Genomic Islands in Bacterial Genome Evolution and Speciation

Abstract

Bacterial genomes are flexible entities due to the complicated and dynamic makeup of the bacterial chromosomes. The plasticity and evolution of the bacterial genome are facilitated by genome rearrangements, point mutations, and lateral or horizontal gene transfer (HGT). Bacteria benefit from HGT as it facilitates them to adapt to their environment, colonize new niches, and steer evolution in “quantum leaps.” Analyses of thousands of bacterial genome sequences have shown that there exist two major divisions in the bacterial genome: the primary core genome and the accessory gene containing flexible genome. Accessory gene acquisition might be mediated by entities designated as genomic islands (GIs), facilitating the process of HGT. GI represents horizontally acquired genes frequently clustered together in bacterial genomes with different GC content, dinucleotide frequencies, codon use, etc., than the neighboring genes. GIs make the genome flexible enough to adapt novel functions over a short life span and encode a diverse range of accessory genes for improved fitness, pathogenicity, resistance potential, metabolic flexibility, ecological adaptability, symbiosis, etc., in the harboring bacteria. Niche dynamicity is the key to having highly flexible genomes in bacteria. The niche exerts selection pressure to retain only helpful information and optimizes genomes based upon the costs and benefits of different strains. This strain-specific propensity to have high island variability contributes to genome plasticity and subsequent genome evolution that might lead to niche specialization of specific bacterial strains. The most significant evolutionary benefit of GI is fostering the genetic flexibility and ability to transmit multiple genes, enabling more effective adaptation and enhancing pertinence in specific ecological niches. The consecutive acquisition and loss of auxiliary genes within the GI and the consequent transmission of chromosomal DNA from the host appear to be the prerequisites for the evolution of bacterial species.