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.
Highlights
Apple (Malus x domestica Borkh) is one of the most important cultivated tree fruit crops in temperate climates
We determined the list of the up- and down-regulated genes and we compared these lists in order to identify common and different regulated genes between the 7 studied research works dealing with biotic stress responses
We found that 16 genes were commonly regulated in responses to fungal pathogens, virus (Apple Stem Grooving Virus) and bacteria (Erwinia amylovora)
Summary
Apple (Malus x domestica Borkh) is one of the most important cultivated tree fruit crops in temperate climates. The identification of up- or down-regulated genes is often not enough to draw meaningful biological conclusions because it is hard to identify which gene plays a key role in specific signaling networks in host responses[1] This issue leads to high difficulties in deriving conclusive models for understanding disease symptomatology. Meta-analysis of transcriptomic data will identify commonalities and differences between differentially regulated gene lists and will allow screen which genes are key players in gene-gene and protein-protein interaction networks. These analyses will allow delivering important information on how a specific environmental factor affects plant molecular responses and how plants activate general stress responses to environmental stresses[6]. We aimed to determine which genes, pathways, gene set categories and predicted protein-protein interaction networks may play key roles in specific responses to pathogen infections
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