Functional and genomic features of piRNAs are conserved. (A) The numbers of piRNA loci predicted based on regulatory motifs and the numbers identified from high-throughput sequencing. (B) The percentage of protein-coding genes in each genome that could be targeted by piRNAs if zero, one, two, or three mismatches are allowed. (C) Density of small RNAs within a 100-nt window centered on the predicted target sites of the top 20% most abundant piRNAs. (Blue) Small RNAs that are antisense to the predicted targets; (red) those that are sense to the targets. (D) Distribution of observed (red) and predicted (blue) piRNA loci per 100-kb window in C. elegans (top) and C. briggsae (bottom). There are two piRNA clusters on C. briggsae chromosome IV: the 0 to 6.9 Mb region largely in synteny with the two C. elegans piRNA clusters (highlighted in lines with arrows); and the 13.1 to 15.1 Mb cluster. In addition, C. briggsae has a third piRNA cluster on chromosome I at position 9.9 to 11.3 Mb.
