Plant & Animal Genomes XIV Conference

January 14-18, 2006
Town & Country Convention Center
San Diego, CA

A Novel Approach To Verifying The Source Of Transcripts From Complex cDNA Libraries

Lecong Zhou^1,2 , Saghai Maroof M.A.² , Brett, M. Tyler¹

¹  Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA24061, USA

²  Department of Crop and Soil Environmental Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA24061, USA

The Affymetrix GeneChip® Soybean Genome Array is a complex high capacity microarray chip that contains over 37,500 soybean (Glycine max) transcripts and over 23,300 transcripts of two important soybean pathogens, Phytophthora soja and Heterodera glycines. This array provides a unique platform for the soybean research community to simultaneously study the gene expression of both the host plant and pathogen(s). However, many of the transcripts represented on the array come from ESTs from pathogen infected soybean tissues. Traditional annotation methods such as GC content and codon usage may not sufficiently distinguish the source of the transcripts, resulting in a small portion of the transcripts being miscategorized. We have recently applied an experimental solution to verify the source of the transcripts on genome scale. By hybridizing the chip with pure soybean and P. sojae RNA samples, we have found approximately 100 soybean transcripts are in fact P.sojae transcripts. On the other hand, a few P.sojae transcripts turned out to be of soybean source. Further rectification of all the transcripts could be done by using pure RNA samples from other relevant microbes like Fusarium solani f.sp. glycines, Pseudomonas syringae pv. glycinea, and Bradyrhizobium japonicus. In addition, we have annotated all the transcripts by searching against the NCBI non-redundant protein database, resulting in a brief functional annotation collection that will be an important resource for the genomic studies of soybean-pathogen interactions.