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Series GSE87651 Query DataSets for GSE87651
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
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.
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.
Contributor(s) Kaur P, Joshi G, Shukla N, Jagannath A, Agarwal M, Goel S, Kumar A
Citation(s) 28426683
Submission date Oct 05, 2016
Last update date May 15, 2019
Contact name Gopal Joshi
Phone +91-11-27662609
Organization name Delhi University
Department Department of Botany
Lab Plant Genomics & Stress Biology
Street address First Floor
City New Delhi
State/province Delhi
ZIP/Postal code 110007
Country India
Platforms (1)
GPL16345 Illumina HiSeq 2000 (Solanum lycopersicum)
Samples (11)
GSM2337660 Stage 0 uninfected
GSM2337661 Stage 1 uninfected
GSM2337662 Stage 1 infected
BioProject PRJNA345485
SRA SRP090890

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Supplementary file Size Download File type/resource
GSE87651_RAW.tar 279.5 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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