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Figure S1. Alignment of YAB genes. Amino acids used in phylogenetic analysis were marked “+”.

Figure S2. Maximum-likelihood tree of YAB genes based on LG model. The tree was generated by PhyML 3.0 on “The ATGC bioinformatics platform” website (http://www.atgc-montpellier.fr/phyml/). Figures around each node indicate support value by approximate likelihood-ratio test (aLRT) based on Shimodaira-Hasegawa-like procedure (Guindon et al., 2010).

Figure S3. Structures of Cabomba YAB genes. Exon is boxed while intron is shown as line. Coding region for Zn finger-like domain is hatched and that for YAB domain is shaded. Translational start and stop positions are pinned by open and solid circles, respectively.

Figure S4. PCR fragments of CcYAB2 on genomic and cDNA (above) and schematic drawing of amplified mRNA position (below). Arrows indicate positions of primers used for the amplification. 5th intron is inferred to exist between nucleotides coding Asparagine and Tryptophan (arrowheads) based on comparison with other YAB genes. Translational stop position is pinned by solid circle.

Figure S5. Alignment of HD-ZIP III genes. All amino acids in this alignment were used for phylogenetic analysis.

Figure S6. Neighbor-Joining tree of HD-ZIPIII genes. Bootstrap values with 1000 trials (>50%) are indicated above each nodes.

Figure S7. Results of negative controls for in situ analyses (a–h, m, r, v) and additional data on expression of YAB genes (i–l, n–q, s–u). Gene names targeted by probe are indicated on the lower left corner of each panel. “s” or “as” preceding gene name indicates sense or antisense probe for the gene, respectively. For correspondences between the results and negative controls, see Table S2. Scale bars = 100 μm.

Figure S8. Results of negative controls for in situ analyses. For correspondences between the results and negative controls, see Table S2. Scale bars = 100 μm.

Table S1. Primers used in this study. *primers used with Universal Amplification Primer (supplied from Invitrogen), **primers used with 5′ Abridged Anchor Primer (supplied from Invitrogen).

Table S2. Correspondence between results and negative controls in in situ hybridization experiments.

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