GSE203627
Transcriptome analysis of tomato seedlings infected by Pepino Mosaic Virus
Pepino Mosaic Virus (PepMV) consists a major pathogenic threat in the greenhouses worldwide and has a devasting impact on tomato global production. PepMV belongs to the Potexvirus genus of the Flexiviridae family. PepMV has a viral RNA genome of approximately 6400 nucleotides long that contains five open reading frames (ORFs) and 4 major genotypes have been characterized. TomCr3, an indigenous virulent PepMV strain derived from the Chilean (CH2) genotype, was isolated in Crete, Greece and was used for the mechanical infection of Belladonna F1 hybrid tomato seedlings. Here, we present the results of a deep RNA-sequencing (RNA-seq) analysis performed to characterize the dynamic expression profile of tomato genes upon PepMV infection, including tomato transcription factors. Overall design: The TomCr3 strain of PepMV was isolated from naturally infected tomato plants in 2012 grown in a greenhouse in Ierapetra area from the Crete island in Southern Greece (35.0119° N, 25.7407° E). The virus was preserved in the laboratory through serial infections of tomato plants (Solanum lycopersicum L., hybrid Belladonna). Mechanical inoculations of tomato plants were performed by applying a suspension culture of PepMV prepared by grinding 0.5g of TomCr3 infected leaves in 5mL of Infection Buffer (0.1M Na2HPO4, 0,2% w/v Na2SO3) onto young leaves at the fourth leaf stage. Mock infected tomato leaves were used as a control. Exactly 10 days post inoculation (dpi), approximately 0.1 g of tissue was cut from the upper two or three leaves of each plant. The material was immediately frozen in liquid nitrogen and stored at -80°C until processing.