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.

Biotechnological strategies and tools for Plum pox virus resistance: trans-, intra-, cis-genesis, and beyond

“…In fact, HR is often the outcome of the direct or indirect recognition of a plant resistance (R) gene with a pathogen avirulence factor, and the largest class of the R genes encode nucleotide-binding leucine-rich repeat (NB-LRR) proteins ( Dangl and Jones, 2001 ). A recent work shows that 354 NB-LRR genes are expressed in ‘Jojo’ plants undergoing PPV-induced HR and that 10 of them were differentially expressed respect the uninfected control plants ( Rodamilans et al, 2014 ). Whether NB-LRR proteins are behind the ‘Jojo’ resistance is not known.…”

RNA Polymerase Slippage as a Mechanism for the Production of Frameshift Gene Products in Plant Viruses of the Potyviridae Family

“…To explore the mechanism by which these additional potyviral proteins can be synthesized, we analyzed available RNA sequencing (RNA-seq) data of two Plum pox virus (PPV) isolates (9). After data filtering (10, 11), sequences were mapped versus the references (12) allowing a maximum of three mismatches per read.…”

Recent advances and prospects in Prunus virology

“…In the first study, a total of 3020 differentially expressed unigenes were observed after PPV inoculation of the resistant plum genotype ‘Jojo’, which developed a hypersensitive response. Out of these unigenes, 154 were characterised as potential resistance genes, and 10 could be placed in the NBS‐LRR class of resistance genes (Rodamilans et al ., ). In the second study, Rubio et al .…”