cholerae strains and several other organisms of related Vibrio species are generally very similar (Tagomori et al., 2002). Interestingly, the CTXϕ region of the Matlab variant of V. cholerae had properties of the CTXϕ region of both V. cholerae Classical and El Tor strains (Safa et al., 2006). In 1990, it was first observed that large blocks of horizontally acquired foreign sequences occur in chromosomes of pathogenic bacteria, and those regions are highly correlated with pathogenicity (Groisman & Ochman,
1996; Hacker et al., 1997; Hacker & Kaper, 1999). Some of these blocks of sequences were observed to possess a gene for specific recombinase and sequences having characteristics of integration sites, the characteristic features of mobile elements. Some others, in spite
of being foreign in nature, lacked insertion sequences, recombinase genes and specific att sites, and might have contained only fragments of mobility genes. In the Selleckchem SB431542 latter case, the mobility sequences were predicted to be lost in the course of evolution after their integration into the bacterial genome (Hacker Antidiabetic Compound Library screening & Kaper, 1999). Subsequently, all foreign gene blocks present in pathogenic and nonpathogenic prokaryotic genomes are collectively named in the literature as genomic islands (GIs) (Hacker & Kaper, 2000; Weinstock, 2000). These gene blocks determine various accessory functions, for example, secondary metabolic activities, antibiotic resistance, symbiosis and other special functions related to survival in harsh environmental conditions (Weinstock, 2000). These foreign DNA blocks were expected to be associated with the virulence of the pathogenic bacteria and, hence, the first of these blocks that were proved to be associated with virulence genes of pathogenic
bacteria were named as pathogenicity islands (Hacker et al., 1990). In this context, the present study has been designed to identify new GIs in three completely sequenced V. cholerae genomes, i.e. V. cholerae Classical O395, V. cholerae El Tor N16961 and V. cholerae MJ1236, using design-island developed in-house (Chatterjee et al., 2008). The program design-island identifies GIs in prokaryotic genomes. GIs thus predicted in these three strains of V. cholerae were then compared to elucidate their relatedness with Edoxaban each other. The complete genome sequences of V. cholerae O395, the O1 classical strain of Ogawa serotype isolated in 1964 from India, V. cholerae N16961, the O1 El Tor Inaba isolated in 1971 in Bangladesh and V. cholerae MJ1236, O1 El Tor Inaba strain isolated from Matlab, Bangladesh in 1994 representing the ‘Matlab variant’ of El Tor were considered for the present study. The chromosomal sequences of all these organisms were downloaded from the ftp server of NCBI (http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi). The program design-island searches for islands in a prokaryotic chromosome using a probing window of varying size that slides over the entire chromosome.