Transcript An Overview of MaizeGDB

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?
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MaizeGDB includes a number of
data types, all available from the
front page.
Genome Browser
Data types available:
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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
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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
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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