ArticleGenome research2010
Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq.
Article in Genome research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 185 papers, 1 of them a synthesis that pooled it.
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Who cites it
185 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Identification of cytokinin-responsive genes using microarray meta-analysis and RNA-Seq in Arabidopsis.Plant physiology · 2013Pooled it
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- Integrated transcriptional and biochemical profiling suggests mechanisms associated with rapid cold hardening in adult Liriomyza trifolii (Burgess).Scientific reports · 2024Article
- Alternative splicing of a potato disease resistance gene maintains homeostasis between growth and immunity.The Plant cell · 2024Article
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- Pan-transcriptomic analysis reveals alternative splicing control of cold tolerance in rice.The Plant cell · 2024Article
- Blocking of amino acid transporter OsAAP7 promoted tillering and yield by determining basic and neutral amino acids accumulation in rice.BMC plant biology · 2024Article
- Nucleotide-level distance metrics to quantify alternative splicing implemented in TranD.Nucleic acids research · 2024Article
- How to explore what is hidden? A review of techniques for vascular tissue expression profile analysis.Plant methods · 2023Review
- Comprehensive Profiling of Alternative Splicing and Alternative Polyadenylation during Fruit Ripening in Watermelon (International journal of molecular sciences · 2023Article
- The Splicing Factor OsSCL26 Regulates Phosphorus Homeostasis in Rice.Plants (Basel, Switzerland) · 2023Article
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- Molecular Mechanism of Cold Tolerance of Centipedegrass Based on the Transcriptome.International journal of molecular sciences · 2023Article
- Alternative Splicing ofInternational journal of molecular sciences · 2023Article
- Transcriptome Analysis of Different Sections of Rhizome in Polygonatum sibiricum Red. and Mining Putative Genes Participate in Polysaccharide Biosynthesis.Biochemical genetics · 2022Article
- Comparative Analysis of Environment-Responsive Alternative Splicing in the Inflorescences of Cultivated and Wild Tomato Species.International journal of molecular sciences · 2022Article
- Alternative Splicing and Its Roles in Plant Metabolism.International journal of molecular sciences · 2022Review
125 more citing papers are in PubMed but not listed here.
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12 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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