Fig 5. A hierarchical cluster analysis of global mRNA expression profiles in response to infection by different SMV isolates.

(A) Heat map displaying 2679 differentially expressed genes (DEGs) in response to infections by three SMV isolates (G2-L, G2-LRB and G7) at 14 dpi. Heat map was generated using Strand NGS (http://www.strand-ngs.com/). (B) A detailed view of an exemplar branch of the heat map showing genes with differential responses following SMV isolate infection. Colors indicate the log₂ fold changes (FC) with a ratio of SMV-infected sample versus the mock-inoculated control according to the average of the normalized signal values. Red colour denotes upregulation, while blue indicates downregulation. Read densities = RPKMs (Read count per kilobase of exon model per million reads); Normalized signal values = log2(RPKMs). Significance was determined by using a fold change threshold of at least 2.