Sweet potato (Ipomoea batatas) ranks among the top 10 most important crops in the world and has played an important role in providing nutritional and economic sustainability for subsistence farmers in Sub-Saharan Africa. Viral disease has been a constant and ever-growing concern for sweet potato production. The most important viral pathogens of sweet potato are Sweet potato chlorotic stunt virus (SPCSV) and Sweet potato feathery mottle virus (SPFMV). Co-infection of sweet potato by SPCSV and SPFMV has been dubbed sweet potato virus disease (SPVD) and can cause upwards of ~90% yield loss in infected plants. Current understanding of sweet potato responses to SPCSV and SPFMV at the molecular level remains very limited. Using deep transcriptome sequencing, we have generated genome-wide mRNA and sRNA profiles of three sweet potato cultivars (with varying degrees of SPVD resistance) inoculated with either SPCSV or SPFMV alone, or both, at three different time points post-inoculation. Comprehensive analysis of these expression profile data allowed us to identify viral responsive mRNAs, which were enriched with those involved in response to biotic stimulus, photosynthesis and primary and secondary metabolisms. Furthermore, viral responsive microRNAs (miRNAs) and phased small-
interfering RNAs (phasiRNAs) were also discovered and their corresponding targets were analyzed. Our results provide a better understanding of regulatory networks underlying the sweet potato responses to the infection of SPCSV and/or SPFMV.