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Indian Journal of Medical Microbiology
Medknow Publications on behalf of Indian Association of Medical Microbiology
ISSN: 0255-0857
EISSN: 1998-3646
Vol. 26, No. 4, 2008, pp. 313-321
Bioline Code: mb08101
Full paper language: English
Document type: Research Article
Document available free of charge

Indian Journal of Medical Microbiology, Vol. 26, No. 4, 2008, pp. 313-321

 en Comparative analysis of codon usage patterns and identification of predicted highly expressed genes in five Salmonella check for this species in other resources genomes
Mondal, UK; Sur, S; Bothra, AK & Sen, A

Abstract

Purpose: To anlyse codon usage patterns of five complete genomes of Salmonella check for this species in other resources , 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.

Keywords
Codon bias and expression, pathogenicity, Salmonella

 
© Copyright 2008 Indian Journal of Medical Microbiology.
Alternative site location: http://www.ijmm.org

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