github link
Accession IconSRP014309

Genomic dissection of small RNAs in wild rice (O.rufipogon): lessons for rice domestication [degradome]

Organism Icon Oryza rufipogon
Sample Icon No Downloadable Samples
Technology Badge IconIllumina Genome Analyzer

Submitter Supplied Information

Description
The lack of MIRNA set and genome sequence of O. rufipogon (the ancestor of the cultivated rice) has limited to answer the role of MIRNA genes in rice domestication.In this study, a genome, three small RNA populations and a degradome of O.rufipogon were sequenced by Illumina platform and miRNA expression were investigated by miRNA chips. A de novo genome was assembled using ~55x coverage of raw sequencing data and a total of 387 MIRNAs were identified in the O. rufipogon genome based on ~5.2 million unique small RNA reads from three different tissues of O. rufipogon. Of these O. rufipogon MIRNAs, 259 were not found in the cultivated rice, suggesting loss of these MIRNAs in the cultivated rice. We also found that 48 MIRNAs were novel in the cultivated rice, suggesting that they were potential targets of domestication selection. Some miRNAs showed significant expression difference in the wild and cultivated rice, suggesting that expression of miRNA could also be a target of domestication, as demonstrated for the miR164 family. Our results illustrated MIRNA genes, like protein-coding genes, were significantly shaped during rice domestication and could be one of the driven forces contributed to rice domestication. Overall design: The 5' end of the 3' degraded mRNAs with polyA tails were collected and generated from seedlings at four-leaves stage of O.rufipogon by degradome highthoughput sequecing using Illumina GAII
PubMed ID
Total Samples
1
Submitter’s Institution
No associated institution
Alternate Accession IDs

Samples

Show of 0 Total Samples
Filter
Add/Remove
Accession Code
Title
Specimen part
Cell line
Subject
Processing Information
Additional Metadata
No rows found
Loading...