sRNA associated genomic islands in Salmonella spp.

Abstract

Genomic Islands are parts of a genome that has evidence of horizontal origins. The present work is a continuation of our earlier work that identified 25 regions downstream of the small RNAs as hotspots of genomic island integration by analyzing three strains of E. coli and one strain of Shigella spp genomes. Till that work, genomic islands have been identified only at tRNA/tmRNA genes in the enterobacterial genomes. Current work reports 11 distinct small RNAs as potent integration sites for genomic islands in 12 Salmonella spp strains. The tRNAcc 1.0 software package has been used to identify genomic islands associated with small RNAs csrC, rprA, ryeB, sraD, sroB, ssrS, rydB, micF, rnpB rtT, and spf. The coordinates of 36 such small RNA associated genomic islands are presented. Also, the nature of genomic sequences encoded within the identified genomic islands were analyzed and validated using virulence factors database, GenBank annotation features, atypical sequence compositions and the genomic block rearrangements.