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| Status |
Public on Aug 21, 2008 |
| Title |
A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains |
| Organism |
Oryza sativa |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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| Summary |
Endogenous small RNAs, including microRNAs (miRNAs) and short-interfering RNAs (siRNAs), function as posttranscriptional or transcriptional regulators in plants. miRNA function is essential for normal development and therefore likely to be important in the growth of the rice grain. To investigate the likely roles of miRNAs in rice grain development we carried out deep sequencing of the small RNA populations of rice grains. A total of 96,091 (including 23,867 reads from vegetative tissues) and 5,379,724 small RNA sequences that are longer than 17nt were generated. Approximately 94% of these small RNAs were 20-24nt in length. The majority of the small RNAs were singletons, indicating that rice genome has a very complex small RNA population, which is harder to be saturated. From these smal RNA sequences we found representatives of all 20 conserved plant miRNA families and evidence for changes in expression of miRNAs during rice grain development. Using an approach based on the presence of the miRNA and miRNA* sequences, we identified 51 novel, non-conserved rice miRNA families expressed in grains with functionally diverse predicted target genes. miRNA-guided cleavage was confirmed for a number of targets genes including ones with roles in sugar signalling and restoration of cytoplasmic male sterility. We identified a likely mirtron, indicating that plants can also use spliced introns as a source of miRNAs. Our sequencing results revealed four TAS3 loci; these all contain dual miR390 sites of which only the 3? site is cleaved. We also found a miRNA-like long hairpin generating phased 21nt small RNAs, strongly expressed in developing grains and show that these small RNAs act in trans to cleave target mRNAs.
Keywords: high throughput pyrosequencing, small RNA, microRNA, grain development, rice
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| Overall design |
Small RNA populations of shoots and roots of 7 days old seedlings, and 1-5 and 6-10 days after fertilization grains were determined using high throughput sequencing technology. The abundance of known miRNAs were compared based on the number of sequence reads. To give a whole picture of the rice small RNA populations and to reflect un-biasly the sequencing results, small RNAs that are longer than 17nt no matter whether or not they matched with the rice genome were included in this submitted dataset. The unmatched sequences may be derived from un-sequenced regions or sequencing errors.
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| Contributor(s) |
Zhu Q, Spriggs A, Helliwell C, Gubler F, Fan L, Matthew L, Kennedy G |
| Citation(s) |
18687877 |
| Submission date |
Apr 01, 2008 |
| Last update date |
Jul 14, 2013 |
| Contact name |
Andrew Spriggs |
| E-mail(s) |
andrew.spriggs@csiro.au
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| Phone |
612-6246-5193
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| Organization name |
CSIRO Plant Industry
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| Department |
Bioinformatics Group
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| Street address |
GPO Box 1600
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| City |
Canberra |
| State/province |
ACT |
| ZIP/Postal code |
2601 |
| Country |
Australia |
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| Platforms (2) |
| GPL9147 |
Illumina Genome Analyzer (Oryza sativa) |
| GPL9388 |
454 GS (Oryza sativa) |
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| Samples (6)
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| Relations |
| SRA |
SRP007800 |
| BioProject |
PRJNA107103 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE11014_RAW.tar |
303.6 Mb |
(http)(custom) |
TAR (of FNA, QUAL, TXT) |
| Processed data included within Sample table |
| Raw data are available in SRA |
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