Additional file 2: of Analysis of Brachypodium miRNA targets: evidence for diverse control during stress and conservation in bioenergy crops

Figure S1. D-Plots of the cold regulated inverse group miRNA targets. PARE data showing evidence for cold regulation of the miRNA guided cleavages of (A) Bradi2g59200.1, (B) Bradi1g11800.5, and (C) Bradi2g35720.1. An additional biological replicate of what is shown in Fig. 6. Red dots indicate the PARE sequences mapping to predicted target sites. Figure S2. Characterization of cold regulated miRNAs and mRNA targets in Biorep #2. Complementary to Fig. 8. Figure S3. Bdi-miR168 Targeting AGO1a. D-Plot of PARE data showing evidence for cleavage of the AGO1a transcript (Bradi3g51077.3) via miR168. Despite this cleavage event being highly conserved it is only Level 1 prominence. Red dot indicates the PARE sequence which mapped to the miR168 target site. (PPTX 1715 kb

Additional file 1: of Analysis of Brachypodium miRNA targets: evidence for diverse control during stress and conservation in bioenergy crops

Table S1. RNAseq Libraries. Summary statistics of Brachypodium RNAseq libraries. Table S2. BDI Prominence Lvls. miRNA target prediction scores and prominence data for predicted Brachypodium miRNA targets. Table S3. SWI miRNAs. Genomic location, folding data, and sequences of conserved miRNAs found in switchgrass. Table S4. SWI Prominence Lvls. miRNA target prediction scores and prominence data for predicted switchgrass miRNA targets. Table S5. SBI Prominence Lvls. miRNA target prediction scores and prominence data for predicted sorghum miRNA targets. Table S6. Inverse and Unchanged. miRNA target prediction scores, annotation information, PARE data, and RNAseq data for all miRNAs/mRNA-targets in the “Inverse” and “Unchanged” groups. Table S7. Primers and Oligos. Primers and oligos used in this study. (XLSX 1498 kb