The VIGNA Project: Genomic Platforms Implementation in Italy

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1 The VIGNA Project: Genomic Platforms Implementation in Italy The French-Italian Public Consortium for the Sequencing of the Grapevine Nuclear Genome M. Enrico Pè Scuola Superiore di Studi Universitari e Perfezionamento Sant Anna di Pisa

2 RESEARCH PHYLOSOPHY Genomic Project with Grape as the Object Organism of Choice Genomic Goals To Implement National Platforms For Genomic Analysis a) technological upgrade b) formation of a new generation of young scientists with genomic skills Applied Research To Develop and Apply Genomic Tools to grape a) Applied Pilot Projects b) Interface with specialists and researchers in the field

3 PROJECT STRUCTURE LEVEL 1 Structural Genomics LEVEL 2 Sequencing Functional Genomics Mapping Physical map High resolution genetic map QTLs for resistance Transcriptomics EST Microarray LEVEL 3 Proteomics 2D-E MS Applied Projects Metabolomics Bioinformatics Web portal Database Data analysis Germplasm characterization Biotic stresses Abiotic stresses Reproduction Development Berry maturation ACTIVITY STARTED AT ALL LEVELS AND IN ALL GROUPS in JANUARY 2006

4 Consorzio Interuniversitario Nazionale per la Biologia Molecolare delle Piante CINBMP 11 research groups ENEA Centro Ricerche Casaccia, Rome Eugenio Benvenuto CNR Dip. di Bioinformatica e Genomica, Bari Sabino Liuni e Cecila Saccone CIB Consorzio Interuniversitario per le Biotecnologie, Trieste Claudio Schneider Università di Bari Dip. di Biologia Molecolare Graziano Pesole Università di Milano Dip. Scienze biomolecolari e Biotecnologie M. Enrico Pè Università di Padova CRIBI Centro per le Biotecnologie Giorgio Valle Università di Siena Dip. di Scienze Ambientali Sciences Mauro Cresti Università di Udine1 Dip. Scienze Agrarie e Ambientali Michele Morgante Università di Udine2 Dip. Scienze Agrarie e Ambientali Raffaele Testolin Università di Verona1 Dip. di Scienze Massimo Delledonne Università di Verona2 Dip. Scienze, Tecnol. e Mercato della vite e del vino Mario Pezzotti

5 Consiglio per la Ricerca in Agricoltura CRA 6 research groups Coordinator: Michele Stanca CRA Istituto Sperimentale per la Cerealicoltura di Fiorenzuola d Arda Plant/Pathogen Interaction Luigi Cattivelli Phytopatology Giampiero Valè Bioinformatics Primetta Faccioli CRA Istituto Sperimentale per la Viticoltura di Conegliano veneto Germplasm characterization - Antonio Calò Sugars Metabolism Angelo Costacurta Plant Development - Manna Crespan

6 GRAPE GENOME SEQUENCING ~480 million bp FINAL GOAL: 12 GENOMES EQUIVALENTS (12x) Using PN40024 homozygous clone (~ 93%) derived from Pinot noir and Helfesteiner after 6 cycles of selfing (Colmar, Fr) FRANCE GENOSCOPE 7 x ITALY 5 x CRIBI Padova 2.0 x IGA Udine 3.0 x Sequencing activity started January 2006 Completed August 2007

7 Progress since April 2007 Accomplished 12 x coverage of PN % sequences organized in < 150 supercontigs > 90% sequences anchored to genetic maps 0.9 x coverage of cultivar Friulano 1 SNP every 98 bp identified 1.3 million SNPs estimated In Progress Deep cdna sequencing by Solexa/Illumina and 454 technology for annotation improvement DNA arrays using Combimatrix technology for Complete transcriptomics analysis

8 Assembling assemblies: positioning supercontigs into a continuous assembly Arachne 8.4X Contig 12 Contig 68 Contig427 Pcap 12X Contig A Contig B Paired supercontig (consensus) Preliminary consensus: whole genome in ~150 ultracontigs

9 Strategy for detecting structural variation Friulano < PN40024: Insertion in PN Friulano paired reads Friulano > PN40024: Insertion in Friulano Friulano paired reads

10 Deep cdna Sequencing for Implementing Gene Prediction and Genome Annotation 1. New sequencing technologies produce millions of short DNA sequences 2. Utilized for sequencing of expressed genes a) from berries at different stage of maturation 350 thousands 250 nucleotide long reads b) from infected tissues 200 thousands 250 nucleotide long reads c) from leaves 40 millions 35 nucleotide long reads Other tissues in progress

11 20 22 nucleotide long MicroRNAs are Important Regulatory Elements Coded by MIR Genes as Precursors

12 Validation of MIR gene prediction by deep cdna sequencing

13 TRAINING ACTIVITY A Major Objective of the VIGNA 43 YOUNG SCIENTISTS CURRENTLY INOLVED IN THE DIFFERENT VIGNA WORKPACKAGES (37 ON VIGNA GRANT)

14 VIGNA FINACIAL RESOURCES MiPAF: 6.5 millions within the French Italian bilateral agreement signed by INRA and CRA Instituto di Genomica Applicata, Udine 2 millions Regione Veneto, Indistrial Sector 1.5 milioni Bank Foundations Cariverona Monte dei Paschi di Siena 0.50 million 0.17 million

15 From the Grape Genome Great Discoveries and Surprises

16 The French-Italian Consortium Olivier Jaillon Jean-Marc Aury Francis Quetier Patrick Wincker Jean Weissenbach et al. Michele Morgante, Alberto Policriti Gabriele De Gaspero, Federica Cattonaro, Alberto Casagrande, Cristian Del Fabbro, Nicoletta Felice, Irena Iurman, Simone Scalabrin, Anne-Francoise Adam- Blondon Christian Clepet Michel Caboche Sebastien Aubourg Fabrice Legeai Didier Merdinoglu et al. CRIBI Padova UniMi Giorgio Valle David Horner Nicola Vitulo Erica Mica Alessandro Vezzi M. Enrico Pè Giorgio Malacrida UniBa Graziano Pesole UniVr Mario Pezzotti Massimo Delledonne