The complete nucleotide sequence of the mitochondrial genome of the lungfish (Protopterus dolloi) supports its phylogenetic position as a close relative of land vertebrates.

The complete DNA sequence (16,646 bp) of the mitochondrial genome of the African lungfish, Protopterus dolloi, was determined. The evolutionary position of lungfish as possibly the closest living relative among fish of land vertebrates made its mitochondrial DNA sequence particularly interesting. Its mitochondrial gene order conforms to the consensus vertebrate gene order. Several sequence motifs and secondary structures likely involved in the regulation of the initiation of replication and transcription of the mitochondrial genome are conserved in the lungfish and are more similar to those of land vertebrates than those of ray-finned fish. A novel feature discovered is that the putative origin of L-strand replication partially overlaps the adjacent tRNA(Cys). The phylogenetic analyses of genes coding for tRNAs and proteins confirm the intermediate phylogenetic position of lungfish between ray-finned fishes and tetrapods. The complete nucleotide sequence of the African lungfish mitochondrial genome was used to estimate which mitochondrial genes are most appropriate to elucidate deep branch phylogenies. Only a combined set of either protein or tRNA mitochondrial genes (but not each gene alone) is able to confidently recover the expected phylogeny among vertebrates that have diverged up to but not over approximately 400 mya.