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Series GSE16507

Query DataSets for GSE16507

Status

Public on Mar 01, 2010

Title

rice whole transcriptome surveyed by high throughput sequencing technology

Organism

Oryza sativa

Experiment type

Expression profiling by SAGE

Summary

Transcriptome analysis is an important approach to associate genotype with phenotype. The content and dynamics of eukaryotic transcriptome are far more complex than previously anticipated. Here we integrated high-throughput RNA-seq and paired-end method to conduct an unprecedentedly deep survey of transcription profile for cultivated rice, one of the oldest domesticated crops species and has since spread worldwide to become one of the major staple foods. Analysis of reads mapping revealed 4,244 previously uncharacterized transcripts, including a mass of protein-coding genes and putative functional non-coding RNA genes. Alignment of junction reads indicated over 42% of rice multiple-exon genes produce two or more distinct splicing isoforms. It’s intriguing that we identified 1,356 putative gene fusion events, indicating the 234 fusion gene produced by trans-splicing vastly increases the complexity of rice transcriptome, together with the pervasive alternative splicing events. Digital gene expression profiling revealed most rice duplicate genes were maintained by the selection constraint on gene dosages, which would increase the genetic robustness of rice to counteract deleterious mutations

Overall design

3' SAGE tags of two rice tissues , booting panicle and callus , were sequenced.

Contributor(s)

Guo G, Zhang G, Hu X, Li Q, Zhuang R, Tian W, Huang Q, He Z, Tao Y

Citation(s)

20305017

Submission date

Jun 08, 2009

Last update date

Mar 21, 2012

Contact name

Guangwu Guo