Mitochondrial genome organization and vertebrate phylogenetics

Abstract

With the advent of DNA sequencing techniques the organization of the vertebrate mitochondrial genome shows variation between higher taxonomic levels. The most conserved gene order is found in placental mammals, turtles, fishes, some lizards and Xenopus. Birds, other species of lizards, crocodilians, marsupial mammals, snakes, tuatara, lamprey, and some other amphibians and one species of fish have gene orders that are less conserved. The most probable mechanism for new gene rearrangements seems to be tandem duplication and multiple deletion events, always associated with tRNA sequences. Some new rearrangements seem to be typical of monophyletic groups and the use of data from these groups may be useful for answering phylogenetic questions involving vertebrate higher taxonomic levels. Other features such as the secondary structure of tRNA, and the start and stop codons of protein-coding genes may also be useful in comparisons of vertebrate mitochondrial genomes.

Evolution of the mitochondrial genome of Metazoa as exemplified by comparison of congeneric species

“…Finally, the gene order of vertebrates is not so invariant as previously reported, and the mtDNA AR appears remarkably dynamic especially in Amphibia and Lepidosauria (see respective AR rate in Table 1), as also indicated by the few cases of vertebrate congeneric comparisons here described. In fact, the dogma of a frozen gene order in vertebrates has been broken by the identification of several deviations from the 'typical' gene order in marsupials, birds, crocodiles, reptiles, amphibians, bony fishes and lampreys (Boore, 1999;Pereira, 2000;Inoue et al, 2003). Many of these alternative gene arrangements involve genes close to the CR or surrounding the Lstrand replication origin (Boore, 1999), and are sometimes associated with duplication of the CR, leading to the hypothesis that errors in mtDNA replication have given rise to these rearrangements.…”

Complete mitochondrial genome sequence of the humphead wrasse, Cheilinus undulatus

“…In vertebrates, each mtDNA strand (heavy strand and light strand) has its own control region, which forms a stable stem-loop structure (Pereira, 2000). The major portion of mtDNA involved in transcription and replication of the heavy strand in vertebrates is called the D-loop region and has been well characterized (Shadel and Clayton, 1997;Sbisa et al, 1997).…”

Relationship between mitochondrial gene rearrangements and stability of the origin of light strand replication

“…With the increasing number of whole mitochondrial genomes now published it is clear that gene order stability within vertebrates is group specific -mammals and birds have relatively stable gene orders, while in amphibians, reptiles and fish rearrangements are more common (Pereira, 2000). Phylogenetic lineages with high levels of gene rearrangements also have higher levels of genetic variation at the nucleotide level (Xu et al, 2006).…”

“…Known O L regions form characteristic stem-loop structures (Clary and Wolstenholme, 1987) and are located in the WANCY transfer RNA (tRNA) genomic region between tRNA Asn and tRNA Cys genes in most vertebrates, although in some groups, such as birds, crocodilians or some reptiles, no obvious O L exist in this region (Pereira, 2000;Macey et al, 1997Macey et al, , 2000. In general, most studies support the strand-displacement replication model and point to a possible involvement of the O L in processes of the mtDNA molecule, such as gene rearrangements (Macey et al, 1997;Mauro et al, 2005), mutation gradients (Faith and Pollock, 2003;Raina et al, 2005) and nucleotide asymmetric compositional bias (Asakawa et al, 1991;Perna and Kocher, 1995).…”