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Status |
Public on Aug 18, 2010 |
Title |
Deep sequencing discovery of novel and conserved microRNAs in trifoliate orange (Citrus trifoliata) |
Organism |
Citrus trifoliata |
Experiment type |
Non-coding RNA profiling by high throughput sequencing
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Summary |
MicroRNAs (miRNAs) play a critical role in post-transcriptional gene regulation. miRNAs have been shown to control many genes involved in various biological and metabolic processes. Deep sequencing technologies have facilitated identification of species-specific or lowly expressed as well as conserved or highly expressed miRNAs in plants. In this research, we used Solexa sequencing to discover new microRNAs in trifoliate orange (Citrus trifoliata) an important rootstock of citrus. A total of 13,106,753 reads representing 4,876,395 distinct sequences were obtained from a short RNA library generated from small RNA extracted from C. trifoliata flower and fruit tissues, Based on sequence similarity and hairpin structure prediction, we found that 178,102 reads representing 89 sequences from 42 highly conserved miRNA families, have perfect matches to known miRNAs. We also identified 10 novel miRNA candidates, whose precursors were all potentially generated from citrus ESTs. And of them five miRNA* sequences were also sequenced. These sequences had not been described in other plant species and accumulation of these 10 novel miRNAs were confirmed by qRT-PCR analysis. Potential target genes were predicted for most conserved and novel miRNAs. Moreover, four target genes included one encoding IRX12 copper ion binding/ oxidoreductase and three genes encoding NB-LRR disease resistance protein have been experimentally verified by detection of the miRNA-mediated mRNA cleavage in C. trifoliata.
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Overall design |
Size fractionated small RNAs (16-30 bp) from total RNA extracts was ligated to 5' and 3' adapters, and reverse transcribed. After PCR amplification the sample was subjected to Solexa sequencing. The resultant 35nt sequence data were filtered according to base quality value. The remained sequences were used to trim 5' and 3' adaptors. The clean tags were used for further analysis.
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Contributor(s) |
Song C, Fang J |
Citation(s) |
20626894 |
Submission date |
Jun 02, 2010 |
Last update date |
May 15, 2019 |
Contact name |
Changnian Song |
E-mail(s) |
2008204002@njau.edu.cn
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Organization name |
Nanjing Agricultural University
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Department |
College of Horticulture
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Lab |
Fruit tree genomics and molecular biology
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Street address |
Weigang No.1
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City |
Nanjing |
ZIP/Postal code |
210095 |
Country |
China |
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Platforms (1) |
GPL10479 |
Illumina Genome Analyzer (Citrus trifoliata) |
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Samples (1) |
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Relations |
SRA |
SRP002607 |
BioProject |
PRJNA128941 |
Supplementary data files not provided |
SRA Run Selector |
Processed data included within Sample table |
Raw data are available in SRA |
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