Transcriptomic dataset of Malus domestica young leaves in response to acibenzolar-S-methyl (ASM) and/or nitrogen nutrition
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PROVIDER: S-EPMC11295710 | biostudies-literature | 2024 Jul
REPOSITORIES: biostudies-literature
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Project description:Plant resistance inducers (PRIs) and nitrogen (N) nutrition are both factors known to act on plant defence but their interaction has been little studied and needs further research. The objective of the study was to further characterize this interaction on apple (Malus domestica) plantlets at the molecular level. The produced dataset allows the investigation of the molecular mechanisms underlying: i) the biotic resistance induced by ASM treatments on apple seedlings, ii) their response to different nitrogen (N) status (N limitation or subsequent N resupply), iii) the combination of both N status and ASM treatment.
2024-07-02 | GSE264541 | GEO
Project description:Transcriptomic data from Malus domestica young leaves response to Acibenzolar-S-Methyl (ASM) treatment and nitrogen limitation or resupply.
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Project description:Phytocytokines belong to a category of small secreted peptides with signaling functions that play pivotal roles in diverse plant physiological processes. However, due to low levels of sequence conservation across plant species and poorly understood biological functions, the accurate detection and annotation of corresponding genes is challenging. The availability of a high-quality apple (Malus domestica) genome has enabled the exploration of five phytocytokine gene families, selected on the basis of their altered expression profiles in response to biotic stresses. These include phytosulfokine, inflorescence deficient in abscission/-like, pathogen-associated molecular pattern induced secreted peptide, plant peptide containing sulfated tyrosine, and C-terminally encoded peptide. The genes encoding the precursors of these five families of signaling peptides were identified using a customized bioinformatics protocol combining genome mining, homology searches, and peptide motif detection. Transcriptomic analyses showed that these peptides were deregulated in response to Erwinia amylovora, the causal agent of fire blight in pome fruit trees, and in response to a chemical elicitor (acibenzolar-S-methyl). Finally, gene family evolution and the orthology relationships with Arabidopsis thaliana homologs were investigated.
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Project description:Investigation of whole genome gene expression level changes in leaves of apple seedlings (Golden delicious) 3 days after treatment by Bion 50WG (ASM) versus water.
2024-04-01 | GSE262538 | GEO
Project description:RNA-Seq analysis is a strong tool to gain insight into the molecular responses to biotic stresses in plants. The objective of this work is to identify specific and common molecular responses between different transcriptomic data related to fungi, virus and bacteria attacks in Malus x domestica. We analyzed seven transcriptomic datasets in Malus x domestica divided in responses to fungal pathogens, virus (Apple Stem Grooving Virus) and bacteria (Erwinia amylovora). Data were dissected using an integrated approach of pathway- and gene- set enrichment analysis, Mapman visualization tool, gene ontology analysis and inferred protein-protein interaction network. Our meta-analysis revealed that the bacterial infection enhanced specifically genes involved in sugar alcohol metabolism. Brassinosteroids were upregulated by fungal pathogens while ethylene was highly affected by Erwinia amylovora. Gibberellins and jasmonates were strongly repressed by fungal and viral infections. The protein-protein interaction network highlighted the role of WRKYs in responses to the studied pathogens. In summary, our meta-analysis provides a better understanding of the Malus X domestica transcriptome responses to different biotic stress conditions; we anticipate that these insights will assist in the development of genetic resistance and acute therapeutic strategies. This work would be an example for next meta-analysis works aiming at identifying specific common molecular features linked with biotic stress responses in other specialty crops.
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Project description:Abscission is the regulated process of detachment of an organ from a plant. In apple the abscission of fruits occurs during their early development to control the fruit load depending on the nutritional state of the plant. In order to control production and obtain fruits with optimal market qualities, the horticultural procedure of thinning is performed to further reduce the number of fruitlets. In this study we have conducted a transcriptomic profiling of seeds from two different types of fruitlets, according to size and position in the fruit cluster. Transcriptomic profiles of central and lateral fruit seeds were obtained by RNAseq. Comparative analysis was performed by the functional categorization of differentially expressed genes by means of Gene Ontology (GO) annotation of the apple genome. Our results revealed the overexpression of genes involved in responses to stress, hormone biosynthesis and also the response and/or transport of auxin and ethylene. A smaller set of genes, mainly related to ion transport and homeostasis, were found to be down-regulated. The transcriptome characterization described in this manuscript contributes to unravelling the molecular mechanisms and pathways involved in the physiological abscission of apple fruits and suggests a role for seeds in this process.
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Project description:Marssonina apple blotch, caused by the fungus Marssonina coronaria, is one of the most destructive apple diseases in China and East Asia. A better understanding of the plant's response to fungi during pathogenesis is urgently needed to improve plant resistance and to breed resistant cultivars. To address this, the transcriptomes of "Qinguan" (a cultivar with high resistance to M. coronaria) apple leaves were sequenced at 12, 24, 48, and 72 h post-inoculation (hpi) with Marssonina coronaria. The comparative results showed that a total of 1956 genes were differentially expressed between the inoculated and control samples at the 4 time points. Gene ontology (GO) term enrichment analysis of differentially expressed genes (DEGs) revealed changes in cellular component, secondary metabolism including chalcone isomerase activity, phytoalexin biosynthetic process, anthocyanin-containing compound biosynthetic process, lignin biosynthetic process, positive regulation of flavonoid biosynthetic process; and molecular functions or biological processes related to the defense response, biotic stimulus response, wounding response and fungus response. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that DEGs were significantly enriched in flavonoid biosynthesis, vitamin B6 metabolism, phenylpropanoid biosynthesis, and the stilbenoid, diarylheptanoid and gingerol biosynthesis pathways. Furthermore, the importance of changes in cellular components and partial polyphenol compounds when encountering M. coronaria are discussed.
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Project description:Modulation of apple leaf trancriptome by Acibenzolar-S-methyl (ASM)
| PRJNA1092251 | ENA
Project description:Background Apple replant disease is a soilborne disease caused by Fusarium proliferatum f. sp. malus domestica strain MR5 (abbreviated hereafter as Fpmd MR5) in China. This pathogen causes root tissue rot and wilting leaves in apple seedlings, leading to plant death. A comparative transcriptome analysis was conducted using the Illumina Novaseq platform to identify the molecular defense mechanisms of the susceptible M.26 and the resistant M9T337 apple rootstocks to Fpmd MR5 infection. Results Approximately 518.1 million high-quality reads were generated using RNA sequencing (RNA-seq). Comparative analysis between the mock-inoculated and Fpmd MR5 infected apple rootstocks revealed 28,196 significantly differentially expressed genes (DEGs), including 14,572 up-regulated and 13,624 down-regulated genes. Among them, the transcriptomes in the roots of the susceptible genotype M.26 were reflected by overrepresented DEGs. MapMan analysis indicated that a large number of DEGs were involved in the response of apple plants to Fpmd MR5 stress. The important functional groups identified via gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment were responsible for fundamental biological regulation, secondary metabolism, plant-pathogen recognition, and plant hormone signal transduction (ethylene and jasmonate). Furthermore, the expression of 33 up-regulated candidate genes (12 related to WRKY DNA-binding proteins, one encoding endochitinase, two encoding beta-glucosidases, ten related to pathogenesis-related proteins, and eight encoding ethylene-responsive transcription factors) were validated by quantitative real-time PCR. Conclusion RNA-seq profiling was performed for the first time to analyze response of apple root to Fpmd MR5 infection. We found that the production of antimicrobial compounds and antioxidants enhanced plant resistance to pathogens, and pathogenesis-related protein (PR10 homologs, chitinase, and beta-glucosidase) may play unique roles in the defense response. These results provide new insights into the mechanisms of the apple root response to Fpmd MR5 infection. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08721-3.
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Project description:Transcriptomic characterization of Malus domestica response to iron and phosphorus deficiency.
2019-05-01 | GSE122554 | GEO