Choosing a genome browser for a Model Organism Database: surveying the Maize community

Database, Vol. 2010, Article ID baq007, doi:10.1093/database/baq007 ............................................................................................................................................................................................................................................................................................. Original article Taner Z. Sen1,2,*, Lisa C. Harper3,4, Mary L. Schaeffer5,6, Carson M. Andorf1, Trent E. Seigfried1, Darwin A. Campbell1 and Carolyn J. Lawrence1,2 1 USDA-ARS Corn Insects and Crop Genetics Research Unit, 2Department of Genetics, Development and Cell Biology, Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50011, 3USDA-ARS Plant Gene Expression Center, 800 Buchanan Street, Albany, CA 94710, 4Department of Molecular and Biology, University of California Berkeley, Berkeley, CA 94720, 5USDA-ARS Plant Genetics Research Unit and 6Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA *Corresponding author: Tel: +1 515 294 5326; Fax: +1 515 294 8280; Email: Submitted 16 November 2009; Revised 8 March 2010; Accepted 9 March 2010 ............................................................................................................................................................................................................................................................................................. As the B73 maize genome sequencing project neared completion, MaizeGDB began to integrate a graphical genome browser with its existing web interface and database. To ensure that maize researchers would optimally benefit from the potential addition of a genome browser to the existing MaizeGDB resource, personnel at MaizeGDB surveyed researchers’ needs. Collected data indicate that existing genome browsers for maize were inadequate and suggest implementation of a browser with quick interface and intuitive tools would meet most researchers’ needs. Here, we document the survey’s outcomes, review functionalities of available genome browser software platforms and offer our rationale for choosing the GBrowse software suite for MaizeGDB. Because the genome as represented within the MaizeGDB Genome Browser is tied to detailed phenotypic data, molecular marker information, available stocks, etc., the MaizeGDB Genome Browser represents a novel mechanism by which the researchers can leverage maize sequence information toward crop improvement directly. Database URL: http://gbrowse.maizegdb.org/ ............................................................................................................................................................................................................................................................................................. Introduction A genome browser is to genomic sequence data as a web browser is to the World Wide Web: both offer logical access to datastreams that are otherwise unintelligible. With the advent of new DNA sequencing technologies and the availability of copious amounts of sequence-based data from many species, genome browsers have been developed as a means for researchers to view, interact with, search through and display sequenced genomes as well as to compare syntenic or similar regions of genomes among related species. Various genome browsers have been created over the years, each with particular strengths and weaknesses. Many provide independent solutions for integrating and visualizing sequence-based data alongside genetic and phenotypic information. Community resources including Model Organism Databases (MODs) [e.g. TAIR (1), FlyBase (2), etc.], Clade-Oriented Databases (CODs) [e.g. Gramene (3), SGN (4), etc.], Automatic Annotation Shops [e.g. PlantGDB (5), JCVI (6, 7), etc.] and others have a responsibility to provide timely access to sequence data well-integrated with existing traditional biological data. Determining how best to choose genome browser software to meet the needs of users within the context of a group’s maintenance capabilities is a major challenge for the groups working to build and maintain these community resources. Described here are the methodologies we used to determine which ............................................................................................................................................................................................................................................................................................. Published by Oxford University Press 2010. This is Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http:// creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. Page 1 of 9 (page number not for citation purposes) Choosing a genome browser for a Model Organism Database: surveying the Maize community Original article Database, Vol. 2010, Article ID baq007, doi:10.1093/database/baq007 ............................................................................................................................................................................................................................................................................................. genome browser to implement at MaizeGDB (8–10), the MOD for maize. The need for a genome browser at MaizeGDB ............................................................................................................................................................................................................................................................................................. Page 2 of 9 These are exciting times for maize researchers and breeders. Not only is maize a major crop worldwide; a reference genome sequence for the inbred line, B73, has been released [www.maizesequence.org; (11)]. As of August 2009, the minimum tiling path included 16 910 sequenced Bacterial Artificial Chromosome (BAC) and fosmid clones and encompassed 2.12 Gb or 93% of the 2.3 Gb B73 genome (12). The B73 pseudomolecules (12) are available through the Arizona Genomics Institute website (http:// www2.genome.arizona.edu/genomes/maize). Other whole-genome sequences include the shotgun sequences of an ancient popcorn landrace, Palomero Toluqueño (13) and the maize inbred line Mo17 (from JGI- the Joint Genome Institute, with D. Rohksar leading the group, http://www.phytozome.net/). In addition, an extensive haplotype map has been published for 27 lines of maize, enabling researchers to establish novel relations between genetic, physical and diversity data (14, 15). Other sequence-based resources include over 2 million public ESTs (http://www.ncbi.nlm.nih.gov/dbEST/dbEST_summary .html) and a large number of genic sequences from gene-enriched libraries (16, 17). Various (...truncated)