis","year":"2021","unstructured":"Dennis EJ, Kneipp M. 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