Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1016149 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR26047700.fastq.gz | Fastqsanger.gz | |||
| SRR26047701.fastq.gz | Fastqsanger.gz | |||
| SRR26047702.fastq.gz | Fastqsanger.gz | |||
| SRR26047703.fastq.gz | Fastqsanger.gz | |||
| SRR26047704.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: To understand the molecular mechanisms involved in disease development during plant-nematode interactions. Methods: We have taken a comprehensive transcriptomic approach to investigate the expression of both tomato and RKN genes in tomato roots at five infection time points from susceptible plants (PR: Pusa Ruby) and two infection time points from resistant plants (M36: Transgenic MM line), grown under soil conditions. Results: Differentially expressed genes during susceptible (1827 tomato, 462 RKN) and resistance (25 tomato, 160 RKN) interactions were identified and a set of genes were validated by qRT-PCR. Conclusion: Our findings, for the first time, provide insights into the transcriptome dynamics of both tomato and RKN during susceptible and resistance interactions and reveal involvement of a complex network of biosynthetic pathways during disease development.
2017-08-21 | GSE88763 | GEO
Project description:High-throughput sequence analysis of small RNAs of TYLCV-tolerant (containing tolerance gene Ty-1) and susceptible varieties indicated that miRNA-like vsRNAs and secondary vsiRNAs are mainly contributed to hotpots. Interestingly, various characteristics of vsRNAs among each sample are consistent, but in different number of expression; Deep sequencing of degradome provided evidence for the function of vsRNAs-mediated viral transcripts slicing; And bisulfite sequencing PCR suggested the geminivirus DNA methylation induced by vsRNAs. Comparison of the expression quantity and trend of viral DNA, mRNA and vsRNA inferred that the quantity of vsRNAs is significantly corresponding to the expression level of viral mRNA. Nevertheless, vsRNAs had finite effect on inhibition of virus replication and expression. Here, we also speculated that by RDR catalysis of vsRNAs amplification, the tolerance gene Ty-1 may take an effective inhibition of viral transcription at the beginning of TYLCV infection. Examination of 6 different sRNA and 4 degradome library in 2 tomato material. The main result of our paper is distinguish the host plant sRNA and viral-derived sRNA from the .fa files (MMS_21dpi, 30dpi and TY1S_21dpi, 30dpi).
2016-08-22 | E-GEOD-50085 | biostudies-arrayexpress
Project description:Alternative splicing (AS) is a critical post-transcriptional regulatory mechanism in eukaryotes. While infection with Ralstonia solanacearum GMI1000 significantly alters plant AS patterns, the underlying molecular mechanisms remain unclear. Herein, we investigate the effects of GMI1000 Type III secretion system (T3SS) effector proteins on AS in the tomato cultivar Heinz 1706. RNA sequencing (RNA-seq) confirmed genome-wide AS changes induced by the T3SS in tomato, in-cluding 1386 differential alternative splicing events in 1023 differentially alternatively spliced genes, many of which are associated with plant defense. Seven nucleus-localized Type III effec-tors(T3Es) were transiently expressed in an RLPK splicing reporter system transgenic tobacco, identifying RipP2 as an effector that modulates AS levels. Sequence analysis, protein-protein in-teraction assays, and AlphaFold2 structural predictions revealed that RipP2 interacts with the tomato splicing factor SR34a.Furthermore, RipP2 acetylates a conserved lysine at position 132 within the SWQDLKD motif of SR34a, regulating its splicing pattern in defense-related genes and modulating plant immunity. This study elucidates how the "Rip-SR34a module" influences plant immune responses by regulating the alternative splicing of immune-related genes, providing new insights into the molecular mechanisms of pathogen-plant interactions, particularly in splicing regulation.
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Project description:BACKGROUND: The tomato psyllid, Bactericera cockerelli Šulc (Hemiptera: Triozidae), is a pest of solanaceous crops such as tomato (Solanum lycopersicum L.) in the U.S. and vectors the disease-causing pathogen ‘Candidatus Liberibacter solanacearum’. Currently, the only effective strategies for controlling the diseases associated with this pathogen involve regular pesticide applications to manage psyllid population density. However, such practices are unsustainable and will eventually lead to widespread pesticide resistance in psyllids. Therefore, new control strategies must be developed to increase host-plant resistance to insect vectors. For example, expression of constitutive and inducible plant defenses can be improved through selection. Currently, it is still unknown whether psyllid infestation has any lasting consequences on tomato plant defense or tomato plant gene expression in general. RESULTS: To characterize the genes putatively involved in tomato defense against psyllid infestation, RNA was extracted from psyllid-infested and uninfested tomato leaves (Moneymaker) three weeks post-infestation. Transcriptome analysis identified 362 differentially expressed genes. These differentially expressed genes were primarily associated with defense responses to abiotic/biotic stress, transcription/translation, cellular signaling/transport, and photosynthesis. These gene expression changes suggested that tomato plants underwent a reduction in plant growth/health in exchange for improved defense against stress that was observable three weeks after psyllid infestation. Consistent with these observations, tomato plant growth experiments determined that the plants were shorter three weeks after psyllid infestation. Furthermore, psyllid nymphs had lower survival rates on tomato plants that had been previously psyllid infested. CONCLUSION: These results suggested that psyllid infestation has lasting consequences for tomato gene expression, defense, and growth.
