Increasing genomic diversity and evidence of constrained lifestyle evolution due to insertion sequences in Aeromonas salmonicida. (December 2016)

• Record Type: Journal Article
• Authors: Vincent, Antony; Trudel, Mélanie; Freschi, Luca; Nagar, Vandan; Gagné-Thivierge, Cynthia; Levesque, Roger; Charette, Steve
• Is Part Of: BMC genomics. Volume 17:Number 1(2016)
• Page Start: 1
• Page End: 12
• Publication Date: 2016-12
• Subjects: Aeromonas salmonicida -- Phylogeny -- Mesophilic -- Psychrophilic -- Insertion sequence; Genomes -- Periodicals; Gene mapping -- Periodicals; Genomics -- Periodicals; Base Sequence -- Periodicals; Chromosome Mapping -- Periodicals; Genetic Techniques -- Periodicals; Sequence Analysis, DNA -- Periodicals; 572.8605
• DOI: 10.1186/s12864-016-2381-3
• Languages: English
• ISSNs: 1471-2164

Abstract

Abstract Background Aeromonads make up a group of Gram-negative bacteria that includes human and fish pathogens. TheAeromonas salmonicida species has the peculiarity of including five known subspecies. However, few studies of the genomes ofA. salmonicida subspecies have been reported to date. Results We sequenced the genomes of additionalA. salmonicida isolates, including three from India, using next-generation sequencing in order to gain a better understanding of the genomic and phylogenetic links betweenA. 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 withA. salmonicida subsp.pectinolytica, were able to grow at either at 18 °C and 37 °C, unlike theA. 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 inA. 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.