Research
Comparative and functional genomics provide insights into the pathogenicity of dermatophytic fungi
- † Equal contributors
1 Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Beutenbergstrasse 11a, Jena, 07745, Germany
2 Institute of Microbiology, Friedrich Schiller University (FSU) Jena, Neugasse 24, Jena, 07743, Germany
3 Systems Biology/Bioinformatics group, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Beutenbergstrasse 11a, Jena, 07745, Germany
4 Genome Analysis group, Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, Jena, 07745, Germany
5 Department of Infection Biology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Beutenbergstrasse 11a, Jena, 07745, Germany
6 Friedrich Schiller University (FSU) Jena, Fürstengraben 26, Jena, 07743, Germany
7 Junior Research Group Fundamental Molecular Biology of Pathogenic Fungi, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Beutenbergstrasse 11a, Jena, 07745, Germany
8 Biocomputing group, Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, Jena, 07745, Germany
9 Swiss-Prot group, SIB, Swiss Institute of Bioinformatics, 1 rue Michel Servet, Geneve, 1204, Switzerland
10 Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Beutenbergstrasse 11a, Jena, 07745, Germany
11 Department of Molecular Genetics and Microbiology, Duke University Medical Center, 322 CARL Building, Box 3546 DUMC, Durham, NC 27710, USA
12 Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Beutenbergstrasse 11a, Jena, 07745, Germany
13 Seattle Biomedical Research Institute, University of Washington, 307 Westlake Ave, N., Suite 500, Seattle, WA 98109-5219, USA
14 Department of Dermatology, Centre Hospitalier Universitaire Vaudois, Lausanne, CH-1011, Switzerland
Genome Biology 2011, 12:R7 doi:10.1186/gb-2011-12-1-r7
Published: 19 January 2011Additional files
Additional file 1:
Supplementary information to Figures 1and 3.
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Additional file 2:
Supplementary data on genome structure of dermatophytes. Table S1a: a detailed description of the sequencing. Table S1b: information on combined assembly. Figure S1: found translocations and the inverson.
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Additional file 3:
Generation of the phylogenetic tree. The file contains the whole phylogenetic tree (Figure S2) and a table of genes used for its construction.
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Additional file 4:
Species-specific genes. The Excel file contains lists of genes that do not have counterparts in the other genome.
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Additional file 5:
Table S2: Fast-evolving A. benhamiae genes (dN/dS >1).
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Additional file 6:
supplementary Tables S3, S5, S6, S7, S8, and S9. Table S3: predicted proteases with marked proteases with secretion signal according to SignalP predictions. Table S5: identification and prediction of secretion signals of protein spots shown in Figure 3. Table S6: comparison of dermatophyte secretome data of Giddey et al. [4 ] and the present study. Table S7: differentially expressed genes of A. benhamiae during co-cultivation with human keratinocytes. Table S8: genes implicated in sexual reproduction and meiosis-specific genes. Table S9: numbers of reads obtained in the transcriptome analysis of infection and control samples.
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Additional file 7:
Table S4: secreted proteases in A. benhamiae, T. verrucosum, Aspergillus fumigatus and Coccidioides spp.
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Additional file 8:
Phylogenetic trees of secreted proteases. The file contains the phylogenies of the A. benhamiae, T. verrucosum, and Coccidioides secreted proteases of the most distinguishing families S8, M35, and M36 (Figure S3.1, S3.2, and S3.3, respectively).
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Additional file 9:
Figure S4: Northern Blot analysis.
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Additional file 10:
Phylogenetic trees of A. benhamiae, T. verrucosum, and Coccidioides immitis PKSs and NRPSs. The file contains phylogenetic trees built for NRPSs (Figure S5.1) and PKSs (Figure S5.2), comparing the corresponding genes sets of the three species.
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