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“Sequencing and analyzing Procaryotic genomes : the story of tree Acinetobacter species”
Valérie Barbe(mail) supported his thesis on Febrary 8th in Evry. His research was carried out in the “Metabolic thesaurus” team led by Marcel salanoubat (mail) and in the “comparative genomics” team led by Claudine Médigue (mail).
The development of sequencing techniques in the last forty years has led to the evolution of a new biological discipline, genomics. Although the production of sequence data has increased exponentially, there are still problems in the assembly and finishing of complete genomes. The first part of this thesis is a presentation of the technical solutions which have been developed at Genoscope to address the main problems in assembly and finishing of complete prokaryotic genomes. A second section describes a complete project, from the sequence to the comparative analysis of three genomes of the Acinetobacter genus. Acinetobacter is a genus of Gram-negative, oxidase-negative, catalase-positive bacteria, which are obligate aerobes. They are gamma-proteobacteria classified in the order Pseudomonales, in the family Moraxellaceae. Acinetobacter baylyi ADP1 is a soil bacterium which is quite versatile and naturally competent for transformation. This strain has been sequenced and annotated, and the analysis has revealed an archipelago of catabolic islands dedicated to the degradation of a large variety of organic compounds. These observations are correlated with its habitat, because this bacterium is notably capable of catabolizing aromatic compounds produced by plants. The recent emergence of the species Acinetobacter baumannii, notably in the hospital environment, is important because of its great capacity to acquire resistance to antibiotics, as well for its role in nosocomial infections. Two strains of this species were sequenced, AYE and SDF, the first multi-resistant and the second not, in order to establish a repertoire of genes important for resistance. An 86-kilobase resistance island was demonstrated in the genome of the AYE srain. Furthermore, the presence of catabolic islands previously described in A. baylyi suggests that the AYE strain is capable of growing on very diverse media. The availability of the sequence and annotation of the three strains of the Acinetobacter genus has made it possible to compare them globally in order to study their metabolic capacities and their role as agents of nosocomial infections.