Comparative RNA-Seq analysis reveals potentially resistance-related genes in response to Bacterial canker of tomato
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ABSTRACT:
PROVIDER: PRJNA639037 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12002100_1.fastq.gz | Fastqsanger.gz | |||
| SRR12002100_2.fastq.gz | Fastqsanger.gz | |||
| SRR12002101_1.fastq.gz | Fastqsanger.gz | |||
| SRR12002101_2.fastq.gz | Fastqsanger.gz | |||
| SRR12002102_1.fastq.gz | Fastqsanger.gz |
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Project description:Tomato is one of the most important crops for human consumption. Unfortunately, its production is affected by diseases caused by pathogens such as the actynomicete Clavibacter michiganensis subsp. michiganens (Cmm). This pathogen is the causal agent of the bacterial canker of tomato, considered one of the most devastating tomato diseases. To date, there are not resistant varieties of commercial tomato against Cmm. However, there are wild tomato species resistant to Cmm. Using massive sequencing, we obtained the transcriptomes of the wild tomato species Solanum arcanum LA2157 and the commercial tomato Solanum lycopersicum cv. Ailsa Craig at 8 and 24 hours after Cmm challenge. We identified potential tomato tolerance-related genes by three approaches: mapping the reads to S. lycopersicum reference genome SL3.0, performing a semi de novo transcriptome assembly and a de novo transcriptome assembly. Some functional groups such as oxylipin biosynthetic process response to wounding, response to cytokinin among others, were enriched in both tomato species, suggesting a similar response, however, genes that encode proteins such as the Polyphenol oxidase E, Ankyrin and Leucine Rich Repeat receptors were overexpressed mainly in the wild tomato species, suggesting a possible role in the defense response. Here, we uncovered new candidate genes potentially related to bacterial canker tomato defense.
2020-06-13 | GSE152330 | GEO
Project description:Tomato is one of the most important crops for human consumption. Its production is affected by the actinomycete Clavibacter michiganensis subsp. michiganensis (Cmm), one of the most devastating bacterial pathogens of this crop. Several wild tomato species represent a source of natural resistance to Cmm. Here, we contrasted the transcriptomes of the resistant wild tomato species Solanum arcanum LA2157 and the susceptible species Solanum lycopersicum cv. Ailsa Craig, during the first 24 h of challenge with Cmm. We used three analyses approaches which demonstrated to be complementary: mapping to S. lycopersicum reference genome SL3.0; semi de novo transcriptome assembly; and de novo transcriptome assembly. In a global context, transcriptional changes seem to be similar between both species, although there are some specific genes only upregulated in S. arcanum during Cmm interaction, suggesting that the resistance regulatory mechanism probably diverged during the domestication process. Although S. lycopersicum showed enriched functional groups related to defense, S. arcanum displayed a higher number of induced genes related to bacterial, oomycete, and fungal defense at the first few hours of interaction. This study revealed genes that may contribute to the resistance phenotype in the wild tomato species, such as those that encode for a polyphenol oxidase E, diacyl glycerol kinase, TOM1-like protein 6, and an ankyrin repeat-containing protein, among others. This work will contribute to a better understanding of the defense mechanism against Cmm, and the development of new control methods.
| S-EPMC8618811 | biostudies-literature
Project description:This submission contains the mass spectrometry files related to the
manuscript by Llorens et al. that describes the characterization of
the proteome profile of the apoplastic fluid in Tomato leaves, and its
changes during the infection with
Pseudomonas syringae and the treatment with the resistance inducer 1-MT.
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Project description:The soil-borne bacterial pathogen Ralstonia solanacearum invades a broad range of plants through roots, resulting in wilting of the plant, but no effective protection against this disease has been developed. Two R. solanacearum resistance-inducing compounds were biochemically isolated from tobacco and identified as sclareol and cis-abienol, diterpenes. When exogenously applied to their roots, these diterpenes induced resistance to R. solanacearum in tobacco, tomato, and Arabidopsis plants without exhibiting any antimicrobial activity. Structure-activity correlation analysis of sclareol-related compounds revealed that the hydroxyl group at the eighth carbon position is responsible for the activity for inducing resistance. Microarray analysis identified many sclareol-responsive Arabidopsis genes, such as those encoding or with role in ABC transporters, biosynthesis and signaling of defense-related signal molecules, and mitogen-activated protein kinase (MAPK) cascades. Sclareol-induced R. solanacearum resistance was partially compromised in Arabidopsis mutants defective in the ABC transporter AtPDR12, the MAPK MPK3, and ethylene and abscisic acid signaling pathways. Transgenic tobacco plants in which NtPDR1, a tobacco homolog of AtPDR12, was silenced exhibited also reduced resistance. These results suggest that multiple host factors are involved in resistance to R. solanacearum induced by sclareol and its related compounds and that these compounds can be used to protect crops from bacterial wilt disease. Genes that were preferentially expressed in Arabidopsis roots 2 hours after treatment with sclareol were explored. The microarray analysis was performed in triplicate.
