Plant & Animal Genomes XIII Conference

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

Deep Transcriptional Profiling Of Rice Using Signature Sequencing

Kan Nobuta¹ , Venu R Channarayappa² , Kalyan Vemeraju¹ , Tam Vu¹ , Maria Bellizzi² , Guo-liang Wang² , Blake C Meyers¹

¹  Delaware Biotechnology Institute, University of Delaware, Newark, DE, 19711, US

²  Department of Plant Pathology, The Ohio State University, Columbus, OH, 43210, US

MPSS (Massively Parallel Signature Sequencing) is a technology that allows the measurement of expression levels for nearly all transcripts expressed in a sample. The method sequences 17 to 20 nucleotides derived from the 3’-most DpnII restriction site (GATC) of each mRNA transcript; each sequence is called a “signature” or “tag”. The expression level is determined by counting the number of occurrences of each signature in the sample and assigning the signature to a known gene. We are currently generating MPSS data for ~65 rice samples. The libraries include diverse untreated tissues, tissues treated with abiotic or biotic stress, and Indica and Japonica hybrids. The recent release of the rice genome annotation from TIGR (v2.0) has facilitated the MPSS data analysis. We are using this sequence and annotation to identify the genomic location of the tags relative to the annotated genes. The MPSS data can be used to identify potential alternative splice products, antisense transcripts, and intergenic transcripts (potentially non-coding transcripts). Molecular biological approaches (e.g. RACE, microarray) will be used to confirm the potential novel transcripts. All the rice MPSS data will be available through our MPSS web-interface (http://mpss.udel.edu); these data will facilitate gene discovery, functional analyses and permit “electronic Northern” analyses of specific genes of interest.