title: Probing the pan-genome of Listeria monocytogenes: new insights into intraspecific niche expansion and genomic diversification.
abstract: BACKGROUND
  Bacterial pathogens often show significant intraspecific variations in ecological fitness, host preference and pathogenic potential to cause infectious disease. The species of Listeria monocytogenes, a facultative intracellular pathogen and the causative agent of human listeriosis, consists of at least three distinct genetic lineages. 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.
  
  
  RESULTS
  Here we compare the genomes of 26 L. monocytogenes strains representing the three lineages based on both in silico comparative genomic analysis and high-density, pan-genomic DNA array hybridizations. We uncover 86 genes and 8 small regulatory RNAs that likely make L. monocytogenes 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 L. monocytogenes strains.
  
  
  CONCLUSIONS
  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 L. monocytogenes sheds new insights into the intraspecific niche expansion and evolution of this important foodborne pathogen.
authors.affiliation: National Center for Food Safety and Technology, Illinois Institute of Technology, Summit, Illinois 60501, USA.
authors.forename: Xiangyu
authors.initials: X
authors.lastname: Deng
authors.forename: Adam M
authors.initials: AM
authors.lastname: Phillippy
authors.forename: Zengxin
authors.initials: Z
authors.lastname: Li
authors.forename: Steven L
authors.initials: SL
authors.lastname: Salzberg
authors.forename: Wei
authors.initials: W
authors.lastname: Zhang
mesh_terms: D002874:Chromosome Mapping; D055028:Comparative Genomic Hybridization; D017124:Conserved Sequence / Q000235:genetics; D005798:Genes, Bacterial / Q000235:genetics; D056426:Genetic Loci / Q000235:genetics; D014644:Genetic Variation; D016680:Genome, Bacterial / Q000235:genetics*; D006801:Humans; D008089:Listeria monocytogenes / Q000235:genetics*; D053858:Metabolic Networks and Pathways / Q000235:genetics; D010802:Phylogeny; D012329:RNA, Bacterial / Q000235:genetics; D012372:ROC Curve; D012015:Reference Standards; D017422:Sequence Analysis, DNA; D012689:Sequence Homology, Nucleic Acid; D013045:Species Specificity
chemical_list: D012329:RNA, Bacterial