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jpy1229-sup-0001-FigS1.pdfapplication/PDF3458KFig. S1. The location of the Porphyra blade tissues used for RNA extraction. The tissue designations are as follows: asexual, low light (CFSP); vegetative, high light (CFST); vegetative, low light (CFSS); olio (CFSU); and blade (CGAG) (see Table S6 for details).
jpy1229-sup-0002-FigS2.pdfapplication/PDF164KFig. S2. A proposed scheme for the synthesis of eicosapentaenoic acid (EPA) in Porphyra and in Cyanidiales.
jpy1229-sup-0003-FigS3.pdfapplication/PDF101KFig. S3. Affiliation of the LCY-type lycopene cyclase paralogs from Porphyra purpurea and P. umbilicalis with LCY from other eukaryotic phototrophs and from cyanobacteria. ML (RAxML) tree constructed from a protein alignment including 383 amino acid positions and rooted with the single LCY sequence from S. elongatus PCC6301. The results of ML bootstrap analysis with RAxML (100 replicates) and PhyML (100 replicates) are shown above and below the branches, respectively (only values >50 are shown); thick branches represent 95% Bayesian posterior probability as observed using MrBayes. Unit of branch lengths is number of substitutions per site. Abbreviations: C, capsanthin/capsorubin synthase; CrtL-b, bacterial lycopene β-cyclase; CrtL-e, bacterial lycopene ε-cyclase; LCYB, eukaryotic lycopene β-cyclase; LCYE, eukaryotic lycopene ε-cyclase; N, putative neoxanthin synthase / fruit-specific lycopene β-cyclase. See Table S8 in the Supporting Information for database accession numbers of the sequences used for the phylogenetic analyses.
jpy1229-sup-0004-FigS4.pdfapplication/PDF80KFig. S4. Affiliation of the CYP97 proteins from Porphyra purpurea and P. umbilicalis with CYP97 proteins from other eukaryotic phototrophs. ML (RA × ML) tree constructed from a protein alignment including 458 amino acid positions. The results of ML bootstrap analysis with RA × ML (100 replicates) and PhyML (100 replicates) are shown above and below the branches, respectively (only values >50 are shown); thick branches represent 95% Bayesian posterior probability as observed using MrBayes. Unit of branch lengths is number of substitutions per site. See Table S8 in the Supporting Information for database accession numbers of the sequences used for the phylogenetic analyses.
jpy1229-sup-0005-TableS1.pdfapplication/PDF98KTable S1. Experimental conditions for each of the Porphyra cDNA libraries used in this study, and the corresponding number of filtered EST sequences that were generated.
jpy1229-sup-0006-TableS2.pdfapplication/PDF167KTable S2. Fisher's Exact Test for enrichment of GO terms associated to mesophile-specific contig set in comparison to reference set, for three principal categories of cellular component (C), molecular function (F), and biological process (P).
jpy1229-sup-0007-TableS3.pdfapplication/PDF64KTable S3. Differential expression of subtypes of histone genes in Porphyra purpurea between blade and conchocelis.
jpy1229-sup-0008-TableS4.pdfapplication/PDF62KTable S4. The list of 79 cytoplasmic ribosomal proteins (RPs) identified in this study from the Porphyra EST data.
jpy1229-sup-0009-TableS5.pdfapplication/PDF71KTable S5. Ribosomal protein (RP) genes of Porphyra purpurea which paralogs showed the opposite expression patterns between blade and conchocelis.
jpy1229-sup-0010-TableS6.pdfapplication/PDF73KTable S6. Proteins putatively encoded in Porphyra that are involved in the extension of fatty acids.
jpy1229-sup-0011-TableS7.pdfapplication/PDF97KTable S7. Enzymes that are putatively encoded in Porphyra and involved in the biosynthesis of carotenoids and sterols.
jpy1229-sup-0012-TableS8.pdfapplication/PDF121K

Table S8. Database accession numbers of the sequences that were used for the phylogenetic analyses.

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