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  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

Pfeiffer, F., Zamora-Lagos, M.-A., Blettinger, M., Yeroslaviz, A., Dahl, A., Gruber, S., et al. (2018). 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. BMC Genomics, 19: 20. doi:10.1186/s12864-017-4301-6.

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12864_2017_4301_MOESM1_ESM.pdf (Supplementary material), 2MB
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Availability of data and materials The genome was submitted to GenBank under accession number CP022426. PacBio sequencing data have been submitted to the SRA archive under accession SRP121438. Transposons identified in the course of this project were submitted to ISFinder (https://www-is.biotoul.fr/). Transposons can be retrieved under their name, which begins with ISAs or TnAs and are a stable identifier in ISFinder. Software developed in the course of this project is available at: https://github.com/BCF-calanques.
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 Creators:
Pfeiffer, Friedhelm1, Author              
Zamora-Lagos, Maria-A.1, Author              
Blettinger, Martin2, Author              
Yeroslaviz, Assa1, Author              
Dahl, Andreas3, Author
Gruber, Stephan2, Author              
Habermann, Bianca H.1, Author              
Affiliations:
1Habermann, Bianca / Computational Biology, Max Planck Institute of Biochemistry, Max Planck Society, ou_1832284              
2Gruber, Stephan / Chromosome Organization and Dynamics, Max Planck Institute of Biochemistry, Max Planck Society, ou_1565151              
3external, ou_persistent22              

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Free keywords: INSERTION SEQUENCES; GENUS AEROMONAS; EVOLUTION; DATABASE; PROTEIN; RESISTANCE; VIRULENCE; ALIGNMENT; GENESBiotechnology & Applied Microbiology; Genetics & Heredity; Aeromonas; Complete circular genome; Transposon; Mobilome; PacBio; Long-read sequencing; High-precision sequencing; Mobilome-dependent evolution; Pathogenic; Environmental;
 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.

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Language(s): eng - English
 Dates: 2018-01-05
 Publication Status: Published online
 Pages: 15
 Publishing info: -
 Table of Contents: -
 Rev. Type: -
 Identifiers: ISI: 000419676500003
DOI: 10.1186/s12864-017-4301-6
 Degree: -

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Project name : “ChroCoDyle”
Grant ID : 724482
Funding program : ERC starting grant
Funding organization : -

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Title: BMC Genomics
Source Genre: Journal
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Publ. Info: BioMed Central
Pages: - Volume / Issue: 19 Sequence Number: 20 Start / End Page: - Identifier: ISSN: 1471-2164
CoNE: https://pure.mpg.de/cone/journals/resource/111000136905010