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| Status |
Public on Jul 28, 2021 |
| Title |
Non-coding RNAs in the interaction between rice and Meloidogyne graminicola |
| Organism |
Oryza sativa Japonica Group |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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| Summary |
In this study we generated small RNA libraries from tissues rice plants infected with Meloidogyne graminicola (Mg)3 days postinoculation as well as from uninfected rice plants. The goal was to study the behaviour of small RNA (miRNA and siRNAs) in response to Mg infection. We combine the expression data gathered from this experiment together with degradome sequencing to predict the targets of differentially expressed miRNAs. Expression was validated using RT-qPCR. The small RNA sequencing datasets were also used with literature annotated siRNA loci for differential expression analysis. DNA methylation data and total RNA sequencing data were used to find siRNAs that were candidates to regulate gene expression through DNA methylation of promoter regions.
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| Overall design |
Small RNA sequencing was done on RNA extracted from rice roots under two experimental conditions: infection with Meloidogyne graminicola and mock infection (three replicates per condition).
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| Contributor(s) |
Verstraeten B, Reza Atighi M, De Meyer T, Kyndt T |
| Citation(s) |
34284724 |
| |
| Submission date |
Aug 14, 2020 |
| Last update date |
Jul 28, 2021 |
| Contact name |
Bruno Verstraeten |
| E-mail(s) |
bruno.verstraeten@ugent.be
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| Organization name |
Ghent University
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| Street address |
/
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| City |
Ghent |
| State/province |
Oost-Vlaanderen |
| ZIP/Postal code |
9000 |
| Country |
Belgium |
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| Platforms (1) |
| GPL22250 |
Illumina HiSeq 3000 (Oryza sativa Japonica Group) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA657181 |
| SRA |
SRP277501 |
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