slightly elevated levels of miR165/166 and slightly reduced levels of miR164. The other examined miRNAs were not obviously affected. The levels of siR255 (from TAS1), siR1511 (from TAS2), and 5D8(+) (from TAS3), were not affected by ago10 mutations. The U6 blots served as loading controls for the overlying small RNA blots. The numbers below the small RNA blots indicate the relative abundance of the small RNAs. (B) Realtime RT-PCR to determine the levels of miRNA- and siRNA-targeted mRNAs. Most of the examined mRNAs were not significantly different between ago10-13 and Ler inflorescences. A small elevation was observed for CUC1 mRNA targeted by miR164. Bars represent standard deviation of three technical replicates. Three biological replicates yielded similar results. Found at: doi:10.1371/journal.pgen.1001358.s002 (4.92 MB TIF) Figure S3 Floral phenotypes of various genotypes. (A) An ago10- 13 flower; ago10-13 flowers resembled wild-type flowers except for the narrower petals. (B) Siliques from ago10-13 plants. ago10-13 siliques were shorter and wider than those of wild-type plants. (C) An SEM image of an ago1-11 flower. (D) An ago1-11 ago10-13/+ inflorescence with obviously enlarged floral meristems (arrow). (E) A wus-1 flower. (F, G) hua1 hua2 ago10-12 and clv3-1 exhibited synergistic effects in terms of floral determinacy. (F) A hua1 hua2 ago10-12 clv3-1 flower with an enlarged gynoecium. (G) A hua1 hua2 ago10-12 clv3-1 silique with a massive amount of internal stigma tissue bursting out of the primary gynoecium. (H) Third whorl organs in hua1 hua2 ago10-12 flowers. Some had petaloid features (the two on the left) while others resembled stamens. (I-L) SEM images of anthers and anther epidermal cells in hua1 hua2 ago10-12 (I and J) and hua1 hua2 ago10-12 ap2-2 (K and L). (M) Siliques of ag-10 ap2-2 plants. (N) Siliques of ag-10 ago10-13 plants. Note the elongated gynophore (arrow). (O) Siliques of ag-10 ago10- 13 ap2-2 plants. (P) Quantification of gynophore length in the two genotypes. (Q) Siliques of phb-1d/+ plants. (R) ag-10 ago10-13/+ phb-1d/+ siliques showing gynoecia enlargement and the presence of ectopic organs (indicated by the arrows). (S) Bulged siliques and ectopic floral organs, indicated by the arrows, were found in ag-10 phv-5d/+ plants. (T) An ag-10 amiR165/166 plant showing SAM defects reminiscent of ago10 mutants. Scale bar, 500 mm in (C), 300 mm in (I), (K), 50 mm in (J), (L), and 1 mm in the rest of the panels. Found at: doi:10.1371/journal.pgen.1001358.s003 (15.43 MB TIF) References 1. Sablowski R (2007) Flowering and determinacy in Arabidopsis. J Exp Bot 58: 899–907. 2. Laux T, Mayer KF, Berger J, Jurgens G (1996) The WUSCHEL gene is required for shoot and floral meristem integrity in Arabidopsis. Development 122: 87–96. 3. Smyth DR, Bowman JL, Meyerowitz EM (1990) Early flower development in Arabidopsis. Plant Cell 2: 755–767. 4. Schoof H, Lenhard M, Haecker A, Mayer KF, Jurgens G, et al. (2000) The stem cell population of Arabidopsis shoot meristems in maintained by a regulatory loop between the CLAVATA and WUSCHEL genes. Cell 100: 635–644. 5. Irish VF (2010) The flowering of Arabidopsis flower development. Plant J 61: 1014–1028. 6. Lenhard M, Bohnert A, Jurgens G, Laux T (2001) Termination of stem cell maintenance in Arabidopsis floral meristems by interactions between WUSCHEL and AGAMOUS. Cell 105: 805–814. 7. Lohmann JU, Hong RL, Hobe M, Busch MA, Parcy F, et al. (2001) A molecular link between stem cell regulation and floral patterning in Arabidopsis. Cell 105: 793–803. 8. Bowman JL, Smyth DR, Meyerowitz EM (1989) Genes directing flower development in Arabidopsis. Plant Cell 1: 37–52. 9. Jofuku KD, den Boer BG, Van Montagu M, Okamuro JK (1994) Control of Arabidopsis flower and seed development by the homeotic gene APETALA2. Plant Cell 6: 1211–1225. 10. Aukerman MJ, Sakai H (2003) Regulation of flowering time and floral organ identity by a microRNA and its APETALA2-like target genes. Plant Cell 15: 2730–2741. AGO10 and Floral Stem Cell Termination Figure S4 AGO10 does not bind miR390. Northern blots for miR166 and miR390 were performed for total RNAs from wild type (Ler; the three lanes on the right) and immunoprecipitated samples (the first two lanes from the left) using anti-GFP antibodies from Ler (a negative control) and the YFP-ZLL transgenic line. YFP-ZLL was associated with miR166 but not miR390 in vivo. Found at: doi:10.1371/journal.pgen.1001358.s004 (1.75 MB TIF) Figure S5 The expression of ZPR3 in wild type (Ler) and ago10- 13 as determined by realtime RT-PCR. Found at: doi:10.1371/journal.pgen.1001358.s005 (2.62 MB TIF) Figure S6 A diagram of amiR165/166. A modified, partial pri- miR168 is highlighted in black. The amiR165 and amiR166 sequences (in green) were introduced into the pri-miR168 backbone through two rounds of PCR cloning using the SwaI and PmeI sites, respectively. The whole structure was inserted between a 2X35S promoter and a 35S terminator through the restriction sites HindIII and EcoRI. Found at: doi:10.1371/journal.pgen.1001358.s006 (0.11 MB JPG) Table S1 Floral organ counts in various genotypes. Found at: doi:10.1371/journal.pgen.1001358.s007 (0.06 MB PDF) Table S2 Sequences of oligonucleotides used in this study. Found at: doi:10.1371/journal.pgen.1001358.s008 (0.11 DOC) MB Acknowledgments We thank Kathy Barton, David Baulcombe, Jennifer Fletcher, Thomas Laux, Allison Mallory, Elliot Meyerowitz, and Patricia Springer for sharing reagents and strains. We thank Kiet Nguyen for technical assistance and Yuanyuan Zhao for comments on the manuscript. Author Contributions Conceived and designed the experiments: X Chen, L Ji, X Liu, W Wang, RE Yumul, X Cui, X Cao, G Tang. 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