The linear mitochondrial genome of Ochromonas danica is 41.035 kbp in size. The ends of the mtDNA consist of 2.2 kbp-long inverted repeats, which code for several genes. No telomeric sequences
(as occur in the linear mtDNA of Tetrahymena pyriformis) were detected.
The O. danica mitochondrial genome contains genes for the most commonly mtDNA-encoded proteins
(nad1,2,3,4,4L,5,6, cob, cox1,2,3, atp6,8,9),
as well as genes for two rRNAs (rns, rnl) and 25 tRNAs (not counting the 4 duplicated copies in the terminal repeats). The latter would
recognize all codons in protein-coding sequences except threonine, cysteine,
and arginine (CGN codon family). No introns have been found in this mtDNA.
In addition to standard mitochondrial genes, O. danica mtDNA codes for a number of proteins whose genes are not found in the more derived animal or fungal mtDNAs, but instead are rather typical of protist mtDNAs. These genes include nad7,9,11, rpl2,6,14,16, and rps3,7,8,10,12,13,14,19. Further, 14 long unique ORFs and a DNA polymerase gene (dpo) have been identified in this mtDNA. The presence of a mitochondrially encoded dpo is a rather exciting exception, even among protists.
The tightly packed genes are separated by A+T-rich intergenic regions and are transcribed from five distinct blocks located on both DNA strands.
The mitochondrial translation code in O. danica is the standard genetic code, as is also the case in its relatives, Chrysodidymus synuroideus and Phytophthora infestans.