Table II. Differential expression of putative Brachypodium genes involved in JA and ET signaling.

The relative unlogged fold change (≥1.5-fold) in gene expression of PMV and PMV+SPMV infection compared with mock are indicated. Minus sign represents down-regulated fold change. The gene descriptions were deduced from peptide ortholog analysis with Arabidopsis protein sequences using Phytozome (Goodstein et al., 2012). The percentage similarity of Brachypodium proteins with the orthologous Arabidopsis proteins is indicated in parentheses. Note that some Brachypodium genes with low percentage similarity to their respective Arabidopsis orthologs are indicated as “-like.” For additional phylogenetic analyses, see Supplemental Figure S2. The statistical significance of gene expression changes was determined using Student’s t test and was corrected for FDR using the Benjamini and Hochberg method (q-value < 0.05).

Gene ID	PMV	PMV+SPMV	Description
Bradi1g05870	3.60	3.07	BdOPR3 (66%)
Bradi2g35907	2.43	2.51	OPR3-like (52%)
Bradi1g16580	−2.00	−3.03	BdFAD7 (71%)
Bradi1g51330	−1.64	−1.89	VSP1-like (44%)
Bradi3g01110	−1.64	−1.92	BdAOS (56%)
Bradi3g30510	4.02	4.75	BdCYP89A6 (65%)
Bradi3g07010	−1.96	−2.86	BdLOX2 (66%)
Bradi3g07000	−2.56	−2.56	LOX2-like (64%)
Bradi3g39980	6.30	7.68	LOX-like (62%)
Bradi3g11260	1.60	1.74	BdMKK3 (64%)
Bradi3g50490	−2.50	−2.70	BdERF-1 (42%)
Bradi1g72450	−8.33	−7.69	ERF/RAP2.2-like (28%)
Bradi5g25570	−4.76	−5.26	ERF3-like (28%)
Bradi2g52370	−2.63	−2.44	ERF4-like (31%)
Bradi1g75960	2.40	2.51	BdACO1 (82%)