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Nucleic Acids Research 2006 34(Database Issue):D771-D776; doi:10.1093/nar/gkj072
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Nucleic Acids Research, 2006, Vol. 34, Database issue D771-D776
© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

The TIGR Maize Database

Agnes P. Chan1, Geo Pertea1, Foo Cheung1, Dan Lee1, Li Zheng1, Cathy Whitelaw1, Ana C. Pontaroli2, Phillip SanMiguel3, Yinan Yuan4, Jeffrey Bennetzen2, William Brad Barbazuk5, John Quackenbush1,6,7 and Pablo D. Rabinowicz1,*

1The Institute for Genomic Research 9712 Medical Center Drive, Rockville, MD 20850, USA 2Department of Genetics, University of Georgia Athens, GA 30602, USA 3Genomics Center, Purdue University West Lafayette, IN 47906, USA 4Department of Biological Sciences, Purdue University West Lafayette, IN 47906, USA 5Donald Danforth Plant Science Center 975 North Warson Road, St Louis, MO 63132, USA 6Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute 44 Binney Street, Boston, MA 02115, USA 7Department of Biostatistics, Harvard School of Public Health Boston, MA 02115, USA

*To whom correspondence should be addressed. Tel: +1 301 795 7787; Fax: +1 301 838 0208; Email: pablo{at}tigr.org

Received August 15, 2005. Revised October 15, 2005. Accepted October 15, 2005.

Maize is a staple crop of the grass family and also an excellent model for plant genetics. Owing to the large size and repetitiveness of its genome, we previously investigated two approaches to accelerate gene discovery and genome analysis in maize: methylation filtration and high C0t selection. These techniques allow the construction of gene-enriched genomic libraries by minimizing repeat sequences due to either their methylation status or their copy number, yielding a 7-fold enrichment in genic sequences relative to a random genomic library. Approximately 900 000 gene-enriched reads from maize were generated and clustered into Assembled Zea mays (AZM) sequences. Here we report the current AZM release, which consists of ~298 Mb representing 243 807 sequence assemblies and singletons. In order to provide a repository of publicly available maize genomic sequences, we have created the TIGR Maize Database (http://maize.tigr.org). In this resource, we have assembled and annotated the AZMs and used available sequenced markers to anchor AZMs to maize chromosomes. We have constructed a maize repeat database and generated draft sequence assemblies of 287 maize bacterial artificial chromosome (BAC) clone sequences, which we annotated along with 172 additional publicly available BAC clones. All sequences, assemblies and annotations are available at the project website via web interfaces and FTP downloads.


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