Figure 5.

Comparison of transcriptome changes in different virus–host systems. We compared our RNA‐sequencing (RNA‐seq) of Cassava brown streak virus (CBSV)‐infected cassava with three other potyvirus–plant transcriptome studies [late‐stage cassava–CBSV infection, Maruthi et al., 2014; early‐stage peach and late‐stage apricot infection with Plum pox virus (PPV), Rubio et al., 2015a, 2015b]. In addition, we included an RNA‐seq study of cassava infected with South African cassava mosaic virus (SACMV), a single‐stranded DNA (ssDNA) geminivirus pathosystem (Allie et al., 2014), to compare the response of cassava to two different virus types. (a) Pairwise similarity matrix of numbers of differentially expressed genes (DEGs) in each pathosystem, based on comparison of Pfam identifiers associated with each gene. A pairwise percentage similarity score was computed by multiplying the DEGs found in common in both pathosystems by 200 and then dividing this number by the sum of the DEGs in both pathosystems that were compared. (b, c) Venn diagrams were constructed using the Pfam identifiers associated with DEGs from all five studies. The figure shows specific Pfam identifiers common to all five studies, as well as those common to all potyvirus studies. (b) Up‐regulated DEGs. (c) Down‐regulated DEGs. [Correction added on 12 January 2018 after first online publication: the formula in figure 5(a) has been revised. The figure caption has also been revised to reflect the changes in the formula.]