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Moreover, correlations between<jats:italic>C. burnetii<\/jats:italic>genomic groups and human disease presentation (acute versus chronic) have been described, suggesting that isolates have distinct virulence characteristics. To provide a more-complete understanding of<jats:italic>C. burnetii<\/jats:italic>'s genetic diversity, evolution, and pathogenic potential, we deciphered the whole-genome sequences of the K (Q154) and G (Q212) human chronic endocarditis isolates and the naturally attenuated Dugway (5J108-111) rodent isolate. Cross-genome comparisons that included the previously sequenced Nine Mile (NM) reference isolate (RSA493) revealed both novel gene content and disparate collections of pseudogenes that may contribute to isolate virulence and other phenotypes. While<jats:italic>C. burnetii<\/jats:italic>genomes are highly syntenous, recombination between abundant insertion sequence (IS) elements has resulted in genome plasticity manifested as chromosomal rearrangement of syntenic blocks and DNA insertions\/deletions. The numerous IS elements, genomic rearrangements, and pseudogenes of<jats:italic>C. burnetii<\/jats:italic>isolates are consistent with genome structures of other bacterial pathogens that have recently emerged from nonpathogens with expanded niches. The observation that the attenuated Dugway isolate has the largest genome with the fewest pseudogenes and IS elements suggests that this isolate's lineage is at an earlier stage of pathoadaptation than the NM, K, and G lineages.<\/jats:p>","DOI":"10.1128\/iai.01141-08","type":"journal-article","created":{"date-parts":[[2008,12,2]],"date-time":"2008-12-02T01:59:42Z","timestamp":1228183182000},"page":"642-656","update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":203,"title":["Comparative Genomics Reveal Extensive Transposon-Mediated Genomic Plasticity and Diversity among Potential Effector Proteins within the Genus<i>Coxiella<\/i>"],"prefix":"10.1128","volume":"77","author":[{"given":"Paul A.","family":"Beare","sequence":"first","affiliation":[{"name":"Coxiella Pathogenesis Section, Laboratory of Intracellular Parasites"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nathan","family":"Unsworth","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology and Immunology, Texas A&amp;M Health Science Center, College Station, Texas 77843"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Masako","family":"Andoh","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology and Immunology, Texas A&amp;M Health Science Center, College Station, Texas 77843"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel E.","family":"Voth","sequence":"additional","affiliation":[{"name":"Coxiella Pathogenesis Section, Laboratory of Intracellular Parasites"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anders","family":"Omsland","sequence":"additional","affiliation":[{"name":"Coxiella Pathogenesis Section, Laboratory of Intracellular Parasites"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stacey D.","family":"Gilk","sequence":"additional","affiliation":[{"name":"Coxiella Pathogenesis Section, Laboratory of Intracellular Parasites"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kelly P.","family":"Williams","sequence":"additional","affiliation":[{"name":"Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bruno W.","family":"Sobral","sequence":"additional","affiliation":[{"name":"Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"suffix":"III","given":"John J.","family":"Kupko","sequence":"additional","affiliation":[{"name":"Genomics Core Facility, Research Technologies Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, Hamilton, Montana 59840"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephen F.","family":"Porcella","sequence":"additional","affiliation":[{"name":"Genomics Core Facility, Research Technologies Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, Hamilton, Montana 59840"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James E.","family":"Samuel","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology and Immunology, Texas A&amp;M Health Science Center, College Station, Texas 77843"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert A.","family":"Heinzen","sequence":"additional","affiliation":[{"name":"Coxiella Pathogenesis Section, Laboratory of Intracellular Parasites"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_2_2_2","doi-asserted-by":"publisher","DOI":"10.1128\/jb.160.3.994-1002.1984"},{"key":"e_1_3_2_3_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0959-437X(99)00024-6"},{"key":"e_1_3_2_4_2","doi-asserted-by":"publisher","DOI":"10.1038\/24094"},{"key":"e_1_3_2_5_2","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.01767-06"},{"key":"e_1_3_2_6_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.0030003"},{"key":"e_1_3_2_7_2","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2180-6-38"},{"key":"e_1_3_2_8_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1574-6968.2006.00440.x"},{"key":"e_1_3_2_9_2","doi-asserted-by":"publisher","DOI":"10.1196\/annals.1355.007"},{"key":"e_1_3_2_10_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.188.7.2309-2324.2006"},{"key":"e_1_3_2_11_2","first-page":"98","volume":"69","year":"1956","unstructured":"Benenson, A. 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