FIG 3.

The PMV 3′ UTR is notably edited in Brachypodium. (A) mRNA-enriched PMV RNAs contain major truncations and A/U-rich sequences in their 3′ UTRs. The 3′ end of the PMV capsid protein (CP) ORF is shown in green, followed by a horizontal line representing the 3′ UTR. Relative positions of the 3′ termini from 12 mRNA-enriched clones are indicated with vertical lines. The position of the truncated termini within the PMV genome is indicated by subscript numbers. Terminal residues corresponding to the truncation point in the wild-type genome are underlined. Nonviral sequences are shown to the right of the underlined residue, followed by an indicator for the RT-PCR oligo(dT) reverse primer ([AAAAAx30]). (B) Insertion and substitution events within the PMV 3′ UTR identified from short reads in the SRA. The scale of the UTR is the same as described for panel A. “Conflict” indicates substitution or deletion events; “insertion” indicates base insertion events.