We have determined the complete nucleotide sequence of the circular mitochondrial DNA (mtDNA) of the zygomycete fungus, Rhizopus oryzae, from a strain that was previously misidentified as R. stolonifer (54,178 bp; A+T content 73.9%). The identified genes that are typical for most fungal mitochondria include those for the large (rnl) and small subunit (rns) ribosomal RNAs, three ATPase subunits (atp6, atp8 and atp9), apocytochrome b (cob), three subunits of the cytochrome oxidase complex (cox1, cox2 and cox3), and seven subunits of the NADH dehydrogenase complex (nad1, nad2, nad3, nad4, nad4L, nad5 and nad6). A total of 9 group I introns are found, five of which contain open reading frames (ORFs) that code for potential endonucleases. All protein coding genes and ORFs can be translated with the universal translation code.
The reduced set of only 24 tRNAs genes in this mtDNA does not include trnI(cau), which would code for a tRNA recognizing AUA codons. Because no AUA codons are found in mitochondrial protein coding genes of Rhizopus, the 24 tRNAs are sufficient to translate the mitochondrial mRNAs.
Like in Allomyces mtDNA, highly structured and conserved DNA elements are inserted in intergenic spacers, introns, and variable regions of the rnl and rns genes.