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Démasquage des gènes spécifiques d'une espèce génomique du complexeAgrobacterium tumefaciens par AFLP et multicapteur à ADN

Abstract : Unmasking species specific genes inspecies G8 by AFLP and microarray. In the frame of studies undertaken to associate a biological concept to the present genomic definition of the bacterial species, a study was done to find species specific genes common to all members of a model species, the genomic species G8 of the species complex Agrobacterium tumefaciens. The study was firstly based upon the identification of the genomic origin of AFLP markers of the species by comparing experimental results to in silico simulations of AFLP of the complete genome sequence of the G8 reference strain C58. Due to size determination uncertainties and possible close co-migration of predicted fragments, only a little number of amplified AFLP markers could be localized without ambiguities in the genome of C58. Nevertheless, the study delivered a catalog of the genes common to all G8 members. Along to standard house-keeping genes, 25% of the G8 core genome also consisted of hypothetical non-conserved or "ORFan" genes. ORFans, which encode unknown functions, are good candidate to encode species specific functions and thus to allow for further studies about the ecological specialization of the species. The study also revealed that AFLP experimental results were influenced by epigenetic determinants that could have artefactually reduced the number of species specific genes delivered in the study, but not the confidence about those readily found common. The still unknown epigenetic phenomenon is thought to prevent the digestion of certain parts of the genomic DNA by endonucleases required for AFLP. It is likely the cause of the significantly higher number of genes experimentally found common to all species members around the centre of the linear chromosome, while the epigenetic phenomenon would have hampered digestions and then delivered artefactual not-common genes in the chromosome lateral branches.The second approach was based on a microarray constructed against the whole genome of C58. A comparative genome hybridization study conducted with members of all the A. tumefaciens complex allowed us to determine genes specific of the genomic species G8. Most of these genes are ORFans and knowing their functions requires additionnal studies. Nevertheless, the study showed that the species specific genes as well as other accessory genes were much more abundant on the linear than on the circular chromosome. The linear chromosome of A. tumefaciens therefore looks to be the preferred genome place for genetic innovations.
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Submitted on : Wednesday, June 3, 2020 - 8:01:48 PM
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  • HAL Id : hal-02753900, version 1
  • PRODINRA : 48751


Perrine Portier, Denis Costechareyre, Daniel Muller, David Chapulliot, Christine Oger, et al.. Démasquage des gènes spécifiques d'une espèce génomique du complexeAgrobacterium tumefaciens par AFLP et multicapteur à ADN. 7. Colloque national du Bureau des Ressources Génétiques, 2008, Strasbourg, France. ⟨hal-02753900⟩



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