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FIGURE S1. De novo contig building and tiling of Aureoumbra lagunensis chloroplast fosmid clones. (A) Eighteen clones were subjected to Multiple Complete Digest (MCD) analysis, and the overlap of the resulting fingerprints generated a preliminary contig of 12 clones. The top candidate clone (by bioinformatic analysis of their end sequences) was sequenced as the “anchor” clone, and four additional clones (numbered 2–5) were selected for sequencing. (B) The complete sequences of the five clones were aligned into a 94 Kbp sequence contig, and tiling of end-sequenced and MCD data from all other clones (only nine clones aligned once the sequence-based contig was used) revealed a sixth clone (labeled “fin.”), which was partially sequenced using custom primers to complete the genome sequence.

FIGURE. S2. A larger and more detailed version of Figure 4 with gene names listed to the right of the heat map.

Table S1. Gene presence (black boxes) and absence (white boxes) among 25 genomes analyzed in Figure 4. Genes and taxa are listed in alphabetically for Aa (Aureococcus anophagefferens), Al (Aureoumbra lagunensis), Bn (Bigelowiella natans), Cr (Chlamydomonas reinhardtii), Cm (Cyanodioschyzon merolae), Cc (Cyanidium caldarium), Eh (Emiliania huxleyi), Eg (Euglena gracilis), Gte (Gracilaria tenuistipitata), Gth (Guillardia theta), Ha90 (Heterosigma akashiwo NIES 293), Ha91 (Heterosigma akashiwo CCMP452 ), Lt (Leptosira terrestris), Ms (Micromonas sp.), Os (Odontella sinensis), Ot (Ostreococcus tauri), Pt (Phaeodactylum tricornutum), Ppy (Pinguiococcus pyrenoidosus), Pp (Porphyra purpurea), Py (Porphyra yezoensis), Rs (Rhodomonas salina), So (Scenedesmus obliquus), Sh (Stigeoclonium helveticum), Tp (Thalassiosira pseudonana), and Vt (Vaucheria litorea).

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