Cucumis sativus
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PROVIDER: PRJNA707667 | ENA |
REPOSITORIES: ENA
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Project description:Transcriptome data of cucumber before and after root-knot nematode infection
| PRJNA707668 | ENA
Project description:Root-knot nematodes (RKN) represent extensive challenges to Cucurbitaceae crops. However, Cucumis metuliferus (Cm) is known to be resistant to Meloidogyne incognita (Mi) infections. Thus, analysis of differentially expressed genes may lead to a comprehensive gene expression profiling of the incompatible Cm-Mi interaction. In this study, the time-course transcriptome of Cm against Mi infection was monitored using RNA-Seq. More than 170000 transcripts were examined in Cm roots, and 2430 genes were subsequently identified as differentially expressed in response to Mi infection. Based on function annotation and orthologs finding, the potential mechanism of transcriptional factor, cytoskeleton, pathogen-related genes and plant hormone were assessed at the transcription level. A comparison of gene expression levels between Mi-infected Cm and cucumber plants revealed that cytoskeleton-related genes are key regulators of Cm resistance to Mi. We herein discuss the dual nature of cytoskeleton-related genes in the susceptibility and resistance of plant hosts to Mi. Our observations provide novel insights into the responses of Cm to Mi at the transcriptome level. The data generated in this study may be useful for elucidating the mechanism underlying resistance to RKNs in cucurbitaceous crops.
2017-01-01 | S-EPMC5471208 | BioStudies
Project description:BACKGROUND: Nitrogen is a principal limiting nutrient in plant growth and development. Among factors that may limit NO3- assimilation, Fe potentially plays a crucial role being a metal cofactor of enzymes of the reductive assimilatory pathway. Very few information is available about the changes of nitrogen metabolism occurring under Fe deficiency in Strategy I plants. The aim of this work was to study how cucumber (Cucumis sativus L.) plants modify their nitrogen metabolism when grown under iron deficiency. RESULTS: The activity of enzymes involved in the reductive assimilation of nitrate and the reactions that produce the substrates for the ammonium assimilation both at root and at leaf levels in Fe-deficient cucumber plants were investigated. Under Fe deficiency, only nitrate reductase (EC 1.7.1.1) activity decreased both at the root and leaf level, whilst for glutamine synthetase (EC 6.3.1.2) and glutamate synthase (EC 1.4.1.14) an increase was found. Accordingly, the transcript analysis for these enzymes showed the same behaviour except for root nitrate reductase which increased. Furthermore, it was found that amino acid concentration greatly decreased in Fe-deficient roots, whilst it increased in the corresponding leaves. Moreover, amino acids increased in the xylem sap of Fe-deficient plants. CONCLUSIONS: The data obtained in this work provided new insights on the responses of plants to Fe deficiency, suggesting that this nutritional disorder differentially affected N metabolism in root and in leaf. Indeed under Fe deficiency, roots respond more efficiently, sustaining the whole plant by furnishing metabolites (i.e. aa, organic acids) to the leaves.
2012-01-01 | S-EPMC3539955 | BioStudies
Project description:Trichomes are epidermal hair-like structures that function in plant defence against biotic and abiotic stresses. Extensive studies have been performed on foliar trichomes development in Arabidopsis and tomato, but the molecular mechanism of fruit trichome formation remains elusive. Cucumber fruit is covered with trichomes (spines) that directly affect the appearance and quality of cucumber products. Here, we characterized the fruit spine development in wild-type (WT) cucumber and a spontaneous mutant, tiny branched hair (tbh). Our data showed that the cucumber trichome was multicellular and non-glandular, with malformed organelles and no endoreduplication. Fruit spine development was generally homogenous and marked by a rapid base expansion stage. Trichomes in the tbh mutant were tiny and branched, with increased density and aberrant cell shape. Transcriptome profiling indicated that meristem-related genes were highly enriched in the upregulated genes in the tbh versus the WT, as well as in WT spines after versus before base expansion, and that polarity regulators were greatly induced during spine base expansion. Quantitative reverse transcription PCR and in situ hybridization confirmed the differential expression of CUP-SHAPED COTYLEDON3 (CUC3) and SHOOT MERISTEMLESS (STM) during spine development. Therefore, cucumber trichomes are morphologically different from those of Arabidopsis and tomato, and their development may be regulated by a distinct pathway involving meristem genes and polarity regulators.
