Tutorial

General information

The MitoFun resource is based on the GBrowse platform for navigating through genome data and presents complete mitochondrial genomes of fungal species (MitoFun v1.0 contains genomes published up to 31 Dec 2012). Each MitoFun entry also contains useful metadata on the fungal species/strain, as for example their systematic classification, intron length and number. Most importantly, the MitoFun team re-annotates genomes before uploading them to the system. Moreover, a MitoFun user may generate in a dynamic fashion gene order diagrams for the genomes of interest via the Synteny Browser feature.

Browsing genomes

Species taxonomy is based on the respective data of the NCBI Taxonomy site. Within the Genome Browser (GBrowse) environment, for each fungal species/strain from all taxonomic units we have chosen to present at the Menu of "Data Source" the subphylum with the first letter of the subphylum and the Order to which the species belongs. Similarly, the same classification mode has been kept at the Synteny Tools. However, since the aim of this site is not the Taxonomy itself, for those visitors who would like to see the whole taxonomy of the species examined, (a) the MycoBank identity of each species, (b) its Class and Order are provided within the introductory Table at the top of the GBrowse. In addition the following data of the species itself is shown:

For the complete mitochondrial genome, we consider as important data: In every genome at GBrowse, the rnl gene is presented in a different colour (cyan) as it is considered as the starting gene of the genome.

Synteny

Currently, MitoFun supports two different ways of representing syntenic information concerning only the “universal” genes of mt genomes (i.e., atp6, 8 and 9, cob, cox1-3, nad1-6 and 4L, rps3, rns, rnl and trn genes):

Synteny (scaled): Gene order comparisons of complete mt genomes can be performed. All genomic features are plotted to scale, including intergenic regions. Genomes are rearranged so that rnl is the starting feature, facilitating easy inspection/comparison of gene order. Arrowheads indicate the direction of transcription. Using the "Select Tracks" panel/button users may choose the genomes of interest as combination of single genomes, “combo” (i.e., more than one/all genomes of fungi belonging to the same Order of interest) or both. tRNA genes (trn) may be omitted from the user’s analysis, when the appropriate single or “combo-tracks” are selected from menu “select track”. Gene color can be selected for any individual gene from the options available via the “Choose gene colors: Configure” menu. By Default, protein-coding genes for ATP synthase F0 subunits, NADH dehydrogenase subunits, Ribosomal protein S3, Cytochrome c oxidase subunits and apocytochrome b are shown in “tomato”, “greenyellow”, “darkorange” and “dodgerblue” colours, respectively. trn and rRNA genes are presented in “lightgrey” and “aqua” colours, respectively. 

Synteny (by blocks): Gene order comparisons of complete mt genomes can be performed. Each gene is represented by a fixed-width block (measured in fictional "units"), and intergenic regions are stripped. Genomes are rearranged so that rnl is the starting feature, facilitating easy inspection/comparison of gene order. Arrowheads indicate the direction of transcription. When the rps3 gene is located as an ORF within the intron of rnl, rps3 is shown above the rnl gene. Using the "Select Tracks" panel/button users may choose the genomes of interest as combination of single genomes, “combo” (i.e., more than one/all genomes of fungi belonging to the same Order of interest) or both. Gene color can be selected for any individual gene from the options available via the “Choose gene colors: Configure” menu. By Default, protein-coding genes for ATP synthase F0 subunits, NADH dehydrogenase subunits, Ribosomal protein S3, Cytochrome c oxidase subunits and apocytochrome b are shown in “tomato”, “greenyellow”, “darkorange” and “dodgerblue” colours, respectively. trn and rRNA genes are presented in “lightgrey” and “aqua” colours, respectively. 

Contact:
The MitoFun Team welcomes suggestions, comments and submission of novel fungal mt genomes. Please feel free to contact any of the MitoFun Team Members.

Acknowledgements:
MitoFun is a collaborative project between the Department of Genetics and Biotechnology (Faculty of Biology, University of Athens) and the Bioinformatics Research Laboratory (Department of Biological Sciences, University of Cyprus).
This project was partially funded by the University of Athens (Kapodistrias grant no. 70/4/8804) and the University of Cyprus (Grant 3/311).
The MitoFun development team: Ioannis Kirmitzoglou, Maria Ntertili, Stella Tamana, Ioanna Kalvari, Michalis Vasiliadis, Vassili N. Kouvelis, Vasilis J. Promponas, and Milton A. Typas
© 2006-2013 Bioinformatics Research Laboratory, University of Cyprus
© 2006-2013 Department of Genetics and Biotechnology, University of Athens