The mitochondrial genome of Amoebidium parasiticum consists of several hundred linear
molecules (chromosomes) with an approximate total size of ~300 kbp.
The chromosomes share a common and unusually short and unique terminal repeat structure. The ends
consist invariably of a 44-bp sequence motif in inverted orientation (repx)
followed by one copy of repa (97 bp) at one end and one copy of repb (92 bp) at the
other end.
In all gene-carrying chromosomes, transcription is in direction repa ==> repb.
Some chromosomes contain several
genes, others just one gene, and a large number of smaller chromosomes (<1.6 bkp) appear to have
no coding content, but include numerous and diverse combinations of distinct repeat elements that
are 24 - 265 bp in length.
At the current status, we have sequenced about 1/2 of A. parasiticum mtDNA. A total of different 53 genes and at least 30 ORFs have been found. Especially tRNA genes are duplicated, and numerous gene fragments were observed as well. The genome specifies genes commonly found in other mtDNAs, i.e., the protein-coding genes nad1,2,3,4L,5,6 cob, cox1,2,3 and atp6,8,9, as well as the large and small subunit rRNA genes (rnl, rns) and a large set of tRNA genes. Of nad1, 2 and 6, only gene fragments have been found so far. Translation in A. parasiticum mitochondria uses the standard genetic code, except that UGA specifies tryptophan.
Only a few genes typical of protist are present, namely rps4 and rps13, coding for ribosomal proteins. Otherwise, the gene set is characteristic for animal or fungal mtDNAs.
Introns are abundant in A. parasiticum mtDNA (21 group I and two group II introns). Despite that genes are tightly packed on the gene-containing molecules, intergenic spacers being only ~ 80 - 200 bp on average, the overall gene density is extremely low: Only ~20% of the genome has an identified coding function.