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Additional file 4: Figure S2. 24-nt phasiRNAs generated from the novel PHAS lociin wild-type and DCL3 mutant. 24-nt phasiRNAs generated from transcripts of LOC_Os01g37325.1 (A), LOC_Os02g20200.1 (B), LOC_Os02g55550.1 (C), LOC_Os04g45834.2 (D) and LOC_Os09g14490.1 (E) in wild-type and osdcl3–1 mutant seedling, respectively. The black arrows indicate the sRNA trigger cleavage sites, the x-axis represent the phasiRNA position mapped within the PHAS loci, the y-axis represent the read abundance (in RMP, reads per million) of the small RNAs mapped to the sense and antisense strands of PHAS loci.

Additional file 3: Figure S1. 21-nt phasiRNAs generated from the novel PHAS loci in wild-type and DCL4 mutant. 21-nt phasiRNAs generated from transcripts of LOC_Os01g57968.1 (A) and LOC_Os05g43650.1 (D) in wild-type and osdcl4-1 seedling, LOC_Os02g18750.1 (B), LOC_Os04g25740.1 (C) and LOC_Os06g30680.1(E) in wild-type and osdcl4-1 mutant panicle, respectively. The black arrows indicate the sRNA trigger cleavage sites, the x-axis represent the phasiRNA position mapped within the PHAS loci, the y-axis represent the read abundance (in RMP, reads per million) of the small RNAs mapped to the sense and antisense strands of PHAS loci.

Additional file 6: Figure S3. Degradome sequencing-based validation of the phasiRNA-target interactions.Four libraries of degradome sequencing data libraries (GSM434596, GSM455938, GSM455939 and GSM476257) were recruited for T-plot profiling. The IDs of the target transcripts and the corresponding phasiRNAs generated from the transcripts of LOC_Os02g18750.1, LOC_Os05g43650.1, LOC_Os06g30680.1 and LOC_Os12g42380.1 are listed on the top. The y axis measure the normalized reads (in RMP, reads per million) of the degradome signals, and the x axis represent the position of the cleavage signals on the target transcripts. The binding sites of the phasiRNA on their target transcripts were denoted by gray horizontal lines, and the dominant cleavage signals were marked by black arrows.