A brief overview of plant xrRNAs. (A) Depending on the plant virus family, xrRNAs are located within intergenic regions and/or at the beginning of the 3′ UTR. (B) Consensus secondary structure for xrRNALTs. The 95th percentile (η.95) is indicated for all variable regions. Covariation analysis was expanded and updated from Steckelberg et al. (2018b). (C) Alignment of xrRNALT sequences from select plant viruses. Bold sequences (PLRV and SCNMV) indicate a crystal structure is available; *, xrRNA confirmed to be resistant to Xrn1 in vitro; gray highlight in L2ACN; the gray shaded nucleotide aligns 2 nt downstream in three dimensions, as indicated by the arrow pointing to the “=” sign. The G–C pair involving J1/2 and L2B is labeled. The complete alignment is shown in Supplemental Figure S1.
