The mitochondrial DNA of Allomyces macrogynus: the complete genomic sequence from an ancestral fungus.

Bruno Paquin and B. Franz Lang
Departement de Biochimie, Universite de Montreal, C.P. 6128 succ. Centre-Ville, Montreal, PQ, H3C 3J7, CANADA.

Complete fungal mitochondrial (mt) sequences are currently only available from Ascomycetes, which leaves us with an incomplete view of the diversity and evolutionary history of this genome for the fungal kingdom. Therefore, we have determined the complete primary sequence of the circular mt DNA of a lower fungus, the Chytridiomycete Allomyces macrogynus (57434 bp, A+T content 60%). The genes that we find are typical of mitochondria in the Ascomycetes, coding for the large (rnl) and small subunit (rns) ribosomal RNAs, a complete set of 25 tRNAs, three ATPase subunits (atp6, atp8 and atp9), apocytochrome b, three subunits of the cytochrome oxidase complex (cox1, cox2 and cox3), seven subunits of the NADH dehydrogenase complex (nad1, nad2, nad3, nad4, nad4l, nad5 and nad6), a ribosomal protein (rps3) and five additional open reading frames, starting with a methionine and continuing for more than 60 codons. Particular features of the A. marcrogynus mtDNA include: (i) the rps3 gene is the first documented case of a mt ribosomal protein gene that is clearly identified by similarity with bacterial homologues; (ii) a total of 28 introns was found, some of them containing open reading frames that code for potential group I endonucleases or group II reverse- transcriptases; (iii) the presence of an insert in the atp6 gene that may have been acquired by interspecific transfer, and which consists of the carboxy-terminus of a foreign atp6 gene plus an open reading frame encoding an endonuclease (Paquin et al., Proc. Natl. Acad. Sci. USA, in press). (iii) as in most Ascomycetes, all mt genes and ORFs of A. macrogynus are encoded on the same DNA strand, but none of the conserved promoter motifs or repetetive sequences found in other mtDNAs were identified; (iv) intergenic regions contain at least 35 repeated, highly structured and conserved structures that are unusually GC-rich; (v) the mt ribosomal RNA structures are much less derived than in the Ascomycetes. Both primary and secondary structures are more similar to the ones in many eubacterial, plant, green and red algae, than to other eufungi.