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Background  Aeromonads make up a group of Gram-negative bacteria that includes human and fish pathogens. The  Aeromonas salmonicida  species has the peculiarity of including five known subspecies. However, few studies of the genomes of  A. salmonicida  subspecies have been reported to date.    Results  We sequenced the genomes of additional  A. salmonicida  isolates, including three from India, using next-generation sequencing in order to gain a better understanding of the genomic and phylogenetic links between  A. salmonicida  subspecies. Their relative phylogenetic positions were confirmed by a core genome phylogeny based on 1645 gene sequences. The Indian isolates, which formed a sub-group together with  A. salmonicida  subsp.  pectinolytica , were able to grow at either at 18 °C and 37 °C, unlike the  A. salmonicida  psychrophilic isolates that did not grow at 37 °C. Amino acid frequencies, GC content, tRNA composition, loss and gain of genes during evolution, pseudogenes as well as genes under positive selection and the mobilome were studied to explain this intraspecies dichotomy.    Conclusion  Insertion sequences appeared to be an important driving force that locked the psychrophilic strains into their particular lifestyle in order to conserve their genomic integrity. This observation, based on comparative genomics, is in agreement with previous results showing that insertion sequence mobility induced by heat in  A. salmonicida  subspecies causes genomic plasticity, resulting in a deleterious effect on the virulence of the bacterium. We provide a proof-of-concept that selfish DNAs play a major role in the evolution of bacterial species by modeling genomes.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-016-2381-3) contains supplementary material, which is available to authorized users.

Increasing genomic diversity and evidence of constrained lifestyle evolution due to insertion sequences in Aeromonas salmonicida