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2022-04-07 | MODEL2111120001 | BioModels
Project description:Tomato plants are commonly attacked by herbivorous mites, including by generalist Tetranychus urticae and specialists Tetranychus evansi and Aculops lycopersici. Mite feeding induces plant defense responses that reduce mite performance. However, via poorly understood mechanisms, T. evansi and A. lycopersici suppress plant defenses and, consequently, maintain a high performance on tomato. Accordingly, on a shared host, non-adapted T. urticae can be facilitated by either of the specialist mites, likely via the suppression of plant defenses. To better understand defense suppression and indirect plant-mediated interactions between herbivorous mites, we used microarrays to analyze transcriptomic changes in tomato after attack by either a single mite species (T. urticae, T. evansi, A. lycopersici) or two species simultaneously (T. urticae plus T. evansi or T. urticae plus A. lycopersici). Additionally, we assessed mite-induced changes in defense-associated phytohormones using LC-MS/MS. Compared to non-infested controls, jasmonates (JAs) and salicylate (SA) accumulated to higher amounts upon all mite-infestation treatments, but lowest increases were detected after single infestations with defense-suppressors. Strikingly, whereas 8 to 10% of tomato genes was differentially expressed upon single infestations with T. urticae or A. lycopersici, only 0.1% was altered in T. evansi-infested plants. Transcriptome analysis of dual-infested leaves revealed that T. evansi dampened T. urticae-triggered host responses on a genome-wide scale, while A. lycopersici primarily suppressed T. urticae-induced JA defenses. Our results provide valuable new insights into the mechanisms underlying host defense suppression and the plant-mediated facilitation of competing herbivores.
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Project description:Arbuscular mycorrhizal symbiosis is a predominant relationship between plant and arbuscular mycorrhizal fungi. To idendify arbuscular mycorrhiza responsive miRNAs, small RNA libraries were constructed in tomato roots colonized with Rhizophagus irregularis and without Rhizophagus irregularis. We identify miRNAs in tomato roots and provide a new profile of tomato miRNAs. And we found that some miRNAs were responsive to arbuscular mycorrhiza by comparing miRNAs in treatment with that in control.
2016-07-20 | GSE76204 | GEO
Project description:Tomato plants are submitted to a high diversity of herbivory pests, among them the leafminer Tuta absoluta, considered as one of the most important threat on the tomato worldwide production. In spite of its susceptibility to this pest, a better understanding of the tomato plant response to T. absoluta herbivory will help defining plant resistance traits and enlarging the range of possibilities for an efficient integrated pest management strategy. We analyzed the transcriptomic response in leaves of tomato (cv. Better Bush) submitted to the herbivory of T. absoluta larvae after 5h and 24h.
2022-04-18 | GSE200795 | GEO
Project description:The whitefly, Bemisia tabaci MEAM1 is a devastating vector capable of transmitting hundreds of plant viruses, including Tomato yellow leaf curl virus (TYLCV), to important food and fiber crops. Here we performed genome-wide profiling of micro RNAs (miRNAs) and piwi-interacting RNAs (piRNAs) in whiteflies after feeding on TYLCV-infected tomato or uninfected tomato for 24, 48 and 72 h. Overall, 160 miRNAs were discovered, 68 of which were conserved and 92 were B. tabaci-specific miRNAs. Majority of the genes that were predicted to be targeted by miRNAs had gene ontologies related to metabolic processes. We identified two miRNAs that were differentially expressed in whiteflies when fed on TYLCV-infected tomato compared to whiteflies that fed on uninfected tomato. The identified piRNAs were expressed as clusters throughout the whitefly genome. A total of 53 piRNA clusters were expressed across all time points and treatments, while 5 piRNA clusters were exclusively expressed in whiteflies that fed on TYLCV-infected tomato, and 24 clusters were exclusively expressed in whiteflies that fed on uninfected tomato. Approximately 62% of all identified piRNAs were derived from non-coding sequences that included intergenic regions, introns, and UTRs with unknown functions. The remaining 38% of piRNAs were derived from coding sequences (CDS) and repeat elements. Transposable elements targeted by piRNA clusters included both class I retrotransposons such as Gypsy, Copia, and LINEs and class II DNA transposons such as MITE, hAT, and TcMar. Lastly, six protein coding genes were targeted in whiteflies that fed on TYLCV-infected tomato. Information on how TYLCV influences miRNA and piRNA expression in whiteflies provides a greater understanding of regulatory pathways involved in mediating whitefly-virus interactions, and will facilitate the identification of novel targets for RNAi control.
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