title: Visualization of pseudogenes in intracellular bacteria reveals the different tracks to gene destruction.
abstract: BACKGROUND
  Pseudogenes reveal ancestral gene functions. Some obligate intracellular bacteria, such as Mycobacterium leprae and Rickettsia spp., carry substantial fractions of pseudogenes. Until recently, horizontal gene transfers were considered to be rare events in obligate host-associated bacteria.
  
  
  RESULTS
  We present a visualization tool that displays the relationships and positions of degraded and partially overlapping gene sequences in multiple genomes. With this tool we explore the origin and deterioration patterns of the Rickettsia pseudogenes and find that variably present genes and pseudogenes tend to have been acquired more recently, are more divergent in sequence, and exhibit a different functional profile compared with genes conserved across all species. Overall, the origin of only one-quarter of the variable genes and pseudogenes can be traced back to the common ancestor of Rickettsia and the outgroup genera Orientia and Wolbachia. These sequences contain only a few disruptive mutations and show a broad functional distribution profile, much like the core genes. The remaining genes and pseudogenes are extensively degraded or solely present in a single species. Their functional profile was heavily biased toward the mobile gene pool and genes for components of the cell wall and the lipopolysaccharide.
  
  
  CONCLUSIONS
  Reductive evolution of the vertically inherited genomic core accounts for 25% of the predicted genes in the variable segments of the Rickettsia genomes, whereas 75% stems from the flux of the mobile gene pool along with genes for cell surface structures. Thus, most of the variably present genes and pseudogenes in Rickettsia have arisen from recent acquisitions.
authors.affiliation: Department of Molecular Evolution, Evolutionary Biology Center, Uppsala University, Norbyvägen 18C, S-752 36 Uppsala, Sweden. Hans-Henrik.Fuxelius@ebc.uu.se
authors.forename: Hans-Henrik
authors.initials: HH
authors.lastname: Fuxelius
authors.forename: Alistair C
authors.initials: AC
authors.lastname: Darby
authors.forename: Nam-Huyk
authors.initials: NH
authors.lastname: Cho
authors.forename: Siv G E
authors.initials: SG
authors.lastname: Andersson
mesh_terms: D001483:Base Sequence; D019143:Evolution, Molecular; D005798:Genes, Bacterial; D014644:Genetic Variation; D020071:Interspersed Repetitive Sequences; D016366:Open Reading Frames / Q000235:genetics; D010802:Phylogeny; D020560:Proteobacteria / Q000235:genetics; D011544:Pseudogenes; D012281:Rickettsia / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software