title: Transcriptomic analysis of Prunus domestica undergoing hypersensitive response to plum pox virus infection.
abstract: Plum pox virus (PPV) infects Prunus trees around the globe, posing serious fruit production problems and causing severe economic losses. One variety of Prunus domestica, named 'Jojo', develops a hypersensitive response to viral infection. Here we compared infected and non-infected samples using next-generation RNA sequencing to characterize the genetic complexity of the viral population in infected samples and to identify genes involved in development of the resistance response. Analysis of viral reads from the infected samples allowed reconstruction of a PPV-D consensus sequence. De novo reconstruction showed a second viral isolate of the PPV-Rec strain. RNA-seq analysis of PPV-infected 'Jojo' trees identified 2,234 and 786 unigenes that were significantly up- or downregulated, respectively (false discovery rate; FDR≤0.01). Expression of genes associated with defense was generally enhanced, while expression of those related to photosynthesis was repressed. Of the total of 3,020 differentially expressed unigenes, 154 were characterized as potential resistance genes, 10 of which were included in the NBS-LRR type. Given their possible role in plant defense, we selected 75 additional unigenes as candidates for further study. The combination of next-generation sequencing and a Prunus variety that develops a hypersensitive response to PPV infection provided an opportunity to study the factors involved in this plant defense mechanism. Transcriptomic analysis presented an overview of the changes that occur during PPV infection as a whole, and identified candidates suitable for further functional characterization.
authors: Centro Nacional de Biotecnología-CSIC, Campus Universidad Autónoma de Madrid, Madrid, Spain.
authors: Bernardo
authors: B
authors: Rodamilans
authors: Centro Nacional de Biotecnología-CSIC, Campus Universidad Autónoma de Madrid, Madrid, Spain.
authors: David
authors: D
authors: San León
authors: Center of Life and Food Sciences Weihenstephan, Unit of Fruit Science, Technische Universität München, Freising, Germany.
authors: Louisa
authors: L
authors: Mühlberger
authors: UMR 1332 Biologie du Fruit et Pathologie, CS20032, Villenave d'Ornon, France.
authors: Thierry
authors: T
authors: Candresse
authors: Center of Life and Food Sciences Weihenstephan, Unit of Fruit Science, Technische Universität München, Freising, Germany.
authors: Michael
authors: M
authors: Neumüller
authors: Centro Nacional de Biotecnología-CSIC, Campus Universidad Autónoma de Madrid, Madrid, Spain.
authors: Juan Carlos
authors: JC
authors: Oliveros
authors: Centro Nacional de Biotecnología-CSIC, Campus Universidad Autónoma de Madrid, Madrid, Spain.
authors: Juan Antonio
authors: JA
authors: García
mesh_terms: D016000:Cluster Analysis; D019295:Computational Biology; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D018740:Genetic Heterogeneity; D020022:Genetic Predisposition to Disease; D016679:Genome, Viral; D010935:Plant Diseases / Q000235:genetics* / Q000821:virology; D017801:Plum Pox Virus / Q000145:classification / Q000235:genetics; D027861:Prunus / Q000145:classification / Q000235:genetics* / Q000821:virology*; D059467:Transcriptome