Biojournal of Science and Technology
Volume 2, P-ISSN:2412-5377, E-ISSN:2410-9754, Article ID:m140008
Identification of the positively selected genes governing host-pathogen arm race in Vibrio sp. through comparative genomics approach
Atai Rabby1, Sajib Chakraborty1*, Atiqur Rahman1, Shamma Shakila Rahman1, Shahjalal Soad1 , Kaniz Fatima Chanda1, Rajib Chakravorty2
1 Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka-1000, Bangladesh.
2 Department of EEE, University of Melbourne, National ICT Australia, Victoria 3010, Australia
Date of Acceptance: Monday, June 29, 2015
Date of Published: Friday, July 24, 2015
Address corresponds to
Sajib Chakraborty Assistant Professor, Department of Biochemistry and Molecular Biology, Faculty of Biological Sciences, University of Dhaka, Dhaka-1000, Bangladesh. Email: firstname.lastname@example.org
Acedemic Editor: Dr Md Shahidul Islam
To cite this article
Atai Rabby, Sajib Chakraborty, Atiqur Rahman, Shamma Shakila Rahman, Shahjalal Soad , Kaniz Fatima Chanda, Rajib Chakravorty .Identification of the positively selected genes governing host-pathogen arm race in Vibrio sp. through comparative genomics approach.Biojournal of Science and Technology.Volume 2,2015
Bacterial evolution is due to the adaptive nature of the core bacterial genomes that plays critical role in diversification, fitness and adaptation of the species to different environment and host. Since Vibrio cholerae represents an appropriate model organism for studying the interplay of environment and host driven factors shaping the microbial genome structure and function, the current study aims to identify genes that are under these strong forces in V. cholerae. Here, we employed a comparative genomics approach to identify genes that are under positive selection in ten strains of Vibrio sp. including four pathogenic V. cholerae strains. From the available genome sequence data, a total of 422 orthologous genes were identified by reciprocal BLAST best-hit method, recombination breakpoint frequency analysis and tree comparison method. These 422 genes, representing the core genome of Vibrio sp., constituted the dataset to be analyzed for evolutionary selections. The analysis of natural selection, based on Maximum Likelihood method on synonymous and non-synonymous substitution rate, confirms the hypothesis that the bacterial core genomes are mostly under purifying selection with a few positively selected regions. However, our finding also reveals that positively selected sites in the Vibrio genome occur in a wide range of different genes encompassing diverse functional pathways including cell surface proteins (e.g. outer membrane-specific lipoprotein transporter/assembly proteins etc.), cell motility proteins (e.g. flagellar motor switch proteins, flagellar hook and assembly proteins), nutrient acquisition (e.g. amino acid, carbohydrate and phosphate ABC transporters), DNA repair and transcription related proteins. Interestingly, these positively selected gene products are directly involved with host-pathogen interactions and fitness in gastrointestinal environment. Therefore, the collective evidences of these positively selected genes spanning several pathways raise the possibility of their involvement in evolutionary arms races with other bacteria, phages, and/or the host immune system. This finding points to the natural selections which is the responsible factor for the diversification of Vibrio genus.