title: 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 approximately 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 5' and/or 3' 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.
authors.affiliation: National Center for Gene Research & Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China.
authors.forename: Tingting
authors.initials: T
authors.lastname: Lu
authors.forename: Guojun
authors.initials: G
authors.lastname: Lu
authors.forename: Danlin
authors.initials: D
authors.lastname: Fan
authors.forename: Chuanrang
authors.initials: C
authors.lastname: Zhu
authors.forename: Wei
authors.initials: W
authors.lastname: Li
authors.forename: Qiang
authors.initials: Q
authors.lastname: Zhao
authors.forename: Qi
authors.initials: Q
authors.lastname: Feng
authors.forename: Yan
authors.initials: Y
authors.lastname: Zhao
authors.forename: Yunli
authors.initials: Y
authors.lastname: Guo
authors.forename: Wenjun
authors.initials: W
authors.lastname: Li
authors.forename: Xuehui
authors.initials: X
authors.lastname: Huang
authors.forename: Bin
authors.initials: B
authors.lastname: Han
mesh_terms: D017398:Alternative Splicing; D001483:Base Sequence; D020869:Gene Expression Profiling; D017343:Genes, Plant; D018745:Genome, Plant; D058977:Molecular Sequence Annotation; D020411:Oligonucleotide Array Sequence Analysis; D012275:Oryza / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D017423:Sequence Analysis, RNA