The mitochondrial genome of Pavlova lutheri has been sequenced to 98%. It is ~30 bp in size and codes for a total of ~46 genes. The genes are tightly packed, but overlap is rare. Four sizable group II introns, one with an intronic ORF, appear in the cox1, cox3, atp6 and atp9 genes. Intergenic regions are of higher A+T content (66%) than genes (63%). Translation in P. lutheri mitochondria uses the standard genetic code.
P. lutheri mtDNA specifies those genes commonly found in other mitochondrial genomes, i.e., the protein-coding genes nad1,2,3,4,4L,5,6, cob, cox1,2,3 and atp4,6,8,9, as well as the large and small subunit rRNA genes (rnl, rns) and ~20 tRNA genes. Currently, trnC is missing, otherwise the mitochondrial-encoded tRNAs are sufficient to recognize all codons in protein-coding sequences. Also present are five ribosomal protein genes typical of protist but not animal or fungal mtDNAs; these are rpl14 rpl16 and rps12,14,19. Several free-standing ORFs have been detected as well, one of which, orf196 displays weak similarity to rpl5. In addition, one intronic ORF is present, which is located in the single cox1 intron.
Mito-ribosomal proteins are dispersed in the genome, rather than being clustered as in eubacterial genomes or mtDNAs of plants, Acanthamoeba or Reclinomonas americana. Gene content as well as gene order testify to a moderately derived mtDNA, as, for example, that of red algae.
An orphelin group II intron is found downstream of rns. No corresponding exons could be detected so far. Upstream of rnl and downstream of cox3 occur tandem repeats. We do presently not know whether the Pavlova mtDNA is circular, in which case we would expect that the region between rnl and cox3 contains repeat array. Alternatively, the chromosome could be linear with telomer-like tandem repeats at both termini.
Ribosomal RNA genes (3):
rns, rnl, rrn5
Transfer RNA genes (24):
trnA(ugc) trnD(guc) trnE(uuc) trnF(gaa) trnG(ucc) trnH(gug) trnI(gau) trnI(cau) trnK(uuu) trnL(uaa) trnL(uag) trnM(cau)e trnM(cau)f trnN(guu) trnP(ugg) trnQ(uug) trnR(acg) trnR(ucu) trnS(gcu) trnS(uga) trnT(ugu) trnV(uac) trnW(cca) trnY(gua)
Ribosomal protein genes (5):
small subunit (3 genes): rps12,14,19
large subunit (2 genes): rpl14,16
Genes for respiration and oxidative phosphorylation (14):
Respiratory chain (10): nad1,2,3,4,4L,5,6; cob; cox1,2,3;
ATP synthase complex (4): atp4,6,8,9
Intronic ORFs (1):
orf637 in cox1 intron (group II)