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Home page > Sequencing > Projects > Fungi > Tuber melanosporum > Whole sequence shotgun

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Tuber melanosporum

Whole sequence shotgun

Project: Collaborative
State of the project: In progress



Collaborations :

INRA, UMR 1136, INRA-Nancy Université, Interactions Arbres/Microorganismes, Champenoux, France

Dipartimento di Biochimica e Biologia Molecolare, Università degli studi di Parma, Parma, Italy

Istituto per la Protezione delle Piante del CNR, sez. di Torino c/o Dipartimento Biologia Vegetale – UniTO, Torino, Italy

CNR-IGV: Istituto di Genetica Vegetale, articolazione territoriale di Perugia, Perugia, Italy

Dipartimento di Scienze Biomolecolari, Università degli Studi di Urbino, Urbino (PU), Italy

INRA - URGI/BIOGER, Versailles cedex, France

Dip. Genetica e Biologia molecolare, Instituto di fisiologia generale, Università la Sapienza Roma, Roma, Italy

Architecture et Fonction des Macromolécules Biologiques, UMR 6098 CNRS-Universités Aix-Marseille I & II, Marseille, France

INRA, UMR Amélioration et Santé des Plantes, INRA-Université Blaise Pascal, centre INRA de Clermont-Ferrand-Theix France

Departments of Environmental Sciences and Basic and Applied Biology, University of L’Aquila, L’Aquila, Italy

Università degli Studi di Bologna Ana De Miguel, Bologna, Italy

Université Paul Sabatier (Toulouse III), Unité mixte UPS-CNRS 5546 Surfaces Cellulaires et Signalisation chez les Végétaux, Castanet-Tolosan, France

A whole-genome shotgun strategy (WGS) was adopted for sequencing and assembling the T. melanosporum draft genome. All genomic DNA was obtained from the vegetative mycelium of the haploid strain Mel28. Template DNA was extracted from mycelium using the Genomic Tip DNA extraction kit (Qiagen). This DNA was randomly sheared and size-fractionated to create libraries with roughly 3 kb and 10 kb inserts. From these two libraries, 1,284,900 reads were obtained. After trimming, the removal of multiple read attempts, and the exclusion of overly-short reads, the pool of data available for the assembly consisted of 1,281,391 reads (10X total sequence redundancy). The data was assembled using the ARACHNE assembler. After excluding redundant and short scaffolds, there remained 125 Mbp of scaffold sequence (398 supercontigs, N50= 637 kb).

Contact: Patrick Wincker (Genoscope) - Francis Martin (INRA)

Last update on 11 May 2009

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