title: Reassessment of the Listeria monocytogenes pan-genome reveals dynamic integration hotspots and mobile genetic elements as major components of the accessory genome.
abstract: BACKGROUND
  Listeria monocytogenes is an important food-borne pathogen and model organism for host-pathogen interaction, thus representing an invaluable target considering research on the forces governing the evolution of such microbes. The diversity of this species has not been exhaustively explored yet, as previous efforts have focused on analyses of serotypes primarily implicated in human listeriosis. We conducted complete genome sequencing of 11 strains employing 454 GS FLX technology, thereby achieving full coverage of all serotypes including the first complete strains of serotypes 1/2b, 3c, 3b, 4c, 4d, and 4e. These were comparatively analyzed in conjunction with publicly available data and assessed for pathogenicity in the Galleria mellonella insect model.
  
  
  RESULTS
  The species pan-genome of L. monocytogenes is highly stable but open, suggesting an ability to adapt to new niches by generating or including new genetic information. The majority of gene-scale differences represented by the accessory genome resulted from nine hyper variable hotspots, a similar number of different prophages, three transposons (Tn916, Tn554, IS3-like), and two mobilizable islands. Only a subset of strains showed CRISPR/Cas bacteriophage resistance systems of different subtypes, suggesting a supplementary function in maintenance of chromosomal stability. Multiple phylogenetic branches of the genus Listeria imply long common histories of strains of each lineage as revealed by a SNP-based core genome tree highlighting the impact of small mutations for the evolution of species L. monocytogenes. Frequent loss or truncation of genes described to be vital for virulence or pathogenicity was confirmed as a recurring pattern, especially for strains belonging to lineages III and II. New candidate genes implicated in virulence function were predicted based on functional domains and phylogenetic distribution. A comparative analysis of small regulatory RNA candidates supports observations of a differential distribution of trans-encoded RNA, hinting at a diverse range of adaptations and regulatory impact.
  
  
  CONCLUSIONS
  This study determined commonly occurring hyper variable hotspots and mobile elements as primary effectors of quantitative gene-scale evolution of species L. monocytogenes, while gene decay and SNPs seem to represent major factors influencing long-term evolution. The discovery of common and disparately distributed genes considering lineages, serogroups, serotypes and strains of species L. monocytogenes will assist in diagnostic, phylogenetic and functional research, supported by the comparative genomic GECO-LisDB analysis server (http://bioinfo.mikrobio.med.uni-giessen.de/geco2lisdb).
authors: Institute of Medical Microbiology, German Centre for Infection Research, Justus-Liebig-University, D-35392, Giessen, Germany.
authors: Carsten
authors: C
authors: Kuenne
authors: André
authors: A
authors: Billion
authors: Mobarak Abu
authors: MA
authors: Mraheil
authors: Axel
authors: A
authors: Strittmatter
authors: Rolf
authors: R
authors: Daniel
authors: Alexander
authors: A
authors: Goesmann
authors: Sukhadeo
authors: S
authors: Barbuddhe
authors: Torsten
authors: T
authors: Hain
authors: Trinad
authors: T
authors: Chakraborty
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics; D000818:Animals; D017124:Conserved Sequence; D004251:DNA Transposable Elements / Q000235:genetics; D019143:Evolution, Molecular; D005819:Genetic Markers / Q000235:genetics; D016680:Genome, Bacterial / Q000235:genetics*; D044404:Genomic Islands / Q000235:genetics; D023281:Genomics; D006801:Humans; D020407:Internet; D020071:Interspersed Repetitive Sequences / Q000235:genetics*; D055029:Inverted Repeat Sequences / Q000235:genetics; D008089:Listeria monocytogenes / Q000235:genetics* / Q000472:pathogenicity / Q000502:physiology / Q000821:virology; D008957:Models, Genetic; D010802:Phylogeny; D039002:Prophages / Q000502:physiology; D058727:RNA, Small Untranslated / Q000235:genetics; D011817:Rabbits; D013045:Species Specificity
chemical_list: D004251:DNA Transposable Elements; D005819:Genetic Markers; D058727:RNA, Small Untranslated