Fungal responsive NBS LRR genes in grapevine functional characterization and genomic profiling to identify their pseudogene counterparts

Abstract

In the present study, functional characterization of fungal responsive NBS-LRR genes has been done through overexpression in Arabidopsis thaliana plants. Transgenic lines were evaluated for various physiological characteristics and exhibited overall improvement in height, flowering, and seed numbers. XP_010660247.1 gene overexpression lines were exhibiting the best overall physiological features. The pseudogenes of Resistance (R) genes were predicted using PlantPseudo and PseudoPipe pipelines and their characterization was done for their roles in antifungal response by protein-protein docking with Erysiphe necator fungal proteins. Seven EKA-peptides with fungal response were screened out and can be further validated using wet-lab analysis. Further, gene regulation with miRNA/tasiRNAs/Transcription factors/mRNA sequences enabled us to devise a hypothesis on how these pseudo-R genes modulate gene expression of their parent gene sequences. The differential gene expression analysis in powdery mildew stress reported 79 differentially expressed pseudo-R genes. Further, 179 differentially expressed pseudo-R genes were exhibiting tissue specific expression patterns. The WGCN network analysis of pseudo-R genes with lncRNAs and coding genes predicted six pseudo-R genes as crucial hubs during powdery mildew infection. Their ancestor sequences were also predicted and their domains were analyzed for presence of transposon sites so that they can be utilized for further functional characterization studies. newline