Additional file 1.

Figures S1 to S14 and Tables S1 to S8. Figure S1: transcriptional profiling experimental design. Figure S2: differentially expressed genes identified by hierarchical clustering. Figure S3: identification of upregulated genes. Figure S4: gene expression correlates with cell type. Figure S5: S. rosetta cadherin expression. Figure S6: Hedgehog signal domain-encoding genes are upregulated in thecate and colonial cell types. Figure S7: protein domain architecture of S. rosetta septins. Figure S8: septin sequence conservation. Figure S9: septin gene family phylogeny. Figure S10: ortholog cluster origin enrichment is robust to species composition. Figure S11: ortholog cluster origin enrichment is robust to changes in MCL (Markov Cluster algorithm) species inflation value. Figure S12: expression levels of receptor tyrosine kinase families. Figure S13: the phylogenetic distribution of important metazoan development genes or domains. Figure S14: synteny between the S. rosetta and M. brevicollis genomes. Table S1: S. rosetta and M. brevicollis genome statistics. Table S2: mapping of de novo transcript assembly. Table S3: telomeres predicted in the S. rosetta genome. Table S4: genomes used for comparative genomics. Table S5: Gene Ontology enrichment of novel genes. Table S6: S. rosetta tyrosine kinases. Table S7: phylogenetic distribution of genes upregulated in different cell types. Table S8: genes missing from choanoflagellate.

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Fairclough et al. Genome Biology 2013 14:R15   doi:10.1186/gb-2013-14-2-r15