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Dernière mise à jour : Mai 2018

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Genomic of Photorhabdus et Xenorhabdus

Genomic diversity and phylogenomic of Photorhabdus and Xenorhabdus

The laboratory has entered the era of genomics subsequent to the complete sequencing of the first genome of an entomopathogenic bacterium, the TT01 strain of P. luminescens (Duchaud et al., 2003) (tri-partite agreement between the Institut Pasteur, Bayer CropScience and our laboratory). Since the publication of the TT01 genome, our panel of entomopathogenic genomes, especially Xenorhabdus genomes has grown: (i) a genome from the Photorhabdus asymbiotica species, virulent on insects and opportunist on humans (sequenced and published by the Sanger Institute and the Richard ffrench-Constant’s group in England), (ii) the genomes of Xenorhabdus nematophila ATCC19061 and Xenorhabdus bovienii SS-2004, two virulent strains for insects, sequenced and published by an US consortium in which we are involved (Chaston et al., 2011); (iii) the genome of X. poinarii G6, X. doucetiae FRM16 and X. bovienii CS03, among which strains G6 and CS03 are avirulent in our two models Lepidoptera, Galleria mellonella and Spodoptera littoralis (grant from Genoscope), (iv) 17 partially assembled genomes of different strains of the Xenorhabdus genus (collaboration with a private company, Nosopharm, Nîmes, 4 strains and the US consortium, 13 strains). We currently have 24 genomes covering much of the phylogeny of the two genera. The following tools are available for these genomes:

  • A genomic sequence databases containing the 24 genomes (PhotoScope and XenorhabduScope, hosted at Genoscope, CEA, Evry).
  • Using the MaGe platform and tools for genomic analysis (ProPhinder, OrthoMCL, ...), we annotate these genomes, we identify the mobile genetic elements and we perform genomic comparisons.
  • A Xenorhabdus - Photorhabdus pan-genome DNA chip (Agilent) for genes encoding virulence factors. 

Genomic data drive our research to evolve from phylogenetic to phylogenomic studies. Indeed, the multigene approach previously used to study the phylogenies of Photorhabdus and Xenorhabdus had shown its limits. The individual gene phylogenetic topologies are not always congruent depending on the bacterial isolates (shown on 5 genes of the core genome). This observation suggests that the gene sequences of the core genome used for the phylogeny do not have an unique evolutionary history.

See also

DUCHAUD E, RUSNIOK C, FRANGEUL L, BUCHRIESER C, GIVAUDAN A, TAOURIT S, BOCS S, BOURSAUX-EUDE C, CHANDLER M, CHARLES JF, DASSA E, DEROSE R, DERZELLE S, FREYSSINET G, GAUDRIAULT S, MEDIGUE C, LANOIS A, POWELL K, SIGUIER P, VINCENT R, WINGATE V, ZOUINE M, GLASER P, BOEMARE N, DANCHIN A, KUNST F. 2003. The genome sequence of the entomopathogenic bacterium Photorhabdus luminescens. Nat Biotechnol21:1307-1313.

CHASTON JM, SUEN G, TUCKER SL, ANDERSEN AW, BHASIN A, BODE E, BODE HB, BRACHMANN AO, COWLES CE, COWLES KN, DARBY C, de LEON L, DRACE K, DU Z, GIVAUDAN A, TRAN EEH, JEWELL KA, KNACK JJ, KRASOMIL-OSTERFELD KC, KUKOR R, LANOIS A, LATREILLE P, LEIMGRUBER NK, LIPKE CM, LIU R, LU X, MARTENS EC, MARRI PR, MEDIGUE C, MENARD ML, MILLER NM, MORALES-SOTO N, NORTON S,  OGIER J-C, ORCHARD SS, PARK D, PARK Y, QUROLLO BA, SUGAR DR, RICHARDS GR, ROUY Z, SLOMINSKI B, SLOMINSKI K, SNYDER H, TJADEN BC, van der HOEVEN R, WELCH RD, WHEELER C, XIANG B, BARBAZUK B, GAUDRIAULT S, GOODNER B, SLATER SC, FORST S, GOLDMAN BS, GOODRICH-BLAIR H. 2011. The entomopathogenic bacterial endosymbionts Xenorhabdus and Photorhabdus: Convergent lifestyles from divergent genomes. Plos One. 6(11):e27909.