Table VI. Unique Brachypodium nuclear transcription and splicing factors altered by SPMV.

Differential expression of putative splicing factors and transcription factors uniquely altered in PMV+SPMV infection. The fold changes in gene expression in PMV and PMV+SPMV infections compared with mock are shown. Changes in gene expression in PMV+SPMV infection as determined by microarray and qRT-PCR analysis strongly correlate to each other [Pearson correlation coefficient (r) = 0.95 and coefficient of determination (R²) = 0.92] and are statistically significant compared with mock and PMV infections. Changes in gene expression in PMV infection and mock are insignificant. The statistical significance of qRT-PCR changes in gene expression was determined using Student’s t test (P value < 0.05). For the microarray data, FDR correction using the Benjamini and Hochberg method (q-value < 0.05) was used. Primers used for this study are listed in Supplemental Table S6. The gene descriptions were deduced from Pfam and PANTHER functional annotations obtained using the Phytozome (Goodstein et al., 2012).

Gene ID	Microarray		qRT-PCR		Description
	PMV	PMV+SPMV	PMV	PMV+SPMV
Bradi2g09850	1.11	1.58	0.90	1.28	Pre-mRNA splicing factor PRP21 like protein, splicing factor3A subunit1
Bradi5g07850	1.11	2.09	1.30	1.84	Splicing factor1/branch point binding protein (RRM superfamily), zinc knuckle domain
Bradi3g06562	1.16	1.55	1.00	1.34	AP2 domain
Bradi4g34700	1.02	1.63	1.10	1.50	Unknown