2011-08-18 | E-GEOD-31230 | biostudies-arrayexpress
Project description:Leaf mold disease caused by Cladosporium fulvum is a major disease in cultivated tomato plants and affects global tomato production. Some Cf genes, of which Cf-16 is an effective gene for resisting tomato leaf mold, are associated with leaf mold resistance; however, the molecular mechanism is largely unknown. We used comparative transcriptome analysis of C. fulvum-resistant (cv. Ontario7816, including the Cf-16 gene) and C. fulvum-susceptible (cv. Moneymaker) tomato lines to identify differentially expressed genes (DEGs) at 4 and 8 days postinfection with C. fulvum. Our results provide new insights into the resistance response mechanism of Cf genes to C. fulvum, especially the unique characteristics of Cf-16 in response to C. fulvum infection.
2020-01-06 | GSE133678 | GEO
Project description:The soil-borne bacterial pathogen Ralstonia solanacearum invades a broad range of plants through roots, resulting in wilting of the plant, but no effective protection against this disease has been developed. Two R. solanacearum resistance-inducing compounds were biochemically isolated from tobacco and identified as sclareol and cis-abienol, diterpenes. When exogenously applied to their roots, these diterpenes induced resistance to R. solanacearum in tobacco, tomato, and Arabidopsis plants without exhibiting any antimicrobial activity. Structure-activity correlation analysis of sclareol-related compounds revealed that the hydroxyl group at the eighth carbon position is responsible for the activity for inducing resistance. Microarray analysis identified many sclareol-responsive Arabidopsis genes, such as those encoding or with role in ABC transporters, biosynthesis and signaling of defense-related signal molecules, and mitogen-activated protein kinase (MAPK) cascades. Sclareol-induced R. solanacearum resistance was partially compromised in Arabidopsis mutants defective in the ABC transporter AtPDR12, the MAPK MPK3, and ethylene and abscisic acid signaling pathways. Transgenic tobacco plants in which NtPDR1, a tobacco homolog of AtPDR12, was silenced exhibited also reduced resistance. These results suggest that multiple host factors are involved in resistance to R. solanacearum induced by sclareol and its related compounds and that these compounds can be used to protect crops from bacterial wilt disease.
2011-08-19 | GSE31230 | GEO
Project description:Bacillus thuringiensis, a well-known and effective bio-insecticide, has attracted considerable attention as a potential biological control agent for the suppression of plant diseases. Treatment of tomato roots with a filter-sterilized cell-free filtrate (CF) of B. thuringiensis systemically suppresses bacterial wilt caused by Ralstonia solanacearum through systemic activation of the plant defense system. Comparative analysis of the expression of the Pathogenesis-Related 1(P6) [PR-1(P6)] gene, a marker for induced resistance to pathogens, in various tissues of tomato plants treated with CF on their roots suggested that the B. thuringiensis-induced defense system was activated in the leaf, stem, and main root tissues, but not in the lateral root tissue. At the same time, the growth of R. solanacearum was significantly suppressed in the CF-treated main root tissue but not in the CF-treated lateral root tissue. This distinct activation of the defense reaction and suppression of R. solanacearum were reflected by the differences in the transcriptional profiles of the main and lateral tissues in response to the CF. In the CF-treated main root tissue, but not CF-treated lateral root tissue, the expression of several salicylic acid (SA)-responsive defense-related genes was specifically induced, whereas jasmonic acid (JA)-related gene expression was either down-regulated or not induced in response to the CF. On the other hand, genes encoding ethylene (ET)-related proteins were induced equally in both the main and lateral root tissues. Taken together, the co-activation of SA-dependent signaling pathway with ET-dependent signaling pathway and suppression of JA-dependent signaling pathway may play key roles in B. thuringiensis-induced resistance to R. solanacearum in tomato plants. Gene expression was measured in main and lateral root tissues of tomato treated with Bacillus thuringiensis or distilled water-treated control at 48 hours after treatment. Two independent experiments were performed at each tissue (main root or lateral root tissue) for each treatment (Bacillus thuringiensis or distilled water control).
2013-08-29 | E-GEOD-50402 | biostudies-arrayexpress
Project description:Identification of key genes potentially related to intervertebral disc degeneration by microarray analysis
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Project description:Salt stress causes the quality change and significant yield loss of tomato. However, the resources of salt-resistant tomato were still deficient and the mechanisms of tomato resistance to salt stress were still unclear. In this study, the proteomic profiles of two salt-tolerant and salt-sensitive tomato cultivars were investigated to deciphered the salt-resistance mechanism of tomato and provide novel resources for tomato breeding. We found that there is an over-abundant proteins relevant to Nitrate and amino acids metabolisms in the Salt-tolerant cultivars. The significant increase in expression of proteins involved in Brassinolides and GABA biosynthesis were verified in salt-tolerant cultivars, strengthening the salt resistance of tomato. Meanwhile, salt-tolerant cultivars with higher abundance and activity of antioxidant-related proteins have more advantages in dealing with reactive oxygen species caused by salt stress. And the salt-tolerant cultivars had higher photosynthetic activity based on overexpression of proteins functioned in chloroplast, guaranteeing the sufficient nutrient for plant growth under salt stress. Furthermore, three key proteins were identified as important salt-resistant resources for breeding salt-tolerant cultivars, including Sterol side chain reductase, gamma aminobutyrate transaminase and Starch synthase. Our results provided series valuable strategies for salt-tolerant cultivars which can be used in future
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