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Background  In order to get global molecular understanding of one of the most important crop diseases worldwide, we investigated compatible and incompatible interactions between  Phytophthora infestans  and potato ( Solanum tuberosum ). We used the two most field-resistant potato clones under Swedish growing conditions, which have the greatest known local diversity of  P. infestans  populations, and a reference compatible cultivar.    Results  Quantitative label-free proteomics of 51 apoplastic secretome samples (PXD000435) in combination with genome-wide transcript analysis by 42 microarrays (E-MTAB-1515) were used to capture changes in protein abundance and gene expression at 6, 24 and 72 hours after inoculation with  P. infestans.  To aid mass spectrometry analysis we generated cultivar-specific RNA-seq data (E-MTAB-1712), which increased peptide identifications by 17%. Components induced only during incompatible interactions, which are candidates for hypersensitive response initiation, include a Kunitz-like protease inhibitor, transcription factors and an RCR3-like protein. More secreted proteins had lower abundance in the compatible interaction compared to the incompatible interactions. Based on this observation and because the well-characterized effector-target C14 protease follows this pattern, we suggest 40 putative effector targets.    Conclusions  In summary, over 17000 transcripts and 1000 secreted proteins changed in abundance in at least one time point, illustrating the dynamics of plant responses to a hemibiotroph. Half of the differentially abundant proteins showed a corresponding change at the transcript level. Many putative hypersensitive and effector-target proteins were single representatives of large gene families.    Electronic supplementary material  The online version of this article (doi:10.1186/1471-2164-15-497) contains supplementary material, which is available to authorized users.

Quantitative proteomics and transcriptomics of potato in response to Phytophthora infestans in compatible and incompatible interactions