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Genome Information for Oryza sativa
Purpose: The goals of this study are to detect the small RNAs generated from the PMS1T gene and the cleavage sites mediated by small RNAs (microRNAs or phasiRNAs).
Methods: The rice panicles were collected in liquid nitrogen and their total RNA were extracted for library construction and subsequent sequencing on an Illumina HiSeq 2000.
Results: Using an optimized data analysis workflow, we mapped a series of small RNAs generated from the PMS1T region of the rice genome; most of these small RNAs were 21-nt phasiRNAs. The results from PARE sequencing validated the cleavage site on the PMS1T transcript, with the cleavage mediated by miR2118.
Conclusions: Our results show that the 21-nt phasiRNA generated from the PMS1T transcript are associated with photoperiod-sensitive male sterility in rice.
Overall design: The young panicles were collected for the sequencing from different sizes of genotypes Nongken 58S and NIL(MH), plus transgenic plants, all grown under long-day (daylength>14 h) and short-day (daylength<13.5 h) conditions.
| Accession | PRJNA335548; GEO: GSE84885 |
| Scope | Multiisolate |
| Organism | Oryza sativa Japonica Group[Taxonomy ID: 39947] Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa; Oryza sativa Japonica Group |
| Publications | Fan Y et al., "PMS1T, producing phased small-interfering RNAs, regulates photoperiod-sensitive male sterility in rice.", Proc Natl Acad Sci U S A, 2016 Dec 27;113(52):15144-15149 |
| Submission | Registration date: 27-Jul-2016
Meyers lab, Donald Danforth Plant Science Center |
| Relevance | Agricultural |
Project Data:
| Resource Name | Number
of Links |
|---|
| Sequence data |
| SRA Experiments | 36 |
| Publications |
| PubMed | 1 |
| PMC | 1 |
| Other datasets |
| BioSample | 36 |
| GEO DataSets | 1 |