Genome wide identification and functional analysis of long non coding RNAs in Vitis vinifera Grapevine

Abstract

Long non-coding RNAs (lncRNAs) are transcripts gt200 nucleotides, which generally lack potential to code for proteins and have prominently emerged as dynamic regulatory molecules across eukaryotes. In our study, we conducted genome-wide investigation of lncRNAs in Vitis vinifera (grapevine), a fruit crop of commercial and nutritional importance that is susceptible to pathogens. Based on computational approaches, we identified and characterized 56,441 lncRNAs in V. vinifera by harnessing transcriptomic data (~200 GB) from 10 developmental stages corresponding to three different tissues of the plant: leaf, inflorescence, and berry. Additionally, we investigated response of these lncRNAs to three fungal stress conditions: Erysiphe necator (powdery mildew, PM), Plasmopara viticola (downy mildew, DM), and Botrytis cinerea (gray mold, GM) infection, which impose huge agro-economic burden on grape-growers worldwide. Consequently, we identified 71 PM-, 83 DM-, and 47 GM-responsive lncRNAs in V. vinifera. Overall, our results highlight the importance of lncRNAs in coordinating developmental transitions and other biological processes in grapevine such as defense response against biotrophic and necrotrophic pathogens. In view of their regulatory versatility, the identified lncRNAs such as those for which quantitative polymerase chain reaction analysis was conducted in this study or which were identified as potent nodes in miRNA-mediated cascade regulation can be further examined. Such lncRNAs upon subsequent investigation can be leveraged to candidates for biotechnological improvement of the susceptible grapevine crop in addition to the conventional approach of over-expressing defense-related genes. newline