MaizeGDB becomes ‘sequence-centric’

0 USDA-ARS Plant Genetics Research Unit and Division of Plant Sciences, University of Missouri , Columbia, MO 65211 1 Department of Genetics, Development and Cell Biology, Iowa State University , Ames, IA 50011 2 Present address: Michael E. Sparks, USDA-ARS Bovine Functional Genomics Laboratory , Beltsville, MD, USA 3 USDA-ARS Corn Insects and Crop Genetics Research Unit , Ames, IA 50011 4 Department of Statistics, Iowa State University , Ames, IA 50011, USA 5 Department of Molecular and Cell Biology, University of California , Berkeley, CA 94720 6 USDA-ARS Plant Gene Expression Center , Albany, CA 94710 MaizeGDB is the maize research community's central repository for genetic and genomic information about the crop plant and research model Zea mays ssp. mays. The MaizeGDB team endeavors to meet research needs as they evolve based on researcher feedback and guidance. Recent work has focused on better integrating existing data with sequence information as it becomes available for the B73, Mo17 and Palomero Toluquen o genomes. Major endeavors along these lines include the implementation of a genome browser to graphically represent genome sequences; implementation of POPcorn, a portal ancillary to MaizeGDB that offers access to independent maize projects and will allow BLAST similarity searches of participating projects' data sets from a single point; and a joint MaizeGDB/PlantGDB project to involve the maize community in genome annotation. In addition to summarizing recent achievements and future plans, this article also discusses specific examples of community involvement in setting priorities and design aspects of MaizeGDB, which should be of interest to other database and resource providers seeking to better engage their users. MaizeGDB is accessible online at http://www.maizegdb.org. Database URL: http://www.maizegdb.org Introduction Maize is one of very few species that serve both as an important research model and as a crop from which diverse products and resources are generated [reviewed in (1, 2)]. This breadth of scope is recapitulated by the wide variety of informatics needs expressed by the community of maize biologistsnot only are tools for handling genetic and genomic information needed, support for translational and applied research is also of great interest [reviewed in (3)]. To better understand the broad needs of the research community and prioritize development goals, a Working Group (http://www.maizegdb.org/working_group.php) made up of maize geneticists and computational biologists meets annually to discuss the MaizeGDB projects status and to suggest how to further develop the MaizeGDB resource. In addition, the maize community periodically organizes meetings to gather information on key needs to move maize research forward. In March 2007, lab heads met at the Allerton Park and Conference Center in Monticello, IL, to discuss The Future of Maize Genetics [meeting report available at http://www.maizegdb .org/AllertonReport.doc and (4)]. Guidance from the MaizeGDB Working Group and Allerton reports agree that two needs are of the utmost priority: improving access to the genome sequence of inbred line B73 (as well as other maize genome sequences as they become available) and creating tools to improve phenotype data collection, storage and analysis. With this in mind, sequence data and phenotypes constitute much of the current MaizeGDB Project Plan, a document that outlines work to be accomplished by MaizeGDB over a 5-year period (2009 14). In brief, the goals are as follows: (1) to integrate new maize genetic and genomic data into the database by expanding mutant and phenotype data and tools as well as structural and genetic map sets emphasizing the integration of the IBM genetic maps with the B73 genome sequence; creating views that convey the substantial variation in maize genome structure; integrating the next-generation genetic map being generated by the Maize Diversity Project (5) into a genomic view to enable its effective use by plant breeders; providing access to gene models calculated by leading gene structure prediction groups through the MaizeGDB interface; compiling and making accessible the annual Maize Newsletter at MaizeGDB and (2) to provide community support services, such as lending help to the community of maize researchers with respect to developing and publicizing a set of guidelines for researchers to follow to ensure that their data can be made available through MaizeGDB; coordinating annual meetings; and conducting elections and surveys. MaizeGDB currently has a wide range of maize data including genetic maps, gene products, loci, alleles, phenotypes, stocks, sequences and markers. However, centralized access to currently ongoing maize projects that create sequenceindexed data (roughly 1015 projects at any given time) is notably lacking. Reported here are some recent updates to MaizeGDB with emphasis on improving the handling and accessibility to sequence data, especially data generated by the Maize Genome Sequencing Project for B73 (6). Of particular note are (i) the new MaizeGDB Genome Browser (see Genomic sequence data display and integration with genetic maps section), (ii) a new project ancillary to MaizeGDB called POPcorn, which currently serves as a portal to maize research projects with a centralized maize sequence similarity search resource coming soon and (iii) a recently launched project to involve the community of maize geneticists in genome annotation for B73 (outlined in Current endeavors section). MaizeGDBs standard operating procedures, machine architecture, accessibility and a description of how the databases are administered are described elsewhere (1, 2). Data made available via MaizeGDB are in the public domain. Genomic sequence data display and integration with genetic maps Genome browser Based upon the 2006 MaizeGDB Working Group guidance (available at the bottom of http://www.maizegdb.org/ working_group.php) and the Allerton meeting report (4), the MaizeGDB Team began development toward making MaizeGDB become more sequence-centric in early 2007. To this end, an initiative to implement a MaizeGDB Genome Browser was launched in early 2008 and completed in December 2008. The MaizeGDB Genome Browser enables MaizeGDB to become the long-term and centralized keeper of maize gene models (which ensures proper nomenclature) and serves as a way to compare various groups assemblies and annotations simultaneously. A variety of genome browser applications were evaluated via a survey prepared on behalf of the Maize Genetics Executive Committee (accessible online at http:// www.maizegdb.org/blanksurvey.html) to gauge cooperators impressions of existing software and to find out what functionalities they would like to have in a maize genome browser. A summary of the survey results is available online at http://www.maizegdb.org/genome_browser_survey.php. Based upon results of the survey, GBrowse (7) was selected for th (...truncated)