Abstract
Genome tiling microarray studies have consistently documented rich transcriptional activity beyond the annotated genes. However, systematic characterization and transcriptional profiling of the putative novel transcripts on the genome scale are still lacking. We report here the identification of 25,352 and 27,744 transcriptionally active regions (TARs) not encoded by annotated exons in the rice (Oryza. sativa) subspecies japonica and indica, respectively. The non-exonic TARs account for approximately two thirds of the total TARs detected by tiling arrays and represent transcripts likely conserved between japonica and indica. Transcription of 21,018 (83%) japonica non-exonic TARs was verified through expression profiling in 10 tissue types using a re-array in which annotated genes and TARs were each represented by five independent probes. Subsequent analyses indicate that about 80% of the japonica TARs that were not assigned to annotated exons can be assigned to various putatively functional or structural elements of the rice genome, including splice variants, uncharacterized portions of incompletely annotated genes, antisense transcripts, duplicated gene fragments, and potential non-coding RNAs. These results provide a systematic characterization of non-exonic transcripts in rice and thus expand the current view of the complexity and dynamics of the rice transcriptome.
Highlights
Efforts to generate sequence from the rice (Oryza sativa) genome as a model for the Gramineae, the group that includes all major cereal crops, has produced draft sequences of the japonica and indica subspecies [1,2,3]
Our characterization of the japonica transcriptome started with custom full-genome tiling microarrays containing 12,254,374 36mer oligonucleotide probes, with an average space of 10 nucleotides between adjacent probes
The tiling arrays were hybridized to a mixture of cDNA targets derived from four rice tissues or organs to optimize transcript representation
Summary
Efforts to generate sequence from the rice (Oryza sativa) genome as a model for the Gramineae, the group that includes all major cereal crops, has produced draft sequences of the japonica and indica subspecies [1,2,3]. In the context of rice genome annotation, tiling array analysis can be utilized to verify predicted gene models and to identify novel transcription units [14,15]. Of the 43,914 annotated non-TE gene models from indica [3], transcription of 35,970 (82%) was detected by tiling array analysis [15].
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