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Home page > Sequencing > Projects > Microorganisms > Mycobacterium > Whole genome shotgun

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Whole genome shotgun

Project: Collaborative
State of the project: In progress

Collaborations :

Laboratoire de Microbiologie et EA 3647
Faculté de Médecine Paris Ile-de-France Ouest
Garches, France

Laboratoire Génome et Informatique,
CNRS/ Université d’Evry
Evry, France

For more informations :

Griffith DE. Emergence of nontuberculous mycobacteria as pathogens in cystic fibrosis. Am J Respir Crit Care Med 2003;167:810-2.

Tortoli E. Impact of genotypic studies on mycobacterial taxonomy: the new mycobacteria of the 1990s. Clin Microbiol Rev 2003;16:319-54.

Cullen N, Cannon CL, Mark EJ and Colin AA. Mycobacterium abscessus infection in cystic fibrosis : colonization or infection. Am J Respir Crit Care Med 2000;161:641-5.

Brown-Elliott BA, Wallace RJ Jr. Clinical and taxonomic status of pathogenic nonpigmented or late-pigmenting rapidly growing Mycobacteria. Clin. Microbiol. Rev 2002;15:716-46.

M. abscessus is a recently recognized pulmonary pathogen in cystic fibrosis that is susceptible to only a few drugs and is responsible for a severe pseudo-tuberculous disease. By substractive hybridization between M. abscessus (CIP 104536T) and the closely-related species, M. chelonae (CIP 104535T), we have recently identified M. abscessus-specific ORFs homologous to genes involved in the pathogenicity of M. tuberculosis, including members of the pks family. This suggests the presence of pathogenicity regions and genes in the M. abscessus genome.

The goal of this project is:

  • to identify and to map these regions by comparative genomics between the M. abscessus and M. chelonae genomes;
  • to further analyse these regions.

With this objective, Genoscope is undertaking the sequencing of the M. abscessus CIP strain 104536T (= ATCC 19977T, knee abcess, 1953) and the M. chelonae CIP strain 104535 (= ATCC 35752T, tortoise, 1921), which were utilized in the previously mentioned subtractive hybridization study. Each genome will be sequenced at a depth of 12X, using three libraries: a library of 3 kb inserts cloned in the multicopy plasmid vector pNAV, a 10 kb library in the pCNS plasmid vector (small copy number) and a miniBAC library (inserts of about 30 kb) in the pBBC vector (derived from pBeloBAC11).
The shotgun stage should produce about 150,000 reads. A finishing step will increase the quality of the sequences obtained.

Valérie Barbe (Genoscope) - Jean-Louis Gaillard

Last update on 15 January 2008

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