Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1018203 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR26081500_1.fastq.gz | Fastqsanger.gz | |||
| SRR26081500_2.fastq.gz | Fastqsanger.gz | |||
| SRR26081501_1.fastq.gz | Fastqsanger.gz | |||
| SRR26081501_2.fastq.gz | Fastqsanger.gz | |||
| SRR26081502_1.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).
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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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