Figure 1. Two classes of small RNA producing loci in the moss P. patens.

(A) Distribution of small RNA lengths within the 52 of the 100 most prolific, uncharacterized small RNA producing loci dominated by 21 nt small RNAs. Each line represents the small RNA size distribution within a single locus. These are referred to as the Pp21SR loci. (B) As in A for the 48 of the 100 most prolific small RNA producing loci which were typified by a collection of 21–24 nt small RNAs. These are referred to as the Pp23SR loci. (C) Scatterplot depicting the normalized small RNA abundances vs. the sizes of the small RNA producing loci. Blue triangles, Pp21SR loci; red circles, Pp23SR loci. (D) The fraction of the normalized small RNA abundance emanating from the most abundant genomic strand is categorized for Pp23SR loci (red) and Pp21SR loci (blue). The subset of the Pp21SR loci where more than 50% of the abundance stemmed from small RNA dyads (where the same small RNA mapped to both genomic strands within a locus) are indicated by hollow blue bars, while solid blue bars indicate Pp21SR loci with less than 50% dyad abundances. None of the Pp23SR loci had a majority of small RNA abundance derived from such dyads. (E) Fractions of the genome (black), Pp21SR loci (blue), Pp23SR loci (red) and randomized controls (hollow bars) overlapping annotated P. patens genes. (F) Percent identity of inverted repeat arms vs. the percent of Pp21SR (blue) and Pp23SR (red) loci which those arms overlap. Black indicates percentage of the P. patens genome which overlaps inverted repeats, with error bars indicating the first quartile, median, and third quartiles of genome-wide inverted repeat identities. (G) Normalized small RNA abundance within inverted repeat stems vs. the total normalized abundance for Pp21SR (blue) and Pp23SR (red) loci. For loci which overlapped multiple inverted repeats, the one with the maximum abundance is shown. The position corresponding to Pp23SR1 is highlighted.