Fig. 3

Metabolism of plant RNAs and identities of transcripts that enter small RNA pathways. a Number of Dicer overlap read pairs (as defined in Fig. 2b-c) for HiTrap purified mite derived RNAs mapped to the T. urticae genome (HiTrap-endo), those mapping to the P. vulgaris genome (HiTrap to plant), reads cloned from total RNA mapped to the P. vulgaris genome (Total to plant), endogenous plant small RNAs (plant-endo), column purified RNAs first mapped to the P. vulgaris genome that are mapped to the T.urticae genome (HiTrap to plant then to mite), and total RNA extracted RNAs the P. vulgaris genome that are mapped to the T.urticae genome (Total to plant then to mite). Black arrow shows 21 nt size RNAs, red arrow 24 nt. Key to right of each graph shows number of reads in each potential pair. Number above represents reads represented by red color, which scales in a linear fashion to dark blue for zero reads. b 1335 Loci in P. vulgaris (bean) with at least two read depth and greater than 40 nucleotides long identified using total RNAs derived from mites. Loci are plotted by chromosome and number of reads per base pair. Colors of loci alternate between black and grey to distinguish originating chromosome. Green labeled loci are the 199 subset found in HiTrap recovered RNAs from mites. c Heatmaps showing size distribution of small RNA reads for P. vulgaris loci identified in (b). Horizontal of the heatmap is read size ranging from 15 on left and 30 on right. Vertical is individual loci with the highest expressing at top and lowest at bottom. From left is mite-derived HiTrap RNAs (HiTrap), total RNA mite-derived reads (Total), and a bean tissue derived (endo-sRNA) library. Black arrow shows 21 nt size RNAs, red arrow 24 nt. Scales on right are log transformed number of reads. d Venn diagram showing overlap between loci plotted in (b) and loci expressing endogenous small RNAs. Percentage indicates portion of mite library annotated loci that don’t overlap with endogenous sources of small RNAs. e Enrichment of plant mapping reads that exhibit Dicer overhangs in HiTrap purified samples from P. vulgaris, A. thaliana, and mites fed dsRNA raised on P.vulgaris. Enrichment is calculated as the proportion of reads that exhibit the 2 nt overhang associated with Dicer cleavage. This proportion is normalized to what is observed for total RNA extracted RNAs. The portion of reads between 19 and 23 nt long (siRNA size) is also plotted.