Additional file 3.

Supplementary Methods and Figures. The file provides a description of the RT-qPCR as well as of the bioinformatics methods (genome assembly and analysis, setup of the T. oceanica genome browser and phylogenetic analyses). It further contains supplementary Figures S1 to S9. Figure S1: taxonomy of genes acquired by lateral gene transfer (2). An overview of the taxonomic assignments for LGT candidate genes as revealed from a refined phylogenetic analysis. Figure S2: duplications of genes and domains occurring in genes whose regulation is dependent on the cellular supply with iron. Figure S3: metabolic shift. The change in relative abundance of organellar RNA between T. oceanica cells subjected to high or low iron. Figure S4: correlation plot P versus T. The extent of correlation between proteomics (P) and transcriptomics (T) data. Figure S5: FCP proteomics. The variation in the response of different FCP light-harvesting proteins to iron limitation. Figure S6: phylogenetic tree of flavodoxin proteins. A neighbor-joining tree of diatom flavodoxin proteins. Figure S7: phylogenetic tree of FBA proteins. A neighbor-joining tree of diatom fructose bisphosphate aldolase proteins. Figure S8: qPCR ΔΔCT. The differential regulation of genes in response to low iron. Data represent the change in transcript level for iron-limited T. oceanica when compared to an iron-replete control. Figure S9: promoter motif. The conservation across diatom species of a motif found in the promoters of several iron-regulated genes. The file is in .pdf format.

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Lommer et al. Genome Biology 2012 13:R66   doi:10.1186/gb-2012-13-7-r66