maizegdb: a very short overview of a database resource for biological information on zea mays jack...
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MaizeGDB: A Very Short Overview of a Database Resource for
Biological Information on Zea mays
Jack M. Gardiner
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
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
POPCornTwo 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 LamblinThomas LubberstedtOwen HoekengaKaren McGinnisLukas MuellerMihai Pop (Chair)Marty Sachs Pat SchnableAnne SylvesterDoreen 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