Fig. 4.

21-nt PHAS precursor transcripts peak coincidentally with their phasiRNA products. We examined a randomly selected 21-PHAS locus on rice chromosome 3 in wild-type (cultivar 9522) rice to assess the peak of abundance relative to the 21-phasiRNAs that peak at stage 5. Because PHAS loci are highly clustered in the rice genome, we selected a region of ~24kb as an example; in this case, the PHAS loci are interlaced with repetitive sequences. Each dot is a small RNA; light blue represent 21-nt sRNAs, green represent 22-nt, and orange represent 24-nt. Yellow shaded regions are predicted DNA transposons; pink shaded regions are predicted retrotransposons; orange shaded regions are inverted repeats. The small pink box is an annotated miRNA. The phasiRNA loci are essentially the distinct blocks of 21-nt sRNAs (light blue dots). The strand-specific RNA-seq data is represented as an IGV screenshot; blue bars are top-strand reads, and red bars are bottom-strand reads. There was a paucity of RNA-seq reads from these PHAS loci data in stage 7 at this cluster of loci, whereas 21-phasiRNAs were still abundant at stage 7.