2014-01-01 | S-EPMC4144775 | BioStudies
Project description:The oomycete pathogen, Pseudoperonospora cubensis, is the causal agent of downy mildew on cucurbits, and at present, no effective resistance to this pathogen is available in cultivated cucumber (Cucumis sativus). To better understand the host response to a virulent pathogen, we performed expression profiling throughout a time course of a compatible interaction using whole transcriptome sequencing. As described herein, we were able to detect the expression of 15,286 cucumber genes, of which 14,476 were expressed throughout the infection process from 1 day post-inoculation (dpi) to 8 dpi. A large number of genes, 1,612 to 3,286, were differentially expressed in pair-wise comparisons between time points. We observed the rapid induction of key defense related genes, including catalases, chitinases, lipoxygenases, peroxidases, and protease inhibitors within 1 dpi, suggesting detection of the pathogen by the host. Co-expression network analyses revealed transcriptional networks with distinct patterns of expression including down-regulation at 2 dpi of known defense response genes suggesting coordinated suppression of host responses by the pathogen. Comparative analyses of cucumber gene expression patterns with that of orthologous Arabidopsis thaliana genes following challenge with Hyaloperonospora arabidopsidis revealed correlated expression patterns of single copy orthologs suggesting that these two dicot hosts have similar transcriptional responses to related pathogens. In total, the work described herein presents an in-depth analysis of the interplay between host susceptibility and pathogen virulence in an agriculturally important pathosystem.
2012-01-01 | S-EPMC3335828 | BioStudies
Project description:Fifteen years after transfer to hops, hop stunt viroid-grapevine (HSVd-g) was replaced by HSVd-hop (HSVd-h), a sequence variant that contains changes at five different positions. HSVd-g54 is a laboratory mutant derived from HSVd-g that differs from its progenitor by a single G to A substitution at position 54. While infection by HSVd-h induces only mild stunting in cucumber (Cucumis sativus L.), HSVd-g54 induces much more severe symptoms in this indicator host. Comparison of transcriptome profiles of cucumber infected with HSVd-h or HSVd-g54 with those of mock-inoculated controls obtained by whole transcriptome shotgun sequencing revealed that many genes related to photosynthesis were down-regulated following infection. In contrast, genes encoding RNA-dependent RNA polymerase 1 (CsRDR1), especially CsRDR1c1 and CsRDR1c2, as well as those related to basal defense responses were up-regulated. Expression of genes associated with phytohormone signaling pathways were also altered, indicating that viroid infection initiates a complex array of changes in the host transcriptome. HSVd-g54 induced an earlier and stronger response than HSVd-h, and further examination of these differences will contribute to a better understanding of the mechanisms that determine viroid pathogenicity.
2017-01-01 | S-EPMC5733102 | BioStudies
Project description:BACKGROUND:Root-knot nematodes transform vascular host cells into permanent feeding structures to withdraw nutrients from the host plant. Ecotypes of Arabidopsis thaliana can display large quantitative variation in susceptibility to the root-knot nematode Meloidogyne incognita, which is thought to be independent of dominant major resistance genes. However, in an earlier genome-wide association study of the interaction between Arabidopsis and M. incognita we identified a quantitative trait locus harboring homologs of dominant resistance genes but with minor effect on susceptibility to the M. incognita population tested. RESULTS:Here, we report on the characterization of two of these genes encoding the TIR-NB-LRR immune receptor DSC1 (DOMINANT SUPPRESSOR OF Camta 3 NUMBER 1) and the TIR-NB-LRR-WRKY-MAPx protein WRKY19 in nematode-infected Arabidopsis roots. Nematode infection studies and whole transcriptome analyses using the Arabidopsis mutants showed that DSC1 and WRKY19 co-regulate susceptibility of Arabidopsis to M. incognita. CONCLUSION:Given the head-to-head orientation of DSC1 and WRKY19 in the Arabidopsis genome our data suggests that both genes may function as a TIR-NB-LRR immune receptor pair. Unlike other TIR-NB-LRR pairs involved in dominant disease resistance in plants, DSC1 and WRKY19 most likely regulate basal levels of immunity to root-knot nematodes.
| S-EPMC7020509 | BioStudies
Project description:Six putative ?-galactosidase genes (?-Gals), three acid forms (CsGAL1, CsGAL2, CsGAL3) and three alkaline forms (CsAGA1, CsAGA2, CsAGAL3), were found in the cucumber genome. It is interesting to know the expression pattern and possible function of these ?-Gals in the cucumber plant since it is a stachyose-translocating species. In this study, full-length cDNAs of six ?-Gals were cloned and heterologously expressed. The result showed that all recombinant proteins revealed acid or alkaline ?-Gal activities with different substrate specificities and pH or temperature responding curves, indicating their distinct roles in cucumber plants. Phylogenetic analysis of collected ?-Gal amino acid sequences from different plants indicated that the ancestor of both acid and alkaline ?-Gals existed before monocots and dicots separated. Generally, six ?-Gal genes are universally expressed in different cucumber organs. CsGAL2 highly expressed in fasting-growing leaves, fruits and germinating seeds; CsGAL3 mainly distributes in vacuoles and significantly expressed in cucumber fruits, senescent leaves and seeds during late stage germination; The expression of CsAGA1 increased from leaf 1 to leaf 3 (sink leaves) and then declined from leaf 4 to leaf 7 (source leaves), and this isoform also highly expressed in male flowers and germinating seeds at early stage; CsAGA2 significantly expressed in cucumber leaves and female flowers; CsAGA3 is localized in plastids and also actively expressed in senescent leaves and germinating seeds; The role of CsGAL1 in cucumber plants is now unclear since its expression was relatively low in all organs. According to their expression patterns, subcellular localizations and previously reported functions of these isoforms in other plants, combining the data of soluble sugars contents in different tissues, the possible functions of these ?-Gals were discussed.
2021-01-01 | S-EPMC7802950 | BioStudies
Project description:In plants, intracellular Fe trafficking must satisfy chloroplasts' and mitochondrial demands for Fe without allowing its accumulation in the organelles in dangerous redox-active forms. Protein ferritin is involved in such homeostatic control, however its functional role in mitochondria, differently from its role in chloroplasts, is still matter of debate. To test ferritin functionality as a 24-mer Fe-storage complex in mitochondria, cucumber seedlings were grown under different conditions of Fe supply (excess, control, deficiency) and mitochondria were purified from the roots. A ferritin monomer of around 25 KDa was detected by SDS-PAGE in Fe-excess root mitochondria, corresponding to the annotated Csa5M215130/XP_004163524 protein: such a monomer is barely detectable in the control mitochondria and not at all in the Fe-deficient ones. Correspondingly, the ferritin 24-mer complex is abundant in root mitochondria from Fe-excess plants and it stores Fe as Fe(III): such a complex is also detectable, though to a much smaller extent, in control mitochondria, but not in Fe-deficient ones. Cucumber ferritin Csa5M215130/XP_004163524 is therefore a functional Fe(III)-store in root mitochondria and its abundance is dependent on the Fe nutritional status of the plant.
2013-01-01 | S-EPMC3744851 | BioStudies
Project description:Root-knot nematodes are devastating pathogens of crop plants. The draft genome of southern root-knot nematode Meloidogyne incognita was published in 2008 and additional genome and transcriptome data became available later on. However, lack of a publically available annotation for M. incognita genome and transcriptome(s) limits the use of this data for functional and comparative genomics by the interested researchers. Here we present a comprehensive annotation for the M. incognita proteome data available at INRA Meloidogyne Genomic Resources page (https://meloidogyne.inra.fr/Downloads/Meloidogyne-incognita-V2-2017) and European Nucleotide Archive (ENA) (accession number: ERP009887) using a multi-pronged approach.
2018-01-01 | S-EPMC6140804 | BioStudies