MaizeGDB becomes 'sequence-centric'

T Z Sen,J Duvick,C M Andorf,C J Lawrence,L C Harper,D A Campbell,M E Sparks,M L Schaeffer,V P Brendel,E Cannon

doi:10.1093/database/bap020

T Z Sen, J Duvick + Show 8 more

Open Access

https://doi.org/10.1093/database/bap020

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Abstract

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 Toluqueño 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

Highlights

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 biologists— are tools for handling genetic and genomic information needed, support for translational and applied research is of great interest [reviewed in [3]]
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 and creating tools to improve phenotype data collection, storage and analysis

Summary

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]]. 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. Data made available via MaizeGDB are in the public domain

Genome browser

Genome browser integration with the existing MaizeGDB resource

Current endeavors