Sequencing-based measurements of mRNA and small RNA

Abstract

The whole-genome sequence of rice (Oryza sativa subsp. japonica cv Nipponbare) has been sequenced and the annotation of this genome has been performed and continues to be updated and improved by several organizations (Yuan et al. 2003; IRGSP 2005). In this chapter, we used the fourth annotation of the rice genome released from TIGR (The Institute of Genomic Research) to analyze our massively parallel signature sequencing (MPSS) data. In this version (TIGR v4.0), 62,827 gene models or transcription units (TUs) were identified, including 4,734 genes with multiple splice isoforms. Among the 55,890 genes, 13,237 were annotated as transposable element (TE)-related genes, while the rest (42,653) were annotated as protein-coding genes or non-TE genes.