title: The influence of environmental adaptation on bacterial genome structure.
abstract: OBJECTIVE
  Researchers have long been puzzled by the diversity of life. Now that the complete genomic sequence of many organisms has been determined, it is possible to evaluate the impact of organismal variation on sequence structure or vice versa. The aim of this investigation was to explore genomic changes mandated by organismal adaptation to its ecological niches.
  
  
  RESULTS
  Coding sequences from three phylogenetically related bacterial species namely Mycoplasma genitalium, M. pneumoniae and Ureaplasma urealyticum were subject to in depth sequence analyses. M. genitalium and M. pneumoniae both belong to the genus Mycoplasma while U. urealyticum is a member of the genus Ureaplasma. However, M. genitalium and U. urealyticum are urogenital pathogens while M. pneumoniae is a respiratory pathogen. Complete transcriptomes were downloaded from NCBI for each species, and were subject to in silico investigation using in-house software, and public sequence analysis tools. Clear similarities in transcriptome structure were identified among the functionally similar species M. genitalium and U. urealyticum while no such relationship was identified among the phylogenetically related species M. genitalium and M. pneumoniae.
  
  
  CONCLUSIONS
  It is plausible to conclude that, in these bacterial species, environmental stimuli might be more influential in shaping sequence signatures than phylogenetic relationships.
  
  
  CONCLUSIONS
  This study suggests that molecular signatures within the transcriptomes of the species examined are likely to be a product of evolutionary adaptation to diverse environmental ecological stimuli, and not a result of common phylogeny.
authors.affiliation: The Bioinformatics Supercomputing Centre, The Hospital for Sick Children, Toronto, ON, Canada. afadiel@yale.edu
authors.forename: A
authors.initials: A
authors.lastname: Fadiel
authors.forename: S
authors.initials: S
authors.lastname: Lithwick
authors.forename: F
authors.initials: F
authors.lastname: Naftolin
mesh_terms: D000220:Adaptation, Biological; D000595:Amino Acid Sequence; D001482:Base Composition; D003062:Codon / Q000235:genetics*; D019992:Databases as Topic; D019143:Evolution, Molecular; D016680:Genome, Bacterial; D023281:Genomics; D009174:Mycoplasma / Q000235:genetics*; D016366:Open Reading Frames / Q000502:physiology; D010802:Phylogeny; D017386:Sequence Homology, Amino Acid
chemical_list: D003062:Codon