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| Status |
Public on Jul 10, 2009 |
| Title |
High-throughput pyrosequencing of plant virus small RNAs |
| Organisms |
Tomato yellow leaf curl virus; Melon necrotic spot virus; Cymbidium ringspot virus; Potato virus X; Turnip mosaic virus; Pepper mild mottle virus; Tobacco rattle virus; Cucumber mosaic virus; Watermelon mosaic virus |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
|
| Summary |
Plant virus infection involves the production of viral small RNAs (vsRNAs) with the potential to associate with distinct Argonaute (AGO)-containing silencing complexes and mediate diverse silencing effects on RNA and chromatin. We used multiplexed, high-throughput pyrosequencing to profile populations of vsRNAs from plants infected with viruses from different genera. Sense and antisense vsRNAs of 20 to 24 nucleotides (nts) spread throughout the entire viral genomes in an overlapping configuration; virtually all genomic nucleotide positions were represented in the dataset. We present evidence to suggest that every genomic position could be a putative cleavage site for vsRNA formation, although viral genomes contain specific regions that serve as preferential sources of vsRNA production. Hotspots for vsRNAs of 21-, 22-, and 24-nt usually coincide in the same genomic regions, indicating similar target affinities among Dicer-like (DCL) enzymes. In the light of our results, the overall contribution of perfectly base paired double-stranded RNA and imperfectly base paired structures within single-stranded RNA to vsRNA formation is discussed. Our census of vsRNAs extends the current view of the distribution and composition of vsRNAs in virus-infected plants, and contributes to define a more comprehensive scenario of vsRNA biogenesis and their regulatory functions in plants
Raw data files are available on our FTP site:
ftp://ftp.ncbi.nlm.nih.gov/pub/geosup/Series/GSE16996
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| Overall design |
10 samples examined: Arabidopsis plants infected with TRV, TuMV or CMV; Nicothiana benthamiana plants infected with CymRSV, PVX or PMMoV; Cucumis melo plants infected with MNSV, quimeric MNSV or WMV and Solanum lycopersicum plants infected with TYLCV.
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| |
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| Contributor(s) |
Donaire L, Wang Y, Gonzalez-Ibeas D, Mayer KF, Aranda MA, Llave C |
| Citation(s) |
19665162 |
| |
| Submission date |
Jul 08, 2009 |
| Last update date |
Jun 11, 2013 |
| Contact name |
Yu Wang |
| E-mail(s) |
yu.1.wang@googlemail.com
|
| Organization name |
Leibniz Supercomputing Centre
|
| Department |
High performance computing
|
| Lab |
Big Data for Life Science
|
| Street address |
Boltzmannstrasse 1
|
| City |
Garchinig |
| ZIP/Postal code |
85748 |
| Country |
Germany |
| |
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| Platforms (9)
|
| GPL9368 |
454 GS FLX (Tobacco rattle virus) |
| GPL9369 |
454 GS FLX (Turnip mosaic virus) |
| GPL9370 |
454 GS FLX (Cucumber mosaic virus) |
| GPL9371 |
454 GS FLX (Cymbidium ringspot virus) |
| GPL9372 |
454 GS FLX (Potato virus X) |
| GPL9373 |
454 GS FLX (Pepper mild mottle virus) |
| GPL9374 |
454 GS FLX (Melon necrotic spot virus) |
| GPL9375 |
454 GS FLX (Watermelon mosaic virus) |
| GPL9376 |
454 GS FLX (Tomato yellow leaf curl virus) |
|
| Samples (10)
|
| GSM425419 |
Tobacco rattle virus (TRV) derived small RNAs |
| GSM425420 |
Turnip mosaic virus (TuMV) derived small RNAs |
| GSM425421 |
Cucumber mosai virus (CMV) derived small RNAs |
| GSM425422 |
Cymbidium ringspot virus (CymRSV) derived small RNAs |
| GSM425423 |
Potato virus X (PVX) derived small RNAs |
| GSM425424 |
Pepper mild mottle virus (PMMoV) derived small RNAs |
| GSM425425 |
Melon necrotic spot virus (MNSV) derived small RNAs |
| GSM425426 |
Watermelon mosaic virus (WMV) derived small RNAs |
| GSM425427 |
Tomato yellow leaf curl virus (TYLCV) derived small RNAs |
| GSM425428 |
Melon necrotic spot virus (MNSV) chimeric virus derived small RNAs |
|
| Relations |
| BioProject |
PRJNA117319 |
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