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| Status |
Public on Oct 21, 2013 |
| Title |
Phytophthora have distinct endogenous small RNA populations that include short interfering and microRNAs: Phytophthora ramorum small RNA |
| Organism |
Phytophthora ramorum |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
|
| Summary |
Deep sequencing of small RNAs from three Phytophthora species, P. infestans, P. ramorum and P. sojae, was done to systematically analyze small RNA-generating components of Phytophthora genomes. We found that each species produces two distinct small RNA populations that are predominantly 21- or 25-nucleotides long. We present evidence that 25-nucleotide small RNAs are short-interfering RNAs that silence repetitive genetic elements. In contrast, 21-nucleotide small RNAs are associated with inverted repeats, including a novel microRNA family, and may function at the post-transcriptional level.
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| Overall design |
Phytophthora ramorum mycelium small RNAs were sequenced and aligned to the P. ramorum genome for analysis.
*Raw data files (fastq) are unavailable for this study.
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| Contributor(s) |
Fahlgren N, Bollmann SR, Kasschau KD, Cuperus JT, Press CM, Sullivan CM, Chapman EJ, Hoyer JS, Gilbert KB, Grünwald NJ, Carrington JC |
| Citation(s) |
24204767 |
| |
| Submission date |
Aug 20, 2013 |
| Last update date |
Jan 20, 2014 |
| Contact name |
James C Carrington |
| E-mail(s) |
jcarrington@danforthcenter.org
|
| Phone |
314-587-1202
|
| Organization name |
Donald Danforth Plant Science Center
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| Lab |
James C. Carrington
|
| Street address |
975 North Warson Road
|
| City |
Saint Louis |
| State/province |
MO |
| ZIP/Postal code |
63132 |
| Country |
USA |
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| Platforms (1) |
| GPL17597 |
454 GS 20 (Phytophthora ramorum) |
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| Samples (1) |
| GSM1212965 |
Phytophthora ramorum mycelium small RNA |
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| This SubSeries is part of SuperSeries: |
| GSE50033 |
Phytophthora have distinct endogenous small RNA populations that include short interfering and microRNAs |
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| Relations |
| BioProject |
PRJNA215844 |
