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Background  Due to the predominant usage of short-read sequencing to date, most bacterial genome sequences reported in the last years remain at the draft level. This precludes certain types of analyses, such as the in-depth analysis of genome plasticity.    Results  Here we report the finalized genome sequence of the environmental strain  Aeromonas salmonicida subsp. pectinolytica  34mel, for which only a draft genome with 253 contigs is currently available. Successful completion of the transposon-rich genome critically depended on the PacBio long read sequencing technology. Using finalized genome sequences of  A. salmonicida  subsp . pectinolytica  and other Aeromonads, we report the detailed analysis of the transposon composition of these bacterial species. Mobilome evolution is exemplified by a complex transposon, which has shifted from pathogenicity-related to environmental-related gene content in  A. salmonicida  subsp . pectinolytica  34mel.    Conclusion  Obtaining the complete, circular genome of  A. salmonicida  subsp.  pectinolytica  allowed us to perform an in-depth analysis of its mobilome. We demonstrate the mobilome-dependent evolution of this strain’s genetic profile from pathogenic to environmental.    Electronic supplementary material  The online version of this article (10.1186/s12864-017-4301-6) contains supplementary material, which is available to authorized users.

bmc genomics

The complete and fully assembled genome sequence of Aeromonas salmonicida subsp. pectinolytica and its comparative analysis with other Aeromonas species: investigation of the mobilome in environmental and pathogenic strains