The circular mitochondrial genome of Naegleria gruberi is nearly 50 kbp in size. Genes are tightly packed, with non-coding sequence amounting to only 8% of the mtDNA. Most genes are encoded on the same DNA strand and the standard genetic code is used.
Compared to other protists, N. gruberi contains a large set of mitochondrial genes, including all those commonly found in animal and fungal mtDNAs: the protein-coding genes cob, cox1,2,3, nad1,2,3,4,4L,5,6 and atp6,8; the structural RNA genes rnl (large subunit rRNA) and rns (small subunit rRNA); and 23 tRNA genes (trn). The mtDNA-encoded tRNAs are presumably supplemented by additional, nuclear DNA-encoded tRNAs that are imported from the cytosol to permit translation of all codons in protein-coding genes.
In addition to this standard set, N. gruberi mtDNA contains numerous additional genes that are characteristic of plant and protist mitochondrial genomes, including genes encoding ribosomal proteins, additional subunits of the NADH dehydrogenase complex, and components of an ABC transporter. Surprisingly, two genes have been identified that have so far only been detected in jakobid mtDNAs: atp3, coding for subunit gamma of ATP synthase, and cox11, specifying a component involved in heme biosynthesis. The presence of these "extra" genes reflects the ancestral character of the N. gruberi mitochondrial genome.
The order of ribosomal protein genes in N. gruberi mtDNA is reminiscent of the bacterial gene organization in the adjacent str, S10, spc and alpha operons.