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  Phenotypic and genomic comparison of Photorhabdus luminescens subsp laumondii TT01 and a widely used rifampicin-resistant Photorhabdus luminescens laboratory strain

Zamora-Lagos, M.-A., Eckstein, S., Langer, A., Gazanis, A., Pfeiffer, F., Habermann, B., et al. (2018). Phenotypic and genomic comparison of Photorhabdus luminescens subsp laumondii TT01 and a widely used rifampicin-resistant Photorhabdus luminescens laboratory strain. BMC Genomics, 19: 854. doi:10.1186/s12864-018-5121-z.

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Zamora-Lagos, Maria-A.1, Author              
Eckstein, Simone2, Author
Langer, Angela2, Author
Gazanis, Athanasios2, Author
Pfeiffer, Friedhelm1, Author              
Habermann, Bianca1, Author              
Heermann, Ralf2, Author
Affiliations:
1Habermann, Bianca / Computational Biology, Max Planck Institute of Biochemistry, Max Planck Society, ou_1832284              
2external, ou_persistent22              

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Free keywords: SP NOV.; HETERORHABDITIS-BACTERIOPHORA; ESCHERICHIA-COLI; IN-VIVO; PATHOGENICITY; SEQUENCE; ELEMENTS; PROPOSAL; CLASSIFICATION; REPRODUCTIONBiotechnology & Applied Microbiology; Genetics & Heredity;
 Abstract: BackgroundPhotorhabdus luminescens is an enteric bacterium, which lives in mutualistic association with soil nematodes and is highly pathogenic for a broad spectrum of insects. A complete genome sequence for the type strain P. luminescens subsp. laumondii TT01, which was originally isolated in Trinidad and Tobago, has been described earlier. Subsequently, a rifampicin resistant P. luminescens strain has been generated with superior possibilities for experimental characterization. This strain, which is widely used in research, was described as a spontaneous rifampicin resistant mutant of TT01 and is known as TT01-Rif(R).ResultsUnexpectedly, upon phenotypic comparison between the rifampicin resistant strain and its presumed parent TT01, major differences were found with respect to bioluminescence, pigmentation, biofilm formation, haemolysis as well as growth. Therefore, we renamed the strain TT01-Rif(R) to DJC. To unravel the genomic basis of the observed differences, we generated a complete genome sequence for strain DJC using the PacBio long read technology. As strain DJC was supposed to be a spontaneous mutant, only few sequence differences were expected. In order to distinguish these from potential sequencing errors in the published TT01 genome, we re-sequenced a derivative of strain TT01 in parallel, also using the PacBio technology. The two TT01 genomes differed at only 30 positions. In contrast, the genome of strain DJC varied extensively from TT01, showing 13,000 point mutations, 330 frameshifts, and 220 strain-specific regions with a total length of more than 300kb in each of the compared genomes.ConclusionsAccording to the major phenotypic and genotypic differences, the rifampicin resistant P. luminescens strain, now named strain DJC, has to be considered as an independent isolate rather than a derivative of strain TT01. Strains TT01 and DJC both belong to P. luminescens subsp. laumondii.

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Language(s): eng - English
 Dates: 2018
 Publication Status: Published online
 Pages: 17
 Publishing info: -
 Table of Contents: -
 Rev. Type: -
 Identifiers: ISI: 000451692700005
DOI: 10.1186/s12864-018-5121-z
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Title: BMC Genomics
Source Genre: Journal
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Publ. Info: BioMed Central
Pages: - Volume / Issue: 19 Sequence Number: 854 Start / End Page: - Identifier: ISSN: 1471-2164
CoNE: https://pure.mpg.de/cone/journals/resource/111000136905010