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Two of these lineages predominantly cause human sporadic and epidemic infections, whereas the third lineage has never been implicated in human disease outbreaks despite its overall conservation of many known virulence factors.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Here we compare the genomes of 26<jats:italic>L. monocytogenes<\/jats:italic>strains representing the three lineages based on both<jats:italic>in silico<\/jats:italic>comparative genomic analysis and high-density, pan-genomic DNA array hybridizations. We uncover 86 genes and 8 small regulatory RNAs that likely make<jats:italic>L. monocytogenes<\/jats:italic>lineages differ in carbohydrate utilization and stress resistance during their residence in natural habitats and passage through the host gastrointestinal tract. We also identify 2,330 to 2,456 core genes that define this species along with an open pan-genome pool that contains more than 4,052 genes. Phylogenomic reconstructions based on 3,560 homologous groups allowed robust estimation of phylogenetic relatedness among<jats:italic>L. monocytogenes<\/jats:italic>strains.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>Our pan-genome approach enables accurate co-analysis of DNA sequence and hybridization array data for both core gene estimation and phylogenomics. Application of our method to the pan-genome of<jats:italic>L. monocytogenes<\/jats:italic>sheds new insights into the intraspecific niche expansion and evolution of this important foodborne pathogen.<\/jats:p><\/jats:sec>","DOI":"10.1186\/1471-2164-11-500","type":"journal-article","created":{"date-parts":[[2010,9,16]],"date-time":"2010-09-16T18:16:25Z","timestamp":1284660985000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":82,"title":["Probing the pan-genome of Listeria monocytogenes: new insights into intraspecific niche expansion and genomic diversification"],"prefix":"10.1186","volume":"11","author":[{"given":"Xiangyu","family":"Deng","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adam M","family":"Phillippy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zengxin","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Steven L","family":"Salzberg","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wei","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2010,9,16]]},"reference":[{"issue":"6","key":"3094_CR1","doi-asserted-by":"publisher","first-page":"3137","DOI":"10.1128\/AEM.69.6.3137-3143.2003","volume":"69","author":"R Gardan","year":"2003","unstructured":"Gardan R, Cossart P, Labadie J: Identification of Listeria monocytogenes genes involved in salt and alkaline-pH tolerance. 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