The circular mitochondrial genome of Pedinomonas minor is only 25 kbp in size. Compared to other protists, P. minor contains a reduced set of mitochondrial genes, including the protein-coding genes cob, cox1, nad1,2,3,4,4L,5, and atp6,8, but no ribosomal protein genes. Structural RNA genes include rnl (large subunit rRNA) and rns (small subunit) and genes for 10 tRNAs. These mtDNA-encoded tRNAs are presumably supplemented by additional, imported, nuclear DNA-encoded tRNAs to permit translation of all codons in protein-coding genes. Transcribed genes are found on one DNA strand only. The only apparent deviation from the standard genetic code is UGA, which specifies tryptophan.
A novel feature of this genome is the fact that the rnl gene is fragmented into 2 pieces, rnl_a and rnl_b, which are located far apart in the coding portion of the genome. The only intron in this mtDNA (group II) is located in rnl_a.
The genes are clustered and tightly packed within a 16 kbp stretch, with the remaining 9 kbp comprising a complex series of repeated sequences located between nad1 and nad6. The primary repeat elements range in size from 6 to 389 bp and comprise 13 distinct families (element 1 to element 13) based on sequenced relatedness. Most members within an element family are identical, a few are distinguished by a sequence differences of up to 25%. The repeat elements either occur as simple duplications or are integrated into an elaborate superstructure in which primary elements from different families form second order, and those again third order, repeat units. The only identified gene in the repeated region is a trnY2, which differs in sequence at 2 positions from a trnY1 at the end of the gene-containing region.
Features of P. minor mtDNA that are reminiscent of the C. reinhardtii mitochondrial genome include small size, absence of cox2, cox3 and any ribosomal protein genes, limited number of tRNA genes, and fragmentation of rRNA genes.