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Figure S1. Alignment of red algal MADS domains (boxed) with sequences from other eukaryotes, showing predominantly MEF2-like signature residues (shaded gray) as opposed to SRF-like residues (shaded black) (Alvarez-Buylla et al., 2000). Species abbreviations are as follows: Ath: Arabidopsis thaliana; Cel: Caenorhabditis elegans; Ddi: Dictyostelium discoideum Raper; Dme: Drosophila melanogaster; Hsa: Homo sapiens; Ota: Ostreococcus tauri C.Courties & M.-J.Chrétiennot-Dinet; Phy: Petunia hybrida; Pin: Phytophthora infestans (Mont.) de Bary; Ppa: Physcomitrella patens Moss; Ppu: Porphyra purpurea; Pum: Porphyra umbilicalis; Sce: Saccharomyces cerevisiae.

Figure S2. Alignment of the most strongly conserved residues of domain 2 from SWI/SNF family SNF2 proteins, which is required for physical interaction with SNF4 and SWI3 in assembling SWI/SNF multi-subunit complexes (Treich and Carlson 1997). Conserved residues are shaded gray and invariable positions are in bold. Species name abbreviations are as in Fig. S1.

Figure S3. Phylogeny of Argonaute family proteins showing that Porphyra AGO1 belongs to the AGO clade. Bayesian posterior probabilities and ML bootstrap values are provided on key nodes supporting this association.

Figure S4. Porphyra does not share conserved miRNAs with higher plants detectable with RNA gel blots. The small RNA fraction from 50 μg of total RNA was run along side a concentration gradient of Arabidopsis RNA on a 12% polyacrylamide gel. After blotting, The membrane hybridized with oligonucleotides probes for miR156, miR166 and U6. AS, 196; VL, 141; V, 101 TP10M.

Table S1. Experimental conditions for each of the Porphyra cDNA libraries used in this study.

Table S2. Small RNA sequences obtained from SBS sequencing.

Table S3. Potential candidates for conserved miRNA in Porphyra. All sRNA abundances are normalized to TP10M. aOsa Rice, Ath Arabidopsis, Cre Chlamydomonas. bThe miRNA sequence from miRbase for the given species.

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