Abstract
BackgroundLong non-coding RNAs (lncRNAs) are regulatory transcripts of length > 200 nt. Owing to the rapidly progressing RNA-sequencing technologies, lncRNAs are emerging as considerable nodes in the plant antifungal defense networks. Therefore, we investigated their role in Vitis vinifera (grapevine) in response to obligate biotrophic fungal phytopathogens, Erysiphe necator (powdery mildew, PM) and Plasmopara viticola (downy mildew, DM), which impose huge agro-economic burden on grape-growers worldwide.ResultsUsing computational approach based on RNA-seq data, 71 PM- and 83 DM-responsive V. vinifera lncRNAs were identified and comprehensively examined for their putative functional roles in plant defense response. V. vinifera protein coding sequences (CDS) were also profiled based on expression levels, and 1037 PM-responsive and 670 DM-responsive CDS were identified. Next, co-expression analysis-based functional annotation revealed their association with gene ontology (GO) terms for ‘response to stress’, ‘response to biotic stimulus’, ‘immune system process’, etc. Further investigation based on analysis of domains, enzyme classification, pathways enrichment, transcription factors (TFs), interactions with microRNAs (miRNAs), and real-time quantitative PCR of lncRNAs and co-expressing CDS pairs suggested their involvement in modulation of basal and specific defense responses such as: Ca2+-dependent signaling, cell wall reinforcement, reactive oxygen species metabolism, pathogenesis related proteins accumulation, phytohormonal signal transduction, and secondary metabolism.ConclusionsOverall, the identified lncRNAs provide insights into the underlying intricacy of grapevine transcriptional reprogramming/post-transcriptional regulation to delay or seize the living cell-dependent pathogen growth. Therefore, in addition to defense-responsive genes such as TFs, the identified lncRNAs can be further examined and leveraged to candidates for biotechnological improvement/breeding to enhance fungal stress resistance in this susceptible fruit crop of economic and nutritional importance.
Highlights
Long non-coding RNAs are regulatory transcripts of length > 200 nt
The analysis revealed their association with C a2+-binding proteins such as calmodulin/ calmodulin-like proteins, enzymes involved in reactive oxygen species (ROS) metabolism, cell-wall modification/reinforcement, secondary metabolic pathways, phytoalexin production, pathogenesis-related proteins such as protein 1 (PR-1), PR-4 and PR-10, and phytohormone-based signal transduction
LncRNA-miRNA interaction network analysis revealed the possibility of target mimicry in regulation of the underlying mechanisms of plant defense response
Summary
Owing to the rapidly progressing RNA-sequencing technologies, lncRNAs are emerging as considerable nodes in the plant antifungal defense networks We investigated their role in Vitis vinifera (grapevine) in response to obligate biotrophic fungal phytopathogens, Erysiphe necator (powdery mildew, PM) and Plasmopara viticola (downy mildew, DM), which impose huge agro-economic burden on grape-growers worldwide. The initial pace of lncRNAs research in plants was slower compared to that in mammals (especially humans), it has gained momentum in the last few years with the advancement in highthroughput sequencing technologies and the availability of genomic and transcriptomic information of several plants at high resolution One such plant is Vitis vinifera (grapevine), which has been extensively studied owing to its commercial importance and worldwide consumption. Efforts are being made to understand the underlying mechanisms of V. vinifera susceptibility to PM and DM, and in turn engineer the cultivated grapevine for resistance against these phytopathogens [4, 7, 8]
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