title: Comparative analysis of codon usage patterns and identification of predicted highly expressed genes in five Salmonella genomes.
abstract: OBJECTIVE
  To analyse codon usage patterns of five complete genomes of Salmonella , predict highly expressed genes, examine horizontally transferred pathogenicity-related genes to detect their presence in the strains, and scrutinize the nature of highly expressed genes to infer upon their lifestyle.
  
  
  METHODS
  Protein coding genes, ribosomal protein genes, and pathogenicity-related genes were analysed with Codon W and CAI (codon adaptation index) Calculator.
  
  
  RESULTS
  Translational efficiency plays a role in codon usage variation in Salmonella genes. Low bias was noticed in most of the genes. GC3 (guanine cytosine at third position) composition does not influence codon usage variation in the genes of these Salmonella strains. Among the cluster of orthologous groups (COGs), translation, ribosomal structure biogenesis [J], and energy production and conversion [C] contained the highest number of potentially highly expressed (PHX) genes. Correspondence analysis reveals the conserved nature of the genes. Highly expressed genes were detected.
  
  
  CONCLUSIONS
  Selection for translational efficiency is the major source of variation of codon usage in the genes of Salmonella . Evolution of pathogenicity-related genes as a unit suggests their ability to infect and exist as a pathogen. Presence of a lot of PHX genes in the information and storage-processing category of COGs indicated their lifestyle and revealed that they were not subjected to genome reduction.
authors.affiliation: NBU Bioinformatics Facility, University of North Bengal, Siliguri, West Bengal, India.
authors.forename: U K
authors.initials: UK
authors.lastname: Mondal
authors.forename: S
authors.initials: S
authors.lastname: Sur
authors.forename: A K
authors.initials: AK
authors.lastname: Bothra
authors.forename: A
authors.initials: A
authors.lastname: Sen
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics* / Q000378:metabolism; D003062:Codon / Q000235:genetics*; D015964:Gene Expression Regulation, Bacterial; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D006801:Humans; D014176:Protein Biosynthesis; D012269:Ribosomal Proteins / Q000235:genetics / Q000378:metabolism; D012475:Salmonella / Q000145:classification* / Q000235:genetics* / Q000378:metabolism / Q000472:pathogenicity
chemical_list: D001426:Bacterial Proteins; D003062:Codon; D012269:Ribosomal Proteins