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MaizeGDB: A Very Short Overview of a Database Resource for Biological Information on Zea mays

MaizeGDB: A Very Short Overview of a Database Resource for Biological Information on Zea mays. Jack M. Gardiner jack.m.gardiner@gmail.com ASPB 2010. MaizeGDB 101. MaizeGDB strives to: Serve as a central repository for public maize information

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MaizeGDB: A Very Short Overview of a Database Resource for Biological Information on Zea mays

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  1. MaizeGDB: A Very Short Overview of a Database Resource for Biological Information on Zea mays Jack M. Gardiner jack.m.gardiner@gmail.com ASPB 2010

  2. 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.

  3. 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.

  4. 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!

  5. 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

  6. 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

  7. 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

  8. 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

  9. POPCornPrOject 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

  10. POPCornTwo Options for Sequence Searches

  11. Accessing the Maize Genome Sequence through MaizeGDB

  12. MaizeGDB Tutorials

  13. 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 • PalomeroToluqueño Genome • Sequenced at CINVESTAV Irapuato, Mexico • Ancient Mexican popcorn landrace provides diversity comparison with B73 genome sequence

  14. 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

  15. 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.

  16. 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 LamblinThomas LubberstedtOwen HoekengaKaren McGinnisLukas MuellerMihai Pop (Chair)Marty Sachs Pat SchnableAnne SylvesterDoreen Ware

  17. 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 jack.m.gardiner@gmail.com for a meeting

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