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

Abstract

Mitochondrial gene rearrangements are much more frequent in vertebrates than initially thought. It has been suggested that the origin of light strand replication could have an important role in the process of gene rearrangements, but this hypothesis has never been tested before. We used amphibians to test the correlation between light-strand replication origin thermodynamic stability and the occurrence of gene rearrangements. The two variables were correlated in a non-phylogenetic approach, but when tested in a phylogenetically based comparative method the correlation was not significant, although species with unstable light-strand replication origins were much more likely to have undergone gene rearrangements. This indicates that within amphibians there are stable and unstable phylogenetic groups regarding mitochondrial gene order. The species analyzed showed variability in the thermodynamic stability of the secondary structure, in the length of its stem and loop, and several species did not present the 5'-GCCGG-3' motif reported to be necessary for efficient mitochondrial DNA replication. Future studies should focus on the role of the light-strand replication origin in mitochondrial DNA replication and gene rearrangements mechanisms.

Next-generation sequencing of mixed genomic DNA allows efficient assembly of rearranged mitochondrial genomes inAmolops chunganensisandQuasipaa boulengeri

“…Our results supported the observation that the hotspot of gene rearrangement was adjacent to the origin of light-strand replication (San Mauro et al, 2006). The widespread occurrence of gene rearrangement among different vertebrate groups has been examined in relation to variability in the thermodynamic stability of the light-strand replication origin (Fonseca & Harris, 2008). …”

The complete mitochondrial genome sequence of the cutlassfish Trichiurus japonicus (Perciformes: Trichiuridae): Genome characterization and phylogenetic considerations

“…The sequence 5'-ACCGG-3' but conserved motif 5'-GCCGG-3' is exactly shown at the base of the stem within the tRNA Cys gene. Motif 5'-GCCGG-3' is often found in many vertebrates (Zardoya et al, 1995;Macey et al, 1997;Oh et al, 2007b;Fonseca and Harris, 2008), even in scombrid (Manchado et al, 2004; Fig. 2B-F).…”

The complete mitochondrial genome of Microtus fortis calamorum (Arvicolinae, Rodentia) and its phylogenetic analysis

“…However, in M. f. calamorum, we found the T-rich sequence was replaced by Poly C in the O L loop region .The adjacent sequence 5′-TAAGG-3′ at the base of O L stem (not the 5′-GCCGG-3′) was found in three genus Microtus species. The motif 5′-GCCGG-3′ was found in many vertebrates (Fonseca and Harris, 2008;Macey et al, 1997;Zardoya et al, 1995) and was reported to be critical for human mtDNA replication (Hixson et al, 1986). (Huang et al, 1995;Luo et al, 2000): (1) (Hong, 1981).…”