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Nucleic Acids Research 2006 34(Database Issue):D465-D470; doi:10.1093/nar/gkj119
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Nucleic Acids Research, 2006, Vol. 34, Database issue D465-D470
© 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

Phytophthora functional genomics database (PFGD): functional genomics of phytophthora–plant interactions

Kamal Gajendran, Michael D. Gonzales, Andrew Farmer, Eric Archuleta, Joe Win1, Mark E. Waugh and Sophien Kamoun1,*

National Center for Genome Resources Santa Fe, NM, USA 1Department of Plant Pathology, The Ohio State University-Ohio Agricultural Research and Development Center Wooster, OH, USA

*To whom correspondence should be addressed. Tel: +1 330 263 3847; Fax: +1 330 263 3841; Email: kamoun.1{at}osu.edu

Received August 15, 2005. Revised October 19, 2005. Accepted October 19, 2005.

The Phytophthora Functional Genomics Database (PFGD; http://www.pfgd.org), developed by the National Center for Genome Resources in collaboration with The Ohio State University-Ohio Agricultural Research and Development Center (OSU-OARDC), is a publicly accessible information resource for Phytophthora–plant interaction research. PFGD contains transcript, genomic, gene expression and functional assay data for Phytophthora infestans, which causes late blight of potato, and Phytophthora sojae, which affects soybeans. Automated analyses are performed on all sequence data, including consensus sequences derived from clustered and assembled expressed sequence tags. The PFGD search filter interface allows intuitive navigation of transcript and genomic data organized by library and derived queries using modifiers, annotation keywords or sequence names. BLAST services are provided for libraries built from the transcript and genomic sequences. Transcript data visualization tools include Quality Screening, Multiple Sequence Alignment and Features and Annotations viewers. A genomic browser that supports comparative analysis via novel dynamic functional annotation comparisons is also provided. PFGD is integrated with the Solanaceae Genomics Database (SolGD; http://www.solgd.org) to help provide insight into the mechanisms of infection and resistance, specifically as they relate to the genus Phytophthora pathogens and their plant hosts.

Present address: Mark E. Waugh, Los Alamos National Laboratory, Los Alamos, NM, USA


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