Transcriptomic responses to biotic stresses in Malus x domestica: a meta-analysis study

Abstract

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.

Differential gene regulatory pathways and co-expression networks associated with fire blight infection in apple (Malus × domestica)

“…For instance, genes related to metabolic activity, cytochrome P450 gene family, protein modification process, kinase activity, transferase activity, and DNA binding show activation upon fire blight infection. These functional classes have been shown to respond under diverse stress categories 25,32,[46][47][48] and their significant enrichment in this study can be categorized as a general stress response. The activation of general stress pathways illustrates the system-level constraints imposed by bacterial infection on the host machinery.…”

Application of a portable instrument for rapid and reliable detection of SARS‐CoV‐2 infection in any environment

“…To assist the biomarkers discovery, the vast amount of transcriptomic data available in public databases in response to human coronaviruses will allow a deep meta‐analysis using previously customized bioinformatics pipelines Ref. [8–11]. This work consists of re‐analyzing raw data obtained by independent experiments using a normalization and standardization procedure included in a bioinformatics pipeline.…”

Interaction of roses with a biotrophic and a hemibiotrophic leaf pathogen leads to differences in defense transcriptome activation

“…A specific reaction to P. pannosa infection is that the genes involved in the light reaction of photosynthesis were downregulated more strongly than those in response to D. rosae, which is surprising, considering that P. pannosa only infects epidermal cells, which are not photosynthetically active, while D. rosae infects also infects the cell layers below the epidermis. However, the downregulation of the photosynthic genes is often observed in plantpathogen interactions (e.g., Cremer et al 2013;Milli et al 2012;Balan et al 2018). This reaction may be explained by a pathogen-induced source-sink transition of infected leaf tissues (Berger et al 2007).…”