An expression atlas of rice mRNAs and small RNAs.

Identification of all expressed transcripts in a sequencedgenome is essential both for genome analysis and forrealization of the goals of systems biology. We used thetranscriptional profiling technology called ‘massively parallelsignature sequencing’ to develop a comprehensive expressionatlas of rice (Oryza sativa cv Nipponbare). We sequenced46,971,553 mRNA transcripts from 22 libraries, and2,953,855 small RNAs from 3 libraries. The data demonstratewidespread transcription throughout the genome, includingsense expression of at least 25,500 annotated genes andantisense expression of nearly 9,000 annotated genes. Anadditional set of B15,000 mRNA signatures mapped tounannotated genomic regions. The majority of the small RNAdata represented lower abundance short interfering RNAs thatmatch repetitive sequences, intergenic regions and genes.Among these, numerous clusters of highly regulated smallRNAs were readily observed. We developed a genomebrowser (http://mpss.udel.edu/rice) for public access tothe transcriptional profiling data for this important crop.Because of its scientific, economic and cultural importance, thesequencing of the rice (Oryza sativa ssp. japonica cv Nipponbare)genome