Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq

Abstract

The functional complexity of the rice transcriptome is not yet fully elucidated, despite many studies having reported the use of DNA microarrays. Next-generation DNA sequencing technologies provide a powerful approach for mapping and quantifying the transcriptome, termed RNA sequencing (RNA-seq). In this study, we applied RNA-seq to globally sample transcripts of the cultivated rice Oryza sativa indica and japonica subspecies for resolving the whole-genome transcription profiles. We identified 15,708 novel transcriptional active regions (nTARs), of which 51.7% have no homolog to public protein data and >63% are putative single-exon transcripts, which are highly different from protein-coding genes (<20%). We found that~48% of rice genes show alternative splicing patterns, a percentage considerably higher than previous estimations. On the basis of the available rice gene models, 83.1% (46,472 genes) of the current rice gene models were validated by RNA-seq, and 6228 genes were identified to be extended at the 59 and/or 39 ends by at least 50 bp. Comparative transcriptome analysis demonstrated that 3464 genes exhibited differential expression patterns. The ratio of SNPs with nonsynonymous/synonymous mutations was 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.

The Differential Transcription Network between Embryo and Endosperm in the Early Developing Maize Seed

“…Retained intron, in which a single intron is alternatively included or spliced out of the mature mRNA via an intron-definition splicing mechanism, was the most prevalent type of AS event (30.4%; Fig. 3C), consistent with previous studies in plants (Black, 2003;Wang and Brendel, 2006;Barbazuk et al, 2008;Filichkin et al, 2010;Li et al, 2010;Lu et al, 2010;Zhang et al, 2010;Marquez et al, 2012) but in contrast to animal AS events, where exon skipping (cassette exons or coordinate cassette exons) is the predominant mechanism (Sultan et al, 2008;Wang et al, 2008;Daines et al, 2011;Graveley et al, 2011). Furthermore, alternative 39 splice sites (A3SS; 21.0%) or alternative last exons (ALE; 11.5%) and alternative 59 splice sites (A5SS; 12.2%) or alternative first exons (AFE; 11.7%) were other types of common AS events observed in our data (Fig.…”

“…Previous studies have shown that NTRs have fewer and shorter exons, less protein-coding potential, and less tissue-specific expression than annotated protein-coding genes (Bruno et al, 2010;Lu et al, 2010;Wetterbom et al, 2010;Zhang et al, 2010;Aanes et al, 2011;Graveley et al, 2011). To determine whether endospermic and embryonic NTRs have similar features, we analyzed the structure, coding potentials, and expression levels of the NTRs.…”

“…It was reported that at least 42% and 48% of genes are alternatively spliced in Arabidopsis and rice, respectively (Filichkin et al, 2010;Lu et al, 2010).…”

“…RNA-seq data are highly reproducible, with few systematic discrepancies among technical replicates (Marioni et al, 2008). RNA-seq technology has been applied to uncovering the entire transcriptome and identifying alternative splicing (AS) and novel transcribed regions (NTRs) as well as chimeric transcripts produced by trans-splicing in human, yeast, mouse, Arabidopsis, and rice (Oryza sativa; Cloonan et al, 2008;Lister et al, 2008;Mortazavi et al, 2008;Nagalakshmi et al, 2008;Pan et al, 2008;Sultan et al, 2008;Wang et al, 2008;Wilhelm et al, 2008;Filichkin et al, 2010;Lu et al, 2010;Zhang et al, 2010).…”

A physical, genetic and functional sequence assembly of the barley genome

“…Second, recent reports have highlighted the abundance of novel transcriptionally active regions in rice that lack homology to proteincoding genes or open reading frames (ORFs) 40 . In barley as many as 27,009 preferentially single-exon low-confidence genes can be classified as putative novel transcriptionally active regions (Supplementary Note 7.1.4).…”