Multiomics analysis of tolerant interaction of potato with potato virus Y

www.nature.com/scientificdata Multiomics analysis of tolerant Data Descriptor interaction of potato with potato virus Y OPEN Tjaša Stare 1,3* , Živa Ramšak 1,3 , Maja Križnik1,2,3 & Kristina Gruden1 Potato virus Y (PVY) is the most economically important viral pathogen of potato worldwide. Different potato cultivars react to the pathogen differently, resulting in resistant, tolerant or disease outcome of the interaction. Here we focus on tolerant interaction between potato cv. Désirée and PVYNTN. To capture the response in its full complexity, we analyzed the dynamic changes on multiple molecular levels, including transcriptomics, sRNAomics, degradomics, proteomics and hormonomics. The analysis was complemented by the measurements of viral accumulation, photosynthetic activity and phenotypisation of the symptoms. Besides cv. Désirée we also studied its transgenic counterpart depleted for the accumulation of salicylic acid (NahG-Désirée). This multiomics analysis provides better insights into the mechanisms leading to tolerant response of potato to viral infection and can be used as a base in further studies of plant immunity regulation. Background & Summary Plant pathogens are responsible for up to 30% losses in agriculture1. Viral caused plant diseases affect all major crops. Being obligate intracellular organisms, chemical control of these pathogens can only be applied to control their insect vectors. Marker-assisted selection breeding of plants that are tolerant or resistant to viruses is an alternative option of control. For this strategy, understanding molecular responses of plant immunity is crucial2,3. At the molecular level, plant defense mechanisms against viral pathogens are regulated by a network of interconnected signal transduction pathways, which lead to plant metabolism reprogramming4. It is also insufficient to analyze plant status snapshots in a single time point and scale, instead, dynamic changes should be monitored on multiple molecular levels to understand the underlying mechanisms5,6. With this in mind, we performed multiomics analyses of potato (Solanum tuberosum L.) responses following the infection with potato virus Y (PVY). Potato is the world’s most important non-grain staple crop. Viruses pose a serious threat to potato production, not only because of the effects caused by the primary infection, but also because potato is propagated vegetatively and the viruses are transmitted through the tubers and accumulate over time7. The most devastating potato virus is PVY8, which induces severe symptoms in sensitive potato cultivars, including the development of potato tuber necrotic ringspot disease9,10. One of the most widely grown potato cultivars is cv. Désirée, which is in non-stress condition tolerant to PVYNTN, meaning that the virus replicates and spreads systemically, however, symptoms of the disease are reduced or not visible at all11. Tolerance may have an advantage over resistance for crop protection because it does not actively select against virus infection and replication, therefore there is little evolutionary pressure for PVY to mutate. Hence, the tolerant phenotype is likely to be more durable than resistance12. In this study, we performed a comprehensive, time series multiomics analysis of the potato cv. Désirée responses to PVYNTN infection11. The response has been analyzed on the levels of transcriptomics, sRNAomics, degradomics, proteomics and hormonomics. The analysis was complemented by the measurements of viral accumulation, measurements of photosynthetic activity and symptoms development (Figs 1 and 2). The plants were either mock- or PVY- treated and the response was analyzed in infected and systemic (upper noninoculated) leaves at different time points, one day before the infection (-1 days post inoculation (dpi)), on the day of infection (0 dpi) and on the following days after infection: 1, 2, 3, 4, 5, 6, 7, 8, 9 and 11 dpi4,13 (Fig. 1). As salicylic acid (SA) was found to be a crucial component for disease symptoms attenuation14, NahG-Désirée transgenic plants, 1 Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia. 2Jožef Stefan International Postgraduate School, Jamova 39, 1000, Ljubljana, Slovenia. 3These authors contributed equally: Tjaša Stare, Živa Ramšak and Maja Križnik. *email: Scientific Data | (2019) 6:250 | https://doi.org/10.1038/s41597-019-0216-1 1 www.nature.com/scientificdata/ www.nature.com/scientificdata Fig. 1 Overview of experimental design and sampling. (a) Plant scheme, indicating the nomenclature for leaves (1B – first bottom, 2B – second bottom, 3B – third bottom; 1U – first upper, 2U – second upper, 3U – third upper leaf). (b) Leaf sampling scheme, where for each leaf, two lamina samples were collected. (c) For each measurement method, indication of which day post infection (DPI) the samples were collected is given. producing salicylate hydroxylase, which catalyzes the conversion of SA to catechol11,15,16, were also included in experimental design (Fig. 1). Plant growth was unaffected in this tolerant interaction. However, in the inoculated leaves virus multiplication was detected at 5 dpi onwards and virus spread to upper systemic leaves was detected at 7 dpi. Also, leaf yellowing occurred faster in virus-inoculated compared to mock-inoculated plants. SA-depletion rendered NahG-Désirée plants more susceptible to PVYNTN infection, which was manifested as faster virus multiplication and appearance of strong disease symptoms including spot necroses, vein necroses and chlorotic spots beside more pronounced yellowing13. To evaluate dynamic changes in photosynthetic activity, net photosynthesis, stomatal conductance, actual photochemical efficiency, potential photochemical activity, chlorophyll content and electron transport rate were measured on both mock- and PVY-treated plants of both genotypes13. In both, a decrease in net photosynthesis and stomatal conductivity at 5 dpi was observed, which coincided with the onset of the virus accumulation. Additionally, in PVY-infected plants, a transient decrease of photochemical efficiency was observed at 5 dpi. Transcriptomics measurements of infected potato leaves of both genotypes for both mock- and PVY-inoculated plants were performed at 0, 1, 3, 4, 5 and 7 dpi using POCI arrays that are able to capture the expression of 84% of the predicted ITAG genes and 72% of predicted PGSC genes. To evaluate dynamics of systemic response, upper untreated leaves were also analyzed at 0, 1, 3, 4, 5, 7, 8, 9 and 11 dpi, for cv. Désirée. Overall, high similarities were observed between biological triplicates (Fig. 3). In untreated plants (0 dpi), 384 POCI probes were differentially expressed between genotypes (Désirée vs. NahG-Désirée). Infection of potato bottom leaves with PVY caused dynamic reprogramming of transcription, 3,572 POCI probes (out of 42,034) were differentially express (...truncated)