title: Increasing genomic diversity and evidence of constrained lifestyle evolution due to insertion sequences in Aeromonas salmonicida.
abstract: 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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Institut de biologie intégrative et des systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, 1030 avenue de la Médecine, Quebec City, G1V 0A6, QC, Canada. antony.vincent.1@ulaval.ca.|Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (Hôpital Laval), 2725 Chemin Sainte-Foy, Quebec City, G1V 4G5, QC, Canada. antony.vincent.1@ulaval.ca.|Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, 1045 avenue de la Médecine, Quebec City, G1V 0A6, QC, Canada. antony.vincent.1@ulaval.ca.
authors.forename: Antony T
authors.initials: AT
authors.lastname: Vincent
authors.affiliation: Institut de biologie intégrative et des systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, 1030 avenue de la Médecine, Quebec City, G1V 0A6, QC, Canada. melanie.trudel@live.ca.|Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (Hôpital Laval), 2725 Chemin Sainte-Foy, Quebec City, G1V 4G5, QC, Canada. melanie.trudel@live.ca.|Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, 1045 avenue de la Médecine, Quebec City, G1V 0A6, QC, Canada. melanie.trudel@live.ca.
authors.forename: Mélanie V
authors.initials: MV
authors.lastname: Trudel
authors.affiliation: Institut de biologie intégrative et des systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, 1030 avenue de la Médecine, Quebec City, G1V 0A6, QC, Canada. luca.freschi@bio.ulaval.ca.|Département de microbiologie-infectiologie et immunologie, Faculté de médecine, Université Laval, Quebec City, QC, Canada. luca.freschi@bio.ulaval.ca.
authors.forename: Luca
authors.initials: L
authors.lastname: Freschi
authors.affiliation: Food Technology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India. vnagar@barc.gov.in.
authors.forename: Vandan
authors.initials: V
authors.lastname: Nagar
authors.affiliation: Institut de biologie intégrative et des systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, 1030 avenue de la Médecine, Quebec City, G1V 0A6, QC, Canada. cynthia.gagne-thivierge.1@ulaval.ca.|Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (Hôpital Laval), 2725 Chemin Sainte-Foy, Quebec City, G1V 4G5, QC, Canada. cynthia.gagne-thivierge.1@ulaval.ca.|Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, 1045 avenue de la Médecine, Quebec City, G1V 0A6, QC, Canada. cynthia.gagne-thivierge.1@ulaval.ca.
authors.forename: Cynthia
authors.initials: C
authors.lastname: Gagné-Thivierge
authors.affiliation: Institut de biologie intégrative et des systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, 1030 avenue de la Médecine, Quebec City, G1V 0A6, QC, Canada. rclevesq@ibis.ulaval.ca.|Département de microbiologie-infectiologie et immunologie, Faculté de médecine, Université Laval, Quebec City, QC, Canada. rclevesq@ibis.ulaval.ca.
authors.forename: Roger C
authors.initials: RC
authors.lastname: Levesque
authors.affiliation: Institut de biologie intégrative et des systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, 1030 avenue de la Médecine, Quebec City, G1V 0A6, QC, Canada. steve.charette@bcm.ulaval.ca.|Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (Hôpital Laval), 2725 Chemin Sainte-Foy, Quebec City, G1V 4G5, QC, Canada. steve.charette@bcm.ulaval.ca.|Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, 1045 avenue de la Médecine, Quebec City, G1V 0A6, QC, Canada. steve.charette@bcm.ulaval.ca.
authors.forename: Steve J
authors.initials: SJ
authors.lastname: Charette
mesh_terms: D048409:Aeromonas salmonicida / Q000235:genetics* / Q000472:pathogenicity; D000818:Animals; D001482:Base Composition / Q000235:genetics; D004251:DNA Transposable Elements / Q000235:genetics; D005393:Fish Diseases / Q000235:genetics / Q000469:parasitology; D005399:Fishes / Q000469:parasitology; D014644:Genetic Variation; D016678:Genome; D006801:Humans; D010802:Phylogeny
chemical_list: D004251:DNA Transposable Elements