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Genome-Wide Relative Analysis of Codon Usage Bias and Codon Context Pattern in the Bacteria Salinibacter Ruber, Chromohalobacter Salexigens and Rhizobium Etli | Abstract
ISSN: 2161-1009

Biochemistry & Analytical Biochemistry
Open Access

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Research Article

Genome-Wide Relative Analysis of Codon Usage Bias and Codon Context Pattern in the Bacteria Salinibacter Ruber, Chromohalobacter Salexigens and Rhizobium Etli

Mohammad Samir Farooqi1*, DC Mishra1, Niyati Rai1, DP Singh2, Anil Rai1, KK Chaturvedi1, Ratna Prabha2 and Manjeet Kaur1

1Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute, Library Avenue, Pusa, New Delhi-110012, India

2National Bureau of Agriculturally Important Microorganisms, Mau, U.P. - 275101, India

*Corresponding Author:
Mohammad Samir Farooqi
Centre for Agricultural Bioinformatics
Indian Agricultural Statistics Research Institute
Library Avenue, Pusa, New Delhi-110012, India
Tel: 9899038037
Fax: 011-25841564
Email: [email protected]

Received Date: January 22, 2016 Accepted Date: March 10, 2016 Published Date: March 14, 2016

Citation: Farooqi MS, Mishra DC, Rai N, Singh DP, Rai A, et al. (2016) Genome-Wide Relative Analysis of Codon Usage Bias and Codon Context Pattern in the Bacteria Salinibacter ruber, Chromohalobacter Salexigens and Rhizobium etli. Biochem Anal Biochem 5:257. doi:10.4172/2161-1009.1000257

Copyright: © 2016 Farooqi MS, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Abstract

Codon is the basic unit for biological message transmission during synthesis of proteins in an organism. Codon Usage Bias is preferential usage among synonymous codons, in an organisms. This preferential use of a synonymous codon was found not only among species but also occurs among genes within the same genome of a species. This variation of codon usage patterns are controlled by natural processes such as mutation, drift and pressure. In this study, we have used computational as well as statistical techniques for finding codon usage bias and codon context pattern of Salinibacter ruber (extreme halophilic), Chromohalobacter salexigens (moderate halophilic) and Rhizobium etli (nonhalophilic). In addition to this, compositional variation in translated amino acid frequency, effective number of codons and optimal codons were also studied. A plot of ENc versus GC3s suggests that both mutation bias and translational selection contribute to these differences of codon bias. However, mutation bias is the driving force of the synonymous codon usage patterns in halophilic bacteria (Salinibacter ruber and Chromohalobacter salexigens) and translational selection seems to affect codon usage pattern in non-halophilic bacteria (Rhizobium etli). Correspondence analysis of Relative Synonymous Codon Usage revealed different clusters of genes varying in numbers in the bacteria under study. Moreover, codon context pattern was also seen variable in these bacteria. These results clearly indicate the variation in the codon usage pattern in these bacterial genomes.

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