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Solanum lycopersicum

ABSTRACT: Transcriptome of tomato treated with SA and inoculated with Clavibacter michiganensis subsp. michiganensis

PROVIDER: PRJDB15775 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	DRR463155.fastq.gz	Fastqsanger.gz
	DRR463156.fastq.gz	Fastqsanger.gz
	DRR463157.fastq.gz	Fastqsanger.gz
	DRR463158.fastq.gz	Fastqsanger.gz
	DRR463159.fastq.gz	Fastqsanger.gz

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Similar Datasets

Solanum lycopersicum

Project description:Transcriptome of tomato infected with Clavibacter michiganensis subsp. michiganensis

| PRJDB11160 | ENA

Transcriptome analysis of Clavibacter michiganensis subsp. michiganensis infected tomato seedlings

Project description:The gram- positive bacterial pathogen Clavibacter michiganensis subsp. michiganensis (Cmm) causes huge economic losses by infecting tomato plants worldwide. Cmm can be spread by contaminated seeds and transplants, penetrating the plant through natural openings or wounds and is transferred through the plant xylem. While in recent years significant progress has been made to elucidate plant responses to pathogenic gram-negative bacteria by gene expression studies, the molecular mechanisms that lead to disease symptoms caused by gram-positive bacteria like Cmm remain elusive. An indigenous virulent Cmm strain isolated from a farm crop of Pomodoro tomatoes in southern Greece was used for the infection of EKSTASIS F1 hybrid tomato seedlings. Here, we present the results of a deep RNA- sequencing (RNA-seq) analysis performed to characterize the dynamic expression profile of tomato genes upon Cmm infection.

2021-08-10 | GSE160971 | GEO

Proteogenomic study of Clavibacter michiganensis subsp. michiganensis strain NCPPB382

Project description:Clavibacter michiganensis subsp. michiganensis is an important Gram-positive phytopathogenic bacteria that causes bacterial wilt and canker in tomato. The genome of the type strain, NCPPB382, has been sequenced and annotated, however comparative genomics suggests that certain regions are under- or misannotated. In order to improve the genome annotation, we have undertaken a proteogenomic study of this important pathogen. Samples were grown in culture and the proteome of the pellet and supernatant were analyzed separately using shotgun HPLC-MS/MS. These proteomics datasets were analyzed and a number of missing gene were found and a number of existing gene calls were modified.

2019-01-31 | PXD006787 | Pride

Comparative RNA-Seq analysis reveals potentially resistance-related genes in response to Bacterial canker of tomato

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

Solanum lycopersicum

Project description:Tomato plants treated inoculated with Kocuria rhizophila

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Transcriptome analysis of Clavibacter michiganensis subsp. michiganensis infected tomato seedlings

Project description:Transcriptome analysis of Clavibacter michiganensis subsp. michiganensis infected tomato seedlings

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The Solanum lycopersicum WRKY3 Transcription Factor Regulates Salt Stress Tolerance In Tomato

Project description:The tomato SlWRKY3 transcription factor was overexpressed in cultivated tomato (Solanum lycopersicum)and transgenic plants transcriptome was compared to that of wild-type plants.

2016-03-15 | GSE74504 | GEO

RNA-seq of Solanum lycopersicum cv Micro-Tom (wild-type and 35S::AtCKX2) infected with the fungus Moniliophthora perniciosa

Project description:We report that Moniliophthora perniciosa biotype-S, which infects Solanaceae, manipulates the tomato Micro-Tom (MT) cytokinin (CK) metabolism. We evaluated the transcriptome of wild-type MT plants and of the transgenic line that overexpresses the Arabidopsis CYTOKININ OXIDASE-2 gene (35S::AtCKX2) inoculated or not with M. perniciosa at 12, 24, and 48 hours after inoculation (hai), and 5, 10, 20, and 30 days after inoculation (dai).

2021-08-24 | GSE153345 | GEO

iSB09 and iCB elicit ABA-responsive gene expression in Solanum lycopersicum seedlings

Project description:To compare the genome-wide transcriptional effect of ABA and iSB09 in tomato plants, we performed RNA-seq analysis of mock-, 10 uM ABA- or 20 uM iSB09-treated plants. Differential gene expression analysis between mock- and ABA-treated or iSB09-treated seedlings was done with DESeq2 and genes with an absolute value of log2 fold change (log2FC) > 1 or (log2FC) < -1 and p-adjusted value (padj) < 0.05 were selected. iSB09 upregulated and downregulated genes represent a subset of the ABA-responsive genes, which reflects the activation of PYL1-like and PYL4-like ABA receptors in tomato seedlings. Additionally, to compare the genome-wide transcriptional effect of ABA and iCB in tomato plants, we performed RNA-seq analysis of mock-, 10 uM ABA- or 10 uM iCB-treated plants. Differential gene expression analysis between mock- and ABA-treated or iCB-treated seedlings was done with DESeq2 and genes with an absolute value of log2 fold change (log2FC) > 1 or (log2FC) < -1 and p-adjusted value (padj) < 0.05 were selected. iCB mimics ABA transcriptional response through activation of the three subfamilies of ABA receptors.

2024-07-22 | GSE256238 | GEO

Biological Control of Root-Knot Nematode Meloidogyne incognita Infection of Tomato (Solanum lycopersicum L.) by the Oomycete Biocontrol Agent Pythium oligandrum

Project description:The biocontrol agent Pythium oligandrum, which is a member of phylum Oomycota, can control diseases caused by a taxonomically wide range of plant pathogens, including fungi, bacteria, and oomycetes. However, whether P. oligandrum could control diseases caused by plant root-knot nematodes (RKNs) was unknown. We investigated a recently isolated P. oligandrum strain GAQ1, and the P. oligandrum CBS530.74 strain, for the control of RKN Meloidogyne incognita infection of tomato (Solanum lycopersicum L.). Initially, P. oligandrum culture filtrates were found to be lethal to M. incognita second-stage juveniles (J2s) with up to 84% mortality at 24 h after treatment compared to 14% in the control group. Consistent with the lethality to M. incognita J2s, tomato roots treated with P. oligandrum culture filtrates reduced the attraction of nematodes, and the number of nematodes penetrating the roots was reduced by up to 78%. In a greenhouse pot trial, P. oligandrum GAQ1 inoculation of tomato plants significantly reduced the gall number by 58% in plants infected with M. incognita. Notably, P. oligandrum GAQ1 mycelial treatment significantly increased tomato plant height (by 36%), weight (by 27%), and root weight (by 48%). Transcriptome analysis of tomato seedling roots inoculated with the P. oligandrum GAQ1 strain identified ~2,500 differentially expressed genes. The enriched GO terms and annotations in the up-regulated genes suggested modulation of plant hormone-signaling and defense-related pathways in response to P. oligandrum. In conclusion, our results support that P. oligandrum GAQ1 can serve as a potential biocontrol agent for M. incognita control in tomato. Multiple mechanisms appear to contribute to the biocontrol effect involving direct inhibition of M. incognita, potential priming of tomato plant defenses, and plant growth promotion.

2024-04-01 | GSE262653 | GEO

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