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| Status |
Public on Jun 12, 2017 |
| Title |
Genome-wide identification and characterization of miRNAome from tomato roots (Solanum lycopersicum) and root-knot nematode (Meloidogyne incognita) during susceptible and resistant interactions. |
| Organism |
Solanum lycopersicum |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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| Summary |
RKNs are economically most damaging, obligate sedentary endoparasites that form giant cells within host roots to obtain nutrition and complete their life cycle. We report genome-wide identification of miRNAs from both host and RKN using RKN-infected susceptible tomato roots through high-throughput sequencing. Eleven small RNA libraries were made from five disease development stages, their five corresponding uninfected development stages and uninfected development stage 0. A total of 52 conserved miRNAs, 4 variants of conserved miRNAs and 281 novel miRNAs of host were identified. A significantly upregulated expression of majority of the miRNAs was observed during susceptible response and downregulated expression during resistance response through qRT-PCR. The miRNA targets were predicted and validated through 5’RLM-RACE. Furthermore, correlation between the expression profile of selected conserved miRNAs viz., miR164, miR156, miR396, miR159, and novel Sly_miRNA996 with their target transcription factors viz., NAC, SBP, GRF1, GAMYB-like, and MYB-like, respectively was also determined. This study suggests a potential role of host miRNAs in regulating transcription factor genes involved in plant developmental processes and defense responses during RKN infection. Additionally, 328 RKN miRNAs including 38 conserved miRNAs, 106 novel miRNAs, and 184 candidate novel miRNAs were identified from same dataset. The differential expression of conserved and RKN-specific miRNAs at different development stages of nematode in tomato roots suggests their probable role during nematode development and adaptation to parasitic behavior. This is the most comprehensive study reporting the identification and characterization of miRNAs from both tomato and RKN in five different disease development stages under soil grown conditions and their potential roles during RKN infection in tomato roots.
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| Overall design |
Total eleven small RNA libraries of root {Stage 0 uninfected (SO UI), Stage 1 uninfected (S1 UI), Stage 1 infected (S1 I), Stage 2 uninfected (S2 UI), Stage 2 infected (S2 I), Stage 3 uninfected (S3 UI), Stage 3 infected (S3 I), Stage 4 uninfected (S4 UI), Stage 4 infected (S4 I), Stage 5 uninfected (S5 UI), stage 5 infected (S5 I)} were constructed and high-throughput sequencing was performed using HiSeq 200 sequencing system.
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| Contributor(s) |
Kaur P, Joshi G, Shukla N, Jagannath A, Agarwal M, Goel S, Kumar A |
| Citation(s) |
28426683 |
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| Submission date |
Oct 05, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Gopal Joshi |
| E-mail(s) |
gopal_joshii@yahoo.com
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| Phone |
+91-11-27662609
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| Organization name |
Delhi University
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| Department |
Department of Botany
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| Lab |
Plant Genomics & Stress Biology
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| Street address |
First Floor
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| City |
New Delhi |
| State/province |
Delhi |
| ZIP/Postal code |
110007 |
| Country |
India |
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| Platforms (1) |
| GPL16345 |
Illumina HiSeq 2000 (Solanum lycopersicum) |
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| Samples (11)
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| Relations |
| BioProject |
PRJNA345485 |
| SRA |
SRP090890 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE87651_RAW.tar |
279.5 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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