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MaizeGDB: A Very Short Overview of a Database Resource for Biological Information on Zea mays Jack M. Gardiner [email protected] ASPB 2010 MaizeGDB 101 • MaizeGDB strives to: – Serve as a central repository for public maize information – Disseminate the data in a user friendly manner that creates intuitive biological connections – Encourage community involvement in the evolution of the data and user interface • MaizeGDB was established in 1991 by USDA-ARS. Basic Utility of MaizeGDB -Top of of Each Page• Each page at MaizeGDB offers a set of consistent tools for users, from searching to access to popular pages… • These tools are found along the top of each page. Basic Utility of MaizeGDB -Bottom of Each Page• Search bar (duplicate) • Feedback is key to getting what you want and helping us deliver a usable resource! What Data Types are Available from MaizeGDB? • • • MaizeGDB includes a number of data types, all available from the front page. Genome Browser Data types available: – – – – – – – – – – – – Probes (BACs, overgos, SSRs, etc.) Gene Products Locus/Loci Maps Metabolic Pathways People/Organizations Phenotypes QTL References Sequences Stocks Variations Spotlight on Three Resources Available from MaizeGDB • Phenotypes – An overview of the depth and breadth of what’s available • Popcorn – One stop resource for maize sequences • Maize Genome Browser – How to access Phenotype Data at MaizeGDB • Sources – The MGCSC Maize Genetics Cooperation Stock Center, Illinois USA, Marty Sachs, Director – High-throughput projects – Mutants of Maize, eds MG Neuffer, EH Coe, SR Wessler (1997) – Images - Community, MG Neuffer collection – Literature How Many Phenotypes are in MaizeGDB? • > 800 genes in MaizeGDB with a designated phenotype • < 250 with some description in Mutants of Maize. Most unsequenced with only approximate chromosome location known • www.maizegenereview.org, a new peer reviewed, on line community resource seeks to capture new and existing maize phenotypes via community curation POPCorn PrOject Portal for Corn • PopCorn: – Provides a searchable database of 92 maize projects and resources – Allow searching of multiple projects with a single sequence query – Provides behind-the-scenes tools to enable projects to transition their data to MaizeGDB – Funded by NSF DBI 0743804 POPCorn Two Options for Sequence Searches Accessing the Maize Genome Sequence through MaizeGDB MaizeGDB Tutorials A Very Brief Overview of Maize Genome Sequencing Projects • Mo17 Genome – Sequenced at the DOE Joint Genome Institute – 65 Million total 454 shotgun reads • 16 million reads with < 1/3 repeat content • Aligned to the B73 Sequence at http://www.phytozome.net/maize.php • Palomero Toluqueño Genome – Sequenced at CINVESTAV Irapuato, Mexico – Ancient Mexican popcorn landrace provides diversity comparison with B73 genome sequence A Very Brief Overview of Maize Genome Sequencing Projects • B73 Genome – Sequenced by the Maize Genome Sequencing Consortium – Funded by the NSF, DOE, and USDA and completed 2008 – Sequencing of ~16,600 BACs at 6X coverage was based on a well developed integrated genetic and physical map • Current Status of the B73 Genome – Version 2 of the pseudomolecules released in March 2010 – A tremendous resource but many sequence contigs within BACs remain unordered. This presents annotation challenges. – Version 2 of the annotation to be released by the MGSC in summer 2010 Works in Progress at MaizeGDB • SNPs – Working to bring in a large SNP dataset(s) and present on the maize genome browser • Gene Expression Data – Working to bring a large NimbleGen microarray data set across 60 maize tissues • Truman State University Collaboration on Undergraduate-Driven Community Annotation – Focus is on genes involved in Shoot Apical Meristem development. MaizeGDB Team • MaizeGDB Core Team – – – – – – – – Carolyn Lawrence-Director Darwin Campbell-DBA Carson Andorf-Bioinformatics Tanner Sen-Computational Biology Ethy Cannon-Software Dev Mary Schaeffer-Curator Jack Gardiner-Curator Lisa Harper-Curator • Working Group Volker Brendel Mike Freeling Anne-Francoise Lamblin Thomas Lubberstedt Owen Hoekenga Karen McGinnis Lukas Mueller Mihai Pop (Chair) Marty Sachs Pat Schnable Anne Sylvester Doreen Ware Contact at ASPB 2010 • Will be at Plant Genome Resources Outreach Booth – – – – Saturday 11:00 to 2:00 Sunday 11:00 to 1:45 Monday 10:00 to 1:45 Tuesday 11:00 to 1:00 • Email me at [email protected] for a meeting