title: Global analysis of uncapped mRNA changes under drought stress and microRNA-dependent endonucleolytic cleavages in foxtail millet- Dd_PARE
design: Total RNA was extracted from the 14-day-old Yugu1 seedlings using Trizol reagent (Invitrogen, USA) following the manufacturer’s protocol. PARE libraries were prepared according to (German, M.A., et al., Nat Protoc, 2009. 4(3): p. 356-62)but with modifications described in (Ma, Z., et al., Plant Cell, 2010. 22(4): p. 1090-103)./ Foxtail millet is an ideal material to investigate the mechanisms of drought tolerance in plants. To deepen our understanding of mRNA degradation and stress response mechanisms in plants, we therefore used the PARE deep-sequencing approach in this study to analyze uncapped mRNA transcripts under drought stress conditions in foxtail millet. PARE was also used to identify potential targets for miRNA-directed cleavage and to reveal multiple novel examples of miRNA precursor processing in foxtail millet.