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at the roots of diversity

at the roots of diversity

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at the roots of diversity

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  1. IGAIstituto di Genomica ApplicataInstitute of Applied GenomicsScientific & Technological Park, Udine, Italy at the roots of diversity

  2. Legal information • Research Institute (ONLUS) • funded on April 13th, 2006 • legally recognised by FVG Regional Adiministration on August 4th, 2008 • to understand the genetic variation underlying the phenotypic diversity • to develop algorithms for the analysis of biological systems • to promote the scientific culture and the advancement of the society • to promote the technological innovation in agro-food Mission

  3. Research activity The mission is targeted by multidisciplinary approaches bridging genetics, biochemistry, cell biology and bioinformatics that serve to: • analyse structural and functional features of genomes • study evolutionary dynamics of genomes and population genetics • link genetic diversity with phenotypic variation • discover the molecular basis of complex traits • describe, simulate and predict biological processes through algorithms and bioinformatics tools • characterise, protect and exploit natural resources relevant to agriculture, food and non-food industry • promote innovation by transferring the results of research to the industry • disseminate the scientific culture

  4. Fields of Research • strctural & functional genomics (genome sequencing and annotation ...) • bioinformatics (development of algorithms and tools for the management of genomic databases and the interpretation of functional DNA motifs) • assisted breeding (development of breeding programs in food and non-food chains) • molecolare diagnostic (genotyping platforms, forensic fingerprinting , comparative genomics and transcriptomics...)

  5. Core facilities DNA sequencing core • 4 ABI Prism 3730xl 96 capillary Sanger sequencers (5 Mb/giorno) • 2 NG sequencers Illumina/Solexa GALII/ GALIIx (50 Gb/run) • 1 NG sequencer Illumina/Solexa HiSeq2000 (200 Gb/run) • 2 robots Beckmann, 9 PCRs ... Centre of computational biology • bar-coded pipeline and integrated LIMS for lab data management • 64 bit cluster, 180 CPU-cores, 16 with parallel access at 128 GB RAM, 650 Gb RAM computational core • 70 TB data storage • proprietary software for data management, analysis and interpretation

  6. Personnel Staff (17 people) • Michele Morgante, molecular geneticist, CEO of IGA • Federica Cattonaro, molecular biologist, CEO of IGA_TS • Gabriele Di Gaspero, plant molecular geneticist • Alessandro Gervaso, systems administrator • Eleonora Di Centa, molecular biologist • Erica Ietri, administration • Irena Jurman, molecular biologist • Moira Livon, molecular biologist • Federica Magni, molecular biologist • Fabio Marroni, molecular biologist • Elena Misdariis, administration • Felice Nicoletta, chemist • Alberto Policriti, bioinformatician • Simone Scalabrin, bioinformatician • Alberto Stefan, molecular biologist • Raffaele Testolin, plant geneticist • Daniele Trebbi, plant geneticist Visiting scientists (3 people) • Alberto Casagrande, University of Trieste, bioinformatician • Rajora Om P, University of New Brunswick, forest geneticist • Sugavanam Swaminathan, Univ. of Hyderabad, India, bioinformatician PhD students, Post-doc (7 people) • Dario Copetti, molecular biologist • Cristian Del Fabbro, bioinformatician • Stefania Giacomello, molecular biologist • Sara Pinosio, bioinformatician • Alessandro Spadotto, molecular biologist • Vera Vendramin, plant molecular geneticist • Francesco Viezzi, engineer

  7. Projects • VIGNA/VIGNE. Grape genome sequencing project (MiPAF with Genoscope 2006-2010) • Grape. Development of new grapevine varieties (FVG Region, 2007-2009) • Grape. Genotyping grapevine varieties and clones (FVG winemakers, 2008-) • Grape. Rapid analysis of secondary metabolite profiles (FVG Region, 2008-2010) • Coffee. Quality-controlling genes (Illy Co, 2008) • Barley. BAC end sequencing (IPK, Gatersleben, 2008-) • Wheat. Marker-assisted breeding (Barilla SpA, 2008-) • Wheat. Physical map of 4 chromosomes (EU Triticeae, 2008-) • Wheat. Physical map of chromosome 5 (MiPAF, 2009-) • Poplar. Energy poplar: gene mining (EU Energy Poplar, 2008-) • Peach. Peach genome sequencing project (MiPAF-Drupomics with JGI-USA, 2009-) • Citrus. Clementine genome sequencing (MiPAF Citromics with JGI-USA, 2009-) • Bees. Studies on CCD (Colony Collapse Disease) (MiPAF , 2009-) • … other projects on plants, animals, fishes, and microorganisms under negotiation …

  8. Services • DNA and RNA sequencing and re-sequencing • genetic and physical maps • individual genotyping • production of genomic and cDNA libraries • DNA sequence alignment and querries on gene banks • analysis of DNA and set up of client-oriented software • data storage, backup and remote access to data • remote management of computing facilities clients • Universities and public/private Research Institutes • Hospitals • Private Companies (seed firms, agro-industries...) Since September 2009 Services on demand are managed by IGA - TECHNOLOGY SERVICES

  9. Contacts web site: www.appliedgenomics.org e-mail: info@appliedgenomics.org • Raffaele Testolin • Michele Morgante • Alberto Policriti • Gabriele Di Gaspero 1 2 3 4