The circular mitochondrial genome of Jakoba libera strain ATCC 50422 is 96.6 kbp in size. Sequencing is nearly completed. At present, 77 genes have been identified, none of them including an intron. Intergenic regions account for ~ 30% of the genome and contain clusters of tandem repeats whose unit length is ~20 bp. Transcribed genes are found on both DNA strands. The standard genetic code is used for translation.
Encoded genes include those commonly found in mtDNA, including the protein-coding genes nad1,2,3,4,4L,5,6, cob, cox1,2,3, and atp6,8,9, as well as large subunit (rnl) and small subunit (rns) rRNA genes and >22 tRNA genes. Also present are a number of protein genes typical of protist but not animal or fungal mtDNAs. These include nad7,9,11, atp1, rpl2,5,6,14,16, and rps2-4,11-14,19. A number of unique ORFs are also encoded by J. libera mtDNA.
As in the histionid R. americana, a number of J. libera mitochondrial genes are rare or absent in other mitochondrial genomes but are present in bacteria. Among these rare or unique mtDNA-encoded genes are dpo, rpoB,C, rrn5, rnpB, tufA, yejU-W, and several of the ribosomal protein genes. With the exception of dpo, all unusual genes found in the J. libera mtDNA are also present in the R. americana mitochondrial genome.
As observed in R. americana, remnants of a prokaryotic operon organization are evident in several gene clusters such as theose encoding succinate dehydrogenase and NADH dehydrogenase subunits.
A comparison of gene order in the mtDNAs of J. libera and R. americana shows that these two histionids are more closely related than initially assumed. They share clusters that are otherwise not found in bacteria but that evidently appeared during evolution of the mitochondrial genome after the divergence of the proto-mitochondrion from the bacterial lineage. Examples are the clusters sdh3 to nad5, (comprising 5 genes), atp8-[trn]-rps4-atp9 and nad11-nad1-cox11-cox3-tufA.