Figure S5 Schematic drawing of genetic experiment that tests Mop2-1 effect on preventing r1 paramutation. Plants heterozygous for Mop2-1/+ and carrying R-st/r or R-r/r were crossed to produce F1 plants. Although r1 paramutation occurs in the F1, observation of paramutation requires a testcross to a colorless allele that does not participate in paramutation (r) to obtain seeds in which pigment levels reveal the extent of paramutation of R-r to R-r’ [81]. To produce testcross progeny, mottled and fully colored F1 seeds (R-st/R-r’ or r/R-r) were planted. Resulting plants were genotyped for the Mop2-1 mutation and out crossed onto silks carrying the r allele. Seeds resulting from the test cross were sorted to identify mottled and/or full colored seeds and light reflectance was measured to determine the relative color of the seeds. Data summarized in Figure 6C. Found at: doi:10.1371/journal.pgen.1000725.s005 (0.10 MB PDF) Figure S6 Schematic drawing of genetic experiment that tests Mop2-1 effect on Ubi::MS45pIR and Ubi::5126pIR transgene induced silencing. pIR is used to symbolize the inverted repeat transgenes. Dark plant pigmentation specified by B’ in Mop2-1/ Mop2-1 plants was used to classify progeny. Molecular genotyping of a subset of plants revealed close correspondence between the B’ phenotype and the Mop2-1 genotype; 28/33 dark plants were homozygous and 28/30 light plants were heterozygous for Mop2-1. Recombination between the linked b1 and mop2 loci does not influence outcome of this experiment because at least one B’ allele is present to report the Mop2-1 genotype. Found at: doi:10.1371/journal.pgen.1000725.s006 (0.16 MB PDF) Figure S7 Protein models of maize second largest subunits of Pol-I and Pol-II used for phylogenetic analysis. Protein sequences References 1. 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