Mapping of the mRNA cleavage sites by PPM-RACE and RLM-RACE. Each top strand (black) depicts a miRNA complementary site, and each bottom strand depicts the miRNA (red). Watson-Crick pairing (vertical dashes) and G: U wobble pairing (circles) are indicated. The arrows indicate the 5′ termini of mRNA fragments isolated from citrus, as identified by cloned PPM-RACE and RLM-RACE products, with the frequency of clones shown. Only the cloned sequences that matched the correct gene and had 5′ ends within a 100 nt window centered on the miRNA validation are included. The miRNA sequence shown indicated in lower case corresponds to the most common miRNA supported by the miRNA PCR (1 out of 4 PCR clones). PPM-RACE and RLM-RACE were used to map the cleavage sites. The partial mRNA sequences from the target genes were aligned with the miRNAs. The numbers indicate the fraction of cloned PCR products terminating at different positions.