Genomics  


  HEADChristiane Bouchier, PhD / bouchier@pasteur.fr
  MEMBERSSophie Créno, Laurence Ma, Magali Tichit, Catherine Gouyette, Olivier Hélynck
Office Staff : Annie Etienne


  Annual Report

The Genomics platform (PF1) undertakes the sequencing of whole microbial genomes in collaboration with several IP teams in addition to smaller projects analysing genomic regions, sets of cDNAs libraries and PCR products. PF1 performs the sequencing then, transfers, the sequences to the partner who carries out the analysis steps. However, in most cases of genome sequencing projects, PF1 conducts the entire process internally and passes on the assembled, polished sequence for analysis. PF1 aims to group state-of-the-art equipment and corresponding technical and methodological process to provide for the needs of the research teams of the Institut Pasteur and its International Network in the field of sequencing projects. PF1 has a closely collaboration with the « Biological Software and Databases » Group (LBD) for installation of biological softwares and developing bioinformatic programs.


The major projects which have been undertaken concerns an epidemic strain of Helicobacter pylori associated with Mucosa Associated Lymphoid Tissue (MALT); the saprophyte Leptospira biflexa which is a model bacteria of spirochetes; an epidemic strain of streptococcal pathogen Streptococcus pneumonia and a strain of Streptococcus macedonicus.

M. aeruginosa PCC 7806, is a cyanobacterium responsible for water spoliage and, during seasonal blue-green algal blooms, produces a neurotoxin. Its genome has been published as a draft of a scaffold contained one hundred of contigs.

A comparative genomics of Hemiascomycetous yeasts study has been investigated with a low coverage sequencing approach of 6 closely phylogenetic species.

Genomic analysis has also been performed with protozoan parasites of interest to human medicine. Allelic diversity and drug resistance of Plasmodium falciparum and Plasmodium vivax, agents of human malaria, have been studied. EST sequencing of clones from different libraries has also been done with Anopheles gambiae and Entamoeba histolytica.

The complete list of all these projects is available on the website of the platform.

Projects realized in 2008 and current projects

  • Allelic diversity of Plasmodium vivax and Plasmodium falciparum isolates from Madagascar to study diversity and the drug resistance

Didier Ménard – Unité de Recherche sur le Paludisme – Institut Pasteur de Madagascar

  • Molecular typing of CIP Bacteria strains

Chantal Bizet – Collection de l'Institut Pasteur

  • Sequencing of two multi-drug resistant plasmids in Yersinia pseudotuberculosis

Elisabeth Carniel – Unité Yersinia

  • Genome sequencing of a Streptococcus pneumoniae strain (serotype 1)

Philippe Glaser – Unité de Génomique des micro-organismes pathogènes

  • Genome sequencing of a Streptococcus macedonicus strain (CIP105685T)

Patrick Trieu-Cuot – Unité de Biologie des bactéries pathogènes à Gram-positif

  • Genomic variation and natural selection at human IFNs and their receptors

Lluis Quintana-Murci – Unité Génétique Evolutive Humaine


Since july 2008 a next-generation sequencing technologies system, Illumina's Genome Analyser II-has been installed at Genopole. This equipment shared with the DNA micro-arrays Platform (PF2), is used for microbial genome resequencing projects.

Since july 2008, High Throughput Synthesis of Long Oligonucleotides Platform has been attached to PF1. Synthesize oligodeoxynucleotides modified in the 5' and/or 3' end by different fluorophores, quenchers (molecular beacons), by amino-alkyl groups or by modified bases through out the sequence is maintained.

Short RNA and siRNA sequences can be made too.



  Publications

1- Barnadas C, Ratsimbasoa A, Tichit M, Bouchier C, Jahevitra M,Picot S, Ménard D.Plasmodium vivax resistance to chloroquine in Madagascar: clinical efficacy and polymorphisms in pvmdr1 and pvcrt-o genesAntimicrob Agents Chemother. 2008 Vol. 52 No12 4233-4240.

2- Achour I, Cavelier P, Tichit M, Bouchier C, Lafaye P, Rougeon FTetrameric and homodimeric camelid IgGs originate from the same IgH locusJ Immunol. 2008 Aug 1;181(3):2001-9.

3- Frangeul L, Quillardet P, Castets AM, Humbert JF, Matthijs HC, Cortez D,Tolonen A, Zhang CC, Gribaldo S, Kehr JC, Zilliges Y, Ziemert N, Becker S, Talla E, Latifi A, Billault A, Lepelletier A, Dittmann E, Bouchier C, de Marsac NT.Highly plastic genome of Microcystis aeruginosa PCC 7806, a ubiquitous toxic freshwater cyanobacterium BMC Genomics. 2008 Jun 5;9:274.

4- Picardeau M, Bulach DM, Bouchier C, Zuerner RL, Zidane N, Wilson PJ, Creno S, Kuczek ES, Bommezzadri S, Davis JC, McGrathA, Johnson MJ, Boursaux-Eude C, Seemann T, Rouy Z, Coppel RL, Rood JI, Lajus A, Davies JK, Médigue C, Adler B.Genome Sequence of the Saprophyte Leptospira biflexa Provides Insights into the Evolution of Leptospira and the Pathogenesis of LeptospirosisPLoS ONE. 2008 Feb 13;3(2):e1607.

5- Delmas O, Holmes EC, Talbi C, Larrous F, Dacheux L, Bouchier C, Bourhy HGenomic diversity and evolution of the lyssaviruses.PLoS ONE. 2008 Apr 30;3(4):e2057.



  Web Site

More informations on our web site




Activity Reports 2009 - Institut Pasteur
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