Mitochondrial gene rearrangements and partial genome duplications detected by multigene asymmetric compositional bias analysis

Asymmetric compositional and mutation bias between the two strands occurs in mitochondrial genomes, and an asymmetric mechanism of mtDNA replication is a potential source of this bias. Some evidence indicates that during replication the heavy strand is subject to a gradient of time spent in a single-stranded state (D (ssH)) and a gradient of mutational damage. The nucleotide composition bias among genes varies with D (ssH). Consequently, partial genome duplications (PGD) will alter the skew for genes located downstream of the duplication, relatively to nascent light strand synthesis, and in the same way, gene rearrangements (GRr) will affect genes by changing their skews. We examined cases where there had been PGD or GRr and determined whether this left a trace in the form of unusual patterns of base composition. We compared the skew of genes differently located on the mtDNA genome of previously published whole mtDNA genomes from amphibians, a group