FIGURE 3.

Primary and predicted secondary structures of lowest free energy of the fig hammerhead viroid-like RNA variant A1 (FHVd-LR_A1) collected from the island of Oahu. Regions involved in the formation of (+) and (−) hammerhead structures are delimited by flags; arrows and bars indicate the self-cleavage sites and the nucleotides conserved in most natural hammerhead structures, respectively; filled (black) and open symbols refer to (+) and (−) polarity, respectively. Mutated positions in other FHVd-LR variants are indicated in circles, with compensatory mutations, insertions, and deletions reported in green, blue, and pink, respectively. Nucleotide changes with respect to the short VL-RNA from the island of Kauai are in red. Horizontal arrows delimit the regions targeted by primer pairs used in the amplification steps of the cloning and sequencing strategy.