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Fig. S1 Percent similarity at the protein level between Macrocystis pyrifera and Ectocarpus siliculosus (blue) and Laminaria digitata (green) using BLAST for alignments with > 75% of the total read length.

Fig. S2 Distribution of clusters of all EST-derived Macrocystis pyrifera ORFs with the brown alage split up by genus: Laminaria, Fucus (2 species), Sargassum and Ectocarpus. Annotations (when available) for clusters on the outside of the Venn are listed in Table S3.

Table S1 Macrocystis pyrifera quantitative PCR targets, function, primer sets, and closest Ectocarpus siliculosus sequence match

Table S2 Genomes and ESTs used in comparative cluster analysis and their sources

Table S3 Non-redundant annotations for novel clusters in Figs 2 and S2

Table S4 Continuation of Table 2: the top 31–100 open reading frames (ORFs) with non-ribosomal pfam annotation ranked by total reads across the four libraries, the pfam description, the best species match, and significantly differential expression patterns in January and July

Table S5 Differentially expressed open reading frames (ORFs) with pfam annotation and summed read counts across the four libraries, the best species match, and significant differential expression patterns in January and July

Table S6 Light-harvesting complexes identified from isotigs in Macrocystis pyrifera