Plant & Animal Genomes XIII Conference

January 15-19, 2005
Town & Country Convention Center
San Diego, CA

Development Of An Affymetrix Genechip Microarray For Fusarium graminearum Using The Gen-Au / Mips Genome Database

Ulrich Gueldener¹ , Francis Trail² , Jin R Xu³ , Gerhard Adam⁴ , H Corby Kistler⁵

¹  MIPS-Munich Information Center on Protein Sequences, GSF - National Research Center for Environment and Health, Ingolstädter Landstrasse 1, D-85764 Neuherberg, Germany

²  Michigan State University, Department of Plant Biology, East Lansing, MI 48824-1312, USA

³  Purdue University, Botany and Plant Pathology, Lilly Hall, 915 West State Street, West Lafayette, IN 47907-2054, USA

⁴  BOKU - University of Natural Resources and Applied Life Sciences, Vienna, Department of Applied Plant Sciences and Plant Biotechnology, Muthgasse 18, A-1190 Vienna

⁵  USDA-ARS, 1551 Lindig Street, Cereal Disease Laboratory, University of Minnesota, St. Paul, MN 55108 , USA

Shortly after public release of the genome sequence of the plant pathogenic fungus Fusarium graminearum by the Broad Institute, automated draft gene calls were processed both at the Broad Institute and at MIPS. A variety of bioinformatics methods were applied to both gene sets at MIPS using the PEDANT system. Manual inspection of the calls using different gene prediction programs and EST sequences were also conducted to examine under-predicted genes and verify predicted coding regions. Such manual inspection of genes is desirable prior to the design of an Affymetrix GeneChip microarray, in order to reduce mis-designed probe sets.
With the help of the Fusarium community we manually processed 860 entries; 408 of the calls were altered or added as completely new calls. However, only 6.1 % of the putative 14,000 Fusarium genes were manually processed. To integrate all different calls and the applied bioinformatics methods, the F. graminearum Genome Database was created with additional functionality including a synteny viewer and comparative Interpro analysis (http://mips.gsf.de/genre/proj/fusarium/).
A non redundant gene call set for the Affymetrix GeneChip design was produced with the order of preference being 'manually processed new calls' > 'MIPS draft set' > 'Broad Institute set.' The set of full length ORF sequences and an additional EST- and rRNA-sequences were submitted to Affymetrix for initial computation of probe sets. After three rounds of revisions on chip design, the sets were approved for mask design. The first experiments for chip validation are underway.