We have completely sequenced the circular, 49,711 kbp long mitochondrial DNA of the basidiomycete Schizophyllum commune (1). The sequencing data are in agreement with the published physical map (2).
This mt genome is very A+T-rich (78%) and contains a set of genes characteristic of fungal mtDNAs including 24 tRNAs (no tRNAI(cau) recognizing AUA codons, and no AUA codons found in any protein coding gene), the two ribosomal RNA subunits, cytochrome oxidase subunits 1, 2 and 3 (cox1,2 and 3), cytochrome b (cob), ATPase subunits 6, 8 and 9, seven subunits of the NADH dehyrogenase complex (nad1, 2, 3, 4, 4L, 5, and 6) and several long unassigned open reading frame (the longest one continues for 1453 codons). The genes are coded on both DNA strands and are often separated by long, A+T-rich 'non-coding' sequences. It has been postulated by others (3) that the universal translation code is used in S. commune mitochondria, based on the sequence of the cox3 gene. However, the analysis of the complete sequence shows that a few UGA tryptophane codons do occur in many essential mitochondrial protein genes (such as cob or nad5). UGA (trp) codons are not preferentially used as in other examples (e.g., yeast), which likely indicates that the introduction of this codon occured more recently. This is in line with the fact that the ascomycete Schizosaccharomyces pombe uses the universal translation code for its mitochondrial genes, as do many members of several, more ancestral fungi such as the Zygomycetes (Rhizopus stolonifer) and Chytridiomycetes ( Allomyces macrogynus, Harpochytrium sp.).
We have not detected any intron in this fungal mitochondrial genome, which has to be considered a rare exception to the otherwise intron-loaded fungal mtDNAs. Further unusual features of its genome organisation is the presence of very tightly stacked nad genes: the stop codon of the nad2 gene is directly adjacent to the initiation codon of the nad3 gene, and the nad4L and nad5 coding regions are separated by only two nucleotides The nad3 gene is unusual in that it has a 473 amino acids long carboxi-terminal extension, of unknown function and with no significant similarity to any protein sequence in the databases.
(1) Paquin B, Laforest M-J, Forget L, Roewer I, Zhang W, Longcore J, and Lang BF (1997). Current Genetics 31:380-395.
(2) Specht CA, Novotny CP & Ullrich RC (1992) Curr Genet 22:129-134.
(3) Phelps LS, Burke JM, Ullrich RC & Novotny CP (1988) Curr Genet 14:401-403.
(4) Paquin B, Roewer I, Wang Z and Lang BF (1995) Can J Bot 73: S180 - S185