Evolution and diversification of reproductive phased small interfering RNAs in Oryza species
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Article acceptance date: 12 October 2020
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Fig. S1 PHAS loci were mostly in the intergenic regions and 21-PHAS have high GC composition
than 24-PHAS.
Fig. S2 miR2118 could target NLRs and produce no or sparse phasiRNAs in O. sativa.
Fig. S3 Most 21-PHAS and 24-PHAS were unique or with low copies, and examples showing 21-
PHAS loci expanded by segment duplication.
Fig. S4 The syntenic distribution property of PHAS on the 11 chromosomes of five Oryza
genomes.
Fig. S5 Both pms1 and pms3 are 21-PHAS loci in O. sativa.
Fig. S6 21-nt phasiRNA-targets were less stable than miRNA-targets.
Fig. S7 21-nt phasiRNAs with 5′-terminal U tend to induce cis-cleavage in the four Oryza species.
Fig. S8 The sequences of two 21-PHAS loci with cis-cleavage sites in Oryza.
Fig. S9 The expression level of two potential miR2118 NATs in different tissues.
Fig. S10 DNA methylation level of PHAS loci was higher in reproductive yong panicles than
vegetative leaves.Table S1 Summary of reads quantities and genome mapping qualities of sRNA and degradome
data for five Oryza species.
Table S2 The lists of PHAS loci found in the five Oryza genomes (see separate file).
Table S3 miR2118 and miR2275 members in the five Oryza genomes (see separate file).
Table S4 The lists of 21-nt phasiRNAs targets identified by degradome analysis in the five Oryza
species (see separate file).
Table S5 The 553 functional 21-nt phasiRNA-targets found in O. sativa, and their orthologous
21-nt phasiRNA and targets in the other Oryza species (see separate file).
Table S6 The number of total, or subset of the 540 functional 21-nt phasiRNAs, with homology
between O. sativa and the other four Oryza species.
