Rice transcriptome profiling at single-nucleotide resolution by RNA-seq
Novel exon splicing junctions and novel transcriptional active regions in Oryza sativa
The functional complexity of the rice transcriptome is not yet fully elucidated in spite of many efforts on it by using cDNA microarray or DNA tiling array.  Next-generation DNA sequencing technologies provide a revolutionary and powerful approach for transcriptome analysis (RNA-seq).  We applied RNA-seq to globally sample transcripts of the cultivated rice Oryza sativa indica and japonica subspecies for detecting the whole-genome transcription profiling.  Nearly 48% rice genes have alternatively spliced patterns; it is much higher than previous estimation.  Compared to available rice gene models, 46,472 (83.1%) genes could be validated by expression evidence.  We identified 15,708 novel transcriptional active regions (nTARs) and 51.70f them have no homologs to public protein database.  Our analysis suggests that >630f these nTARs are putative single exon transcipts; which are highly different from protein-coding genes (<20%).  Furthermore, we found that 6,228 rice genes are extended at the 5ï¿½ï¿½ and/or 3ï¿½ï¿½ end by at least 50 bp.  We also identified 3,464 genes as differentially expressed between the two rice subspecies.  Catalytic activity and binding proteins dominated the differentially expressed genes.  We found that 8,433 genes were influenced in amino acid level between indica and japonica by reason of SNPs identified in coding regions.  The ratio of SNPs with nonsynonymous/synonymous mutations is nearly 1:1.06.  In total, we interrogated and compared transcriptomes of the two rice subspecies to reveal the overall transcriptional landscape at maximal resolution.