We have determined the complete sequences of the small (19,5 and 24,1 kbp, respectively) circular mitochondrial DNAs (mtDNA) of the chytridiomycete fungi, Harpochytrium #94 (Longcore) and Harpochytrium #105 (Longcore). The sequences obtained from these two species are about 90% identical in gene regions, but are of very low similarity in intergenic spacers.
The the same set of genes typical for fungal are found in both Harpochytrium species (cob, cox1, cox2, cox3, nad1, nad2, nad3, nad4, nad4L, nad5, nad6, atp6, atp8, atp9, rns, rnl, trnP, trnM, trnK, trnW, trnY, trnE, trnD, trnQ, ), all genes are transcribed from the same strand, and their gene order is identical. The gene coding for the small subunit rRNA comes in two pieces (rns_a and rns_b). The protein coding genes are translated with the universal translation code as in Allomyces sp., Rhizopus stolonifer and Schizosaccharomyces pombe. The number of tRNA genes identified so far is small, and 7 of the 8 identified genes are homologs to members of the reduced set of 8 tRNA genes found in Spizellomyces punctatus. In addition, most tRNAs have to be edited in the 5' region in order to conform to the canonical tRNA structure. The type of editing is very similar or identical to the one found in Spizellomyces punctatus and Acanthamoeba castellanii.
The phylogenetic relationships inferred from COX1 protein sequences demonstrate that Harpochytrium clearly belongs into the lineage of the Monoblepharidales, which is a sister lineage to the Chytridiales + Spizellomycetales. The phylogenetic grouping of the Monoblepharidales is consistent in sharing a reduced set of tRNA genes with the Chytridiales + Spizellomycetales. The use of the universal translation code in Monoblepoharidales mitochondria likely reflects a trait derived from a common fungal ancestor, which was also retained in the Blastocladiales and some "higher" fungi.