Welcome to MitoFun!

­MitoFun is a manually curated database and provides data concerning MITOchondrial FUNgal genomes in a uniform manner, for correcting possible erroneous or missing gene assignments. MitoFun data originate from several sources, such as:

  • in-house sequenced genomes
  • publicly available fungal mitochondrial genomes from GenBank
  • mitochondrial genomes mined from web repositories (i.e. the Broad Institute and the Joint Genome Institute sequencing centers) of complete fungal genome projects.

Fungal mitochondrial genomes are flexibly presented through a GBrowse based genome browser. The mt genomes of interest may be easily accessed through an alphabetical list of the species whose mt genome is available or a phylogenetic tree. Synteny comparisons (either by blocks or in a scaled form) are also provided through a unified interface. BLAST search against genomes/genes/coding/protein sequences provides the option to search for similarities for user defined queries. In an overview drop-down menu, a short MitoFun tutorial, the necessary MitoFun assumptions for presenting data in a consistent manner, related literature for mt genomes and genes and useful links, are available for the visitor. In addition, users have the ability to download gene, coding and protein sequences.

The MitoFun Team welcomes suggestions, comments and submission of novel fungal mt genomes. 

Fig. 1 – Structure of a typical mitochondrion (Source: <a href="http://commons.wikimedia.org/wiki/Category:Images" target="_blank">Wikipedia commons</a>)
Fig. 1 – Structure of a typical mitochondrion (Source: Wikipedia commons)

 

 

Mitochondria contain their own genome (mtDNA or mt genome), which range in size and structure. In fungi, the size of mtDNA ranges from ca. 16-110 kbs, and they may be presented as circular (most common map depiction, Fig. 2) or in linear form (with telomeric ends). It does not encode for the majority of mitochondrion’s necessary components, which are encoded from nuclear genes and are imported to the mitochondrion.  However, it usually includes the same set of genes with small exceptions. In detail, in fungal mt genomes, 14 protein-encoded genes (i.e., atp6, atp8, atp9, cob, cox1-3, nad1-6 and nad4L) implicated in oxidative phosporylation and the production of ATP (Fig. 3), 2 genes of rRNA (rns and rnl) and a gene (rps3) of a protein necessary for the composition of the small and large subunit of the mitochondrial ribosome, and a set of genes (trn) for tRNAs (ranging from 8-24). MtDNAs show a great variability which may be attributed to inclusion of many different introns (either group-I or group-II) and the highly variable intergenic regions of these genomes.  

 

 

Mitochondrion (Fig. 1) is a eukarytotic organelle commonly known as the “cellular power plant”, since its main function is the production of ATP. It participates in signaling, cell death, cell differentiation and the control of cell growth as well as the control of the cell cycle. Its origin may be explained by two different hypotheses:

  • Autogenous hypothesis. According to which a DNA portion of the nucleus of the eukaryotic cell during its divergence from the prokaryote has been enclosed by membranes and thus the mitochondrion was created.
  • Endosymbiotic hypothesis (the prevailing supposition). According to this hypothesis, mitochondrion is the result of an emdosymbiosis between a procaryotic cell capable of implementing oxidative mechanisms and the ancestor of the eukaryotic cell.

This ancestor of the mitochondrion, often called proto-mitochondrion, seems to be a close relative of alpha-proteobacteria belonging to the order of Rickettsiales.

 

Fig. 2 – A typical circular map of a mitochondrial genome: the mtDNA of Trichophyton  tonsurans (sequence available by Broad Institute). Map generated by M. Ntertili using CGView Server.)
Fig. 2 – A typical circular map of a mitochondrial genome: the mtDNA of Trichophyton tonsurans (sequence available by Broad Institute)
Map generated by M. Ntertili using CGView Server)

Fig. 3 – The oxidative phosphorylation pathway of Neurospora crassa. Proteins encoded from both nuclear and mitochondrial genes implicated in this pathway are shown.(Image kindly provided by KEGG.)

Fig. 3 – The oxidative phosphorylation pathway of Neurospora crassa.
Proteins encoded from both nuclear and mitochondrial genes implicated in this pathway are shown.
(Image kindly provided by KEGG)

Fungi (Fig. 4) comprise one of the biggest phyla of extant organisms with more than 1M species. They are heterotrophic eukaryotes found in all known habitats. Mitochondrial genome sequences evolve faster than their nuclear counterpart and may be useful for inferring phylogenetic relationships, fungal taxonomy, species evolution and strain/species typing.

  • Fig. 4 – Representative fungal species: A. Basidiomycetes in their natural environment (photos from Ms. M. Ntertili and Dr. V.N. Kouvelis)
  • Fig. 4 – Representative fungal species: B. cultured Ascomycetes from ATHUM collection (curators Dr. E. Kapsanaki-Gotsi and Z. Gonou-Zagou). From upper left (clockwise): Aspergillus flavus, Penicillium miszynskii, Acrodontium crateriforme and Penicillium sclerotiorum. (photos kindly provided by Dr. I. Pyrri, University of Athens)
  • Fig. 4 – Representative fungal species: C. microscopic specimens from ATHUM collection. From upper left (clockwise): Penicillium expansum, Rhizopus oryzae, Fusarium equisetii and Circinella minor (photos kindly provided by Dr. I. Pyrri, University of Athens)

Fig. 4 – Representative fungal species: A. Basidiomycetes in their natural environment (photos from Ms. M. Ntertili and Dr. V.N. Kouvelis) B. cultured Ascomycetes from ATHUM collection (curators Dr. E. Kapsanaki-Gotsi and Z. Gonou-Zagou). From upper left (clockwise): Aspergillus flavus, Penicillium miszynskii, Acrodontium crateriforme and Penicillium sclerotiorum. (photos kindly provided by Dr. I. Pyrri, University of Athens) C. microscopic specimens from ATHUM collection. From upper left (clockwise): Penicillium expansum, Rhizopus oryzae, Fusarium equisetii and Circinella minor (photos kindly provided by Dr. I. Pyrri, University of Athens).

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