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| Status |
Public on Jan 01, 2015 |
| Title |
Genome-wide identification of microRNAs and their targets involved in the phyB-mediated light signaling pathway in rice |
| Organism |
Oryza sativa |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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| Summary |
Phytochrome B (phyB), one member of phytochrome family in rice, plays important roles in regulating a range of developmental processes, and stress responses. However, little information about the mechanism involved in phyB-mediated light signaling pathway has been reported in rice. Another, it has been well-known that microRNAs (miRNAs) perform important roles in plant development and stress responses. Thus it is intriguing to explore the role of miRNAs in phyB-mediated light signaling pathway in rice. In this study, comparative high-throughput sequencing and degradome analysis were adopted to identify candidate miRNAs and their targets that participate in phyB-mediated light signaling pathway. A total of 838 known miRNAs, 663 novel miRNAs and 1,957 target genes were identified from wild-type (WT) and phyB mutant. Among them, 135 miRNAs showed differential expression, suggesting that the expressions of these miRNAs are under the control of phyB. In addition, 32 out of the 135 differentially expressed miRNAs were detected to slice 70 genes in rice genome. Analysis of these target genes showed that members of various transcription factor families constitute the largest proportion, indicating miRNAs are probably involved in phyB-mediated light signaling pathway mainly via regulating the expression of transcription factors. This study presented a comprehensive expression analysis of miRNAs and their targets that might be involved in phyB-mediated light signaling pathway for the first time. The results provide new clues for functional characterization of miRNAs in phyB-mediated light signaling pathway, which would be helpful in comprehensively uncovering molecular mechanism of phytochrome-mediated photomorphogenesis and stress responses in plant.
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| Overall design |
Examination of miRNA profiles in wild type (WT) and phyB mutant at four-leaf stage by deep sequencing using Illumina Hiseq2500.
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| Contributor(s) |
Xie X, Xu XH |
| Citation(s) |
26074936 |
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| Submission date |
Oct 15, 2014 |
| Last update date |
Jun 10, 2019 |
| Contact name |
Xiao Hui Xu |
| E-mail(s) |
xuxiaohui1023@163.com
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| Phone |
86-0531-83178193
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| Organization name |
Shandong Academy of Agricultural Sciences
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| Street address |
No. 202, Gongyebei Road
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| City |
Jinan |
| ZIP/Postal code |
250100 |
| Country |
China |
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| Platforms (1) |
| GPL19290 |
Illumina HiSeq 2500 (Oryza sativa) |
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| Samples (4)
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| Relations |
| BioProject |
PRJNA263869 |
| SRA |
SRP048923 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE62334_Table1_miRNA.txt.gz |
328.1 Kb |
(ftp)(http) |
TXT |
| GSE62334_Table2_targets.txt.gz |
4.5 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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