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BMC Genomics. 2018 Jan 5;19(1):20. doi: 10.1186/s12864-017-4301-6.

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.

Author information

1
Computational Biology Group, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.
2
Research Group Chromosome Organization and Dynamics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.
3
Biotechnology Center (biotec), Technical University Dresden, Tatzberg 47, 1307, Dresden, Germany.
4
Research Group Chromosome Organization and Dynamics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany. stephan.gruber@unil.ch.
5
Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland. stephan.gruber@unil.ch.
6
Computational Biology Group, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany. bianca.habermann@univ-amu.fr.
7
Computational Biology Group, Developmental Biology Institute of Marseille (IBDM) UMR 7288, Aix Marseille Universite, Parc Scientifique de Luminy, 163 Avenue de Luminy, 13009, Marseille, France. bianca.habermann@univ-amu.fr.

Abstract

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.

KEYWORDS:

Aeromonas; Complete circular genome; Environmental; High-precision sequencing; Long-read sequencing; Mobilome; Mobilome-dependent evolution; PacBio; Pathogenic; Transposon

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