Open Access Research

Genome and low-iron response of an oceanic diatom adapted to chronic iron limitation

Markus Lommer1, Michael Specht2, Alexandra-Sophie Roy1, Lars Kraemer3, Reidar Andreson45, Magdalena A Gutowska6, Juliane Wolf2, Sonja V Bergner2, Markus B Schilhabel3, Ulrich C Klostermeier3, Robert G Beiko7, Philip Rosenstiel3, Michael Hippler2 and Julie LaRoche18*

Author Affiliations

1 RD2 Marine Biogeochemistry, Helmholtz Centre for Ocean Research Kiel (GEOMAR), Düsternbrooker Weg 20, Kiel, D-24105, Germany

2 Institute of Plant Biology and Biotechnology, University of Münster, Hindenburgplatz 55, Münster, D-48143, Germany

3 Institute of Clinical Molecular Biology ICMB, Christian-Albrechts-University Kiel, Schittenhelmstrasse 12, Kiel, D-24105, Germany

4 Department of Biology, University of Bergen, Thormøhlensgt. 53 A/B, Bergen, NO-5020, Norway

5 Estonian Biocentre, University of Tartu, Riia 23b, Tartu, EE-51010, Estonia

6 Institute of Physiology, Christian-Albrechts-University Kiel, Hermann-Rodewald-Strasse 5, Kiel, D-24118, Germany

7 Faculty of Computer Science, Dalhousie University, 6050 University Avenue, Halifax, NS B3H 1W5, Canada

8 Department of Biology, Dalhousie University, 1355 Oxford Street, Halifax, NS B3H 4J1, Canada

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Genome Biology 2012, 13:R66  doi:10.1186/gb-2012-13-7-r66

Published: 26 July 2012

Additional files

Additional file 1:

Supplemental table - BLAST analysis of AUGUSTUS-predicted protein models versus the NCBI Non-redundant Protein (nr) database and the Conserved Domain Database. The table lists the best BLAST hits from a BLASTP analysis of AUGUSTUS-predicted protein models against NCBI nr protein and Conserved Domain Database. The file is in .xls format (compressed to .zip).

Format: ZIP Size: 4.1MB Download file

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Additional file 2:

Phylogenetic trees for T. oceanica LGT candidate genes. The file comprises 254 unrooted, Newick-formatted trees containing candidate LGT genes as described in the main manuscript. Trees and corresponding support values were generated using FastTree. Novel T. oceanica genes are identified in the trees by a reference number followed by '_TO'. Homologs from the 'nr' database identified using BLAST are given in the form 'Genus_GI', except for matches to unnamed genera, which are shown as RefSeq GI number followed by 'X'. Visual inspection of trees was performed by importing this file into FigTree (Andrew Rambaut 2007) and assigning a root as described in the Supplementary Methods in Additional file 3. The file is in .tre format (compressed to .gz).

Format: GZ Size: 486KB Download file

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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.

Format: PDF Size: 768KB Download file

This file can be viewed with: Adobe Acrobat Reader

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Additional file 4:

Gene abbreviations list. The file lists gene abbreviations and gene product descriptions for all genes mentioned in this paper. The file is in .xls format.

Format: XLS Size: 31KB Download file

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Additional file 5:

Supplemental sequences - curated protein models. The file lists 436 manually curated protein sequences from nuclear genes (with custom identifiers x1 to x12 and p1 to p455) together with the 158 proteins encoded by the organellar genomes in FASTA format.

Format: FAS Size: 314KB Download file

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Additional file 6:

Supplemental table - manual transcriptome annotation. The table lists annotation information for all protein sequences provided in Additional file 5. The file is in .xls format.

Format: XLS Size: 2.4MB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 7:

Supplemental sequences - selected protein models discussed in the manuscript. The file lists sequences of proteins that we explicitly refer to in the discussion of the low-iron response. The sequences are provided in FASTA format.

Format: FAS Size: 53KB Download file

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Additional file 8:

Supplemental table - overview of low-iron responsive genes. The table contains more detailed annotation information for all protein sequences provided in Additional file 7. Deviation of a custom curated model from its respective official 't1'-AUGUSTUS prediction is indicated as 'mod'. The file is in .xls format.

Format: XLS Size: 57KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 9:

Supplemental table - comparative genomics of selected genes with a putative adaptive relevance. The table contains all official database identifiers for the gene products listed in Table 3. The file is in .xls format.

Format: XLS Size: 17KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 10:

Supplemental table - BLAST mapping of T. oceanica transcript fragments versus NCBI databases and other diatom genomes. The table provides a comprehensive overview for all 11,264 transcript fragments with read statistics, best BLASTX hits to NCBI nr and Conserved Domain Database, and additional best TBLASTX hits to the genomes of T. pseudonana, P. tricornutum and F. cylindrus, notably including worldwide web link-outs to the respective orthologous genes of these species. The file is in .xls format (compressed to .zip).

Format: ZIP Size: 5.7MB Download file

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Additional file 11:

Supplemental table - primers used for RT-qPCR. The table lists the sequences of all primers used in the RT-qPCR experiments. The file is in .xls format.

Format: XLS Size: 28KB Download file

This file can be viewed with: Microsoft Excel Viewer

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