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Open AccessFeature PaperArticle

Comparison between Proteome and Transcriptome Response in Potato (Solanum tuberosum L.) Leaves Following Potato Virus Y (PVY) Infection

1
Department of Biotechnology and Systems Biology, National Institute of Biology, 1000 Ljubljana, Slovenia
2
Department of Ecogenomics and Systems Biology, Faculty of Life Sciences, University of Vienna, 1010 Wien, Austria
*
Author to whom correspondence should be addressed.
Proteomes 2017, 5(3), 14; https://doi.org/10.3390/proteomes5030014
Received: 4 May 2017 / Revised: 27 June 2017 / Accepted: 1 July 2017 / Published: 6 July 2017
(This article belongs to the Special Issue Proteomics in Plant–Environment Interactions)
Plant diseases caused by viral infection are affecting all major crops. Being an obligate intracellular organisms, chemical control of these pathogens is so far not applied in the field except to control the insect vectors of the viruses. Understanding of molecular responses of plant immunity is therefore economically important, guiding the enforcement of crop resistance. To disentangle complex regulatory mechanisms of the plant immune responses, understanding system as a whole is a must. However, integrating data from different molecular analysis (transcriptomics, proteomics, metabolomics, smallRNA regulation etc.) is not straightforward. We evaluated the response of potato (Solanum tuberosum L.) following the infection with potato virus Y (PVY). The response has been analyzed on two molecular levels, with microarray transcriptome analysis and mass spectroscopy-based proteomics. Within this report, we performed detailed analysis of the results on both levels and compared two different approaches for analysis of proteomic data (spectral count versus MaxQuant). To link the data on different molecular levels, each protein was mapped to the corresponding potato transcript according to StNIB paralogue grouping. Only 33% of the proteins mapped to microarray probes in a one-to-one relation and additionally many showed discordance in detected levels of proteins with corresponding transcripts. We discussed functional importance of true biological differences between both levels and showed that the reason for the discordance between transcript and protein abundance lies partly in complexity and structure of biological regulation of proteome and transcriptome and partly in technical issues contributing to it. View Full-Text
Keywords: potato virus Y (PVY); proteomics; transcriptomics; potato (Solanum tuberosum L.) potato virus Y (PVY); proteomics; transcriptomics; potato (Solanum tuberosum L.)
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Stare, T.; Stare, K.; Weckwerth, W.; Wienkoop, S.; Gruden, K. Comparison between Proteome and Transcriptome Response in Potato (Solanum tuberosum L.) Leaves Following Potato Virus Y (PVY) Infection. Proteomes 2017, 5, 14.

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