| Abstract Detail
Tomato sequencing - Morning Regad, Farid [1], Delalande, Corinne [1], Zouine, Mohamed [1], Frasse, Pierre [1], Coriton, Olivier [2], Berges, Helene [3], De Leeuw, Marcel [4], Raffy, Claudine [4], Duborjal, Herve [4], Bouzayen, Mondher [1]. Sequencing the gene-rich space of tomato chromosome 7: Current status of the French effort. THE tomato (Solanum Lycopersicum) genome is comprised of approximately 950 Mb of DNA among which more than 75% is heterochromatin largely devoid of coding sequences. The majority of genes are found in long contiguous stretches of gene-dense euchromatin located on the distal portions of each chromosome arms. The gene-rich euchromatic portion of the tomato genome (approximately 220 Mb) is being sequenced by an international consortium and the GBF (Genomic and Biotechnology of the Fruit) laboratory (http://gbf.ensat.fr) is leading the French effort for sequencing tomato chromosome 7. The strategy used by our laboratory is the clone by clone sequencing and finishing of the gene rich region estimated to cover 27 Mb which correspond to 277 BAC clones to be sequenced. Our aim is to select the tiling path across chromosome 7 with minimal overlaps between neighbouring sequence clones as a mean of reducing redundant sequencing. Because the average size of the FPC contigs assigned to chromosome 7 is small it was decided that before entering the sequencing pipeline, the assignment of the seed BACs is FISH verified. The FISH mapping is performed by Steve Stack’s group at Colorado University (USA) and by the Molecular Cytogenetics platform at INRA Rennes (Olivier Coriton, France). The sequencing is performed by Genome Express company who also implement the Discriminative Analysis of Clone Signatures (DACS) for the finishing phase (De Leeuw et al. 2005, 2nd Solanaceae Genome Workshop, Ishia-Italy). So far, sixteen seed BACs have been selected based on mapping or FISH data and sequenced. Seven new clones are in progress of sequencing. The status of chromosome 7 sequencing progress will be presented as well as the difficulties encountered so far.
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1 - INRA/INP-ENSA Toulouse, Plant Biotechnology, Genomique et de Biotechnologie des Fruits, Chemin de Borde Rouge, BP 52627, Castanet Tolosan, F31326, France
2 - INRA Rennes, Plate-forme Cytogenetique Moleculaire DGAP, Agrocampus Rennes Domaine de la Motte - BP 35327, Le Rheu, F 35650, France
3 - INRA Toulouse, Centre National de Ressources Genomiques Vegetales, Chemin de Borde Rouge - BP 52627 - F31326, Castanet Tolosan, F31326, France
4 - Genome Express, 11 chemin de Pres, Meylan, F38944, France
Keywords:
Chromosome 7
S. lycopersicum
genome sequencing
FISH.
Session: SAT04-8
Location: Hall of Ideas Room E/Monona Terrace
Date: Wednesday, July 26th, 2006
Time: 10:00 AM
Abstract ID:368 |
