title: Comprehensive analysis of pseudogenes in prokaryotes: widespread gene decay and failure of putative horizontally transferred genes.
abstract: BACKGROUND
  Pseudogenes often manifest themselves as disabled copies of known genes. In prokaryotes, it was generally believed (with a few well-known exceptions) that they were rare.
  
  
  RESULTS
  We have carried out a comprehensive analysis of the occurrence of pseudogenes in a diverse selection of 64 prokaryote genomes. Overall, we find a total of around 7,000 candidate pseudogenes. Moreover, in all the genomes surveyed, pseudogenes occur in at least 1 to 5% of all gene-like sequences, with some genomes having considerably higher occurrence. Although many large populations of pseudogenes arise from large, diverse protein families (for example, the ABC transporters), notable numbers of pseudogenes are associated with specific families that do not occur that widely. These include the cytochrome P450 and PPE families (PF00067 and PF00823) and others that have a direct role in DNA transposition.
  
  
  CONCLUSIONS
  We find suggestive evidence that a large fraction of prokaryote pseudogenes arose from failed horizontal transfer events. In particular, we find that pseudogenes are more than twice as likely as genes to have anomalous codon usage associated with horizontal transfer. Moreover, we found a significant difference in the number of horizontally transferred pseudogenes in pathogenic and non-pathogenic strains of Escherichia coli.
authors.affiliation: Department of Molecular Biophysics and Biochemistry, Yale University, PO Box 208114, New Haven, CT 06520-8114, USA. lyang@csb.yale.edu
authors.forename: Yang
authors.initials: Y
authors.lastname: Liu
authors.forename: Paul M
authors.initials: PM
authors.lastname: Harrison
authors.forename: Victor
authors.initials: V
authors.lastname: Kunin
authors.forename: Mark
authors.initials: M
authors.lastname: Gerstein
mesh_terms: D048168:Escherichia coli K12 / Q000235:genetics; D018628:Gene Dosage; D020440:Gene Duplication; D022761:Gene Transfer, Horizontal / Q000235:genetics*; D005798:Genes, Bacterial / Q000235:genetics; D023281:Genomics / Q000379:methods; D008957:Models, Genetic; D005810:Multigene Family / Q000235:genetics; D016296:Mutagenesis / Q000235:genetics; D011387:Prokaryotic Cells / Q000737:chemistry* / Q000378:metabolism*; D011544:Pseudogenes / Q000235:genetics*