Open Access Research

Premetazoan genome evolution and the regulation of cell differentiation in the choanoflagellate Salpingoeca rosetta

Stephen R Fairclough1, Zehua Chen2, Eric Kramer3, Qiandong Zeng2, Sarah Young2, Hugh M Robertson4, Emina Begovic1, Daniel J Richter1, Carsten Russ2, M Jody Westbrook1, Gerard Manning3, B Franz Lang5, Brian Haas2, Chad Nusbaum2* and Nicole King1*

Author Affiliations

1 Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA

2 Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA

3 Department of Computational Biology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA

4 Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA

5 Departement de Biochimie, Universite de Montreal, Montreal, Quebec, Canada

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Genome Biology 2013, 14:R15  doi:10.1186/gb-2013-14-2-r15

Published: 18 February 2013

Additional files

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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Additional file 2:

Number of ortholog pairs shared between S. rosetta and M. brevicollis scaffolds.

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Additional file 3:

The number of genes present in each of the OrthoMCL ortholog clusters.

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Additional file 4:

The genes present in each of the OrthoMCL ortholog clusters.

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Additional file 5:

OrthoMCL ortholog clusters predicted to be present in the ancestors reconstructed in Figure 2.

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Additional file 6:

Kinases identified in the S. rosetta genome.

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Additional file 7:

Read counts and FPKM values (fragments per kilobase per million reads) for genes encoded by the S. rosetta genome.

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Additional file 8:

Differentially expressed genes identified by hierarchical clustering.

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Additional file 9:

Differentially expressed genes identified by pairwise comparison.

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Additional file 10:

Differentially expressed genes identified by group comparison.

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Additional file 11:

Genes identified as upregulated in colonial cells.

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Additional file 12:

Genes identified as upregulated in thecate cells.

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Additional file 13:

Genes identified as upregulated in swimming cells.

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Additional file 14:

Blast2GO annotation of S. rosetta genome.

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Additional file 15:

Interpro annotation of S. rosetta genome.

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