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Open Access Research article

Mitochondrial genome evolution in species belonging to the Phialocephala fortinii s.l. - Acephala applanata species complex

Angelo Duò1, Rémy Bruggmann2, Stefan Zoller3, Matthias Bernt4 and Christoph R Grünig15*

Author Affiliations

1 Forest Pathology and Dendrology, Institute of Integrative Biology (IBZ), ETH Zurich, CH-8092, Zurich, Switzerland

2 Bioinformatics, Department of Biology, University of Berne, Baltzerstrasse 6, CH-3012, Bern, Switzerland

3 Genetic Diversity Centre (GDC), ETH Zurich, CH-8092, Zurich, Switzerland

4 Parallel Computing and Complex Systems Group, Department of Computer Science, University of Leipzig, Johannisgasse 26, D-04009, Leipzig, Germany

5 Microsynth AG, Schützenstrasse 15, CH-9436, Balgach, Switzerland

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BMC Genomics 2012, 13:166  doi:10.1186/1471-2164-13-166

Published: 4 May 2012

Additional files

Additional file 1:

Titel: Transcriptomics landscape in the mt genome of Phialocephala subalpina. Description: Sequence coverage for 5,903 454 cDNA reads (total number of aligned bases: 1.89 Mbp) that mapped to the mt genome of Phialocephala subalpina. 454 reads almost exclusively mapped to coding regions of the mt genome (proteins and rDNAs) but depths of coverage differed considerably among genes.

Format: EPS Size: 686KB Download file

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Additional file 2:

Titel: Protein aligenemts for putative ORFs. Description: Protein alignments of two putative ORFs (ORF_02, ORF_03) for eight PAC species.

Format: DOC Size: 36KB Download file

This file can be viewed with: Microsoft Word Viewer

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Additional file 3:

Titel: Gene order data used for TreeREx and CREx analysis. Descriptions: Gene order data for 13 unique gene orders observed in species belonging to the Pezizomycotina and used for TreeREx and CREx analysis.

Format: TXT Size: 2KB Download file

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Additional file 4:

Titel: CREx and TreeREx analysis. Description: In the first two sections an informal introduction to CREX and TREEREX is given. For a detailed introduction we refer to Bernt et al. (2007, 2008). Sections 3 to 6 include a detailed description of the gene order analyses performed completing the results included in the paper.

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Additional file 5:

Titel: Polymorphism screening in PAC. Description: Amount and distribution of polymorphisms found at four mt loci for five species of the Phialocephala fortinii s.l. – Acephala applanata species complex (PAC). The four loci included approx. 7,800 bp representing 17.8% of the mt genome. The position of protein coding regions and rDNAs are indicated. Thick bars represent the fragment chosen for testing mt loci for species diagnosis in PAC (8 species, 32 strains).

Format: EPS Size: 984KB Download file

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Additional file 6:

Titel: List of primers used to sequence the mt genome of Phialocephala subalpina. Description: List of primers used to amplify and sequence the complete mt genome of Phialocephala subalpina.

Format: XLS Size: 26KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 7:

Titel: Presence/absence of tRNA genes in species belonging to the Pezizomycotina included in CREX and TREEREX analysis.

Format: XLSX Size: 57KB Download file

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Additional file 8:

Titel: Primers used for phylogenetic analyis in the Phialocephala fortinii s.l. – Acephala applanata species complex (PAC). Description: Primers used to amplify three mtDNA loci in eight species belonging to PAC.

Format: XLS Size: 19KB Download file

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