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Online Journal of Bioinformatics ©
Volume 14 (1): 14-31, 2013.
Statistical analysis of codon usage in extremely halophilic bacterium, Salinibacter ruber DSM 13855
Sanjukta RK1 , Farooqi MS1, Sharma N1 , Rai N Mishra DC2, Rai A, Singh DP3 and Chaturvedi KK1
Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute, Pusa, New Delhi Central Drug Research Institute, Jhankipuram, Lucknow, National Bureau of Agriculturally Important Microorganisms, Mau Nath Bhanjan, India
Sanjukta RK, Farooqi MS, Sharma N, Rai N, Mishra DC, Rai A, Singh DP, Chaturvedi KK., Statistical Analysis of codon usage in extremely halophilic bacterium, Salinibacter ruber DSM 13855, Online J Bioinform., 14(1): 15-31, 2013. Synonymous codons are randomly distributed among genes, a phenomenon termed as codon usage bias. Understanding the extent and pattern of codon bias; the forces affecting codon usage are the key steps towards elucidating the adaptive choice of codon at the level of individual genes. Herein, trends in codon usage bias in a set of 1450 genes in Salinibacter ruber, an extremely halophilic bacterium have been evaluated. Notably, synonymous codon usage varies considerably among genes of this bacterium. Base composition (mutational bias) particularly C- and G-ending codons predominate with greater preference of ‘C’ at synonymously variable sites. The effect of natural selection acting at the level of translation has been observed. Certain genes with a high codon bias have been identified by multivariate statistical approach and investigations through various codon bias indices. These genes appearto be highly expressed, and their codon usage seems to have been shaped by selection favouring a limited number of translationally optimal codons. A subset of 27 optimal codons seems to be preferentially used in highly expressed genes. The frequency of these codons appears to be correlated with the level of gene expression, and may be a useful indicator in the case of genes (or open reading frames) whose expression levels are unknown.
Keywords: synonymous codon usage, mutational bias, multivariate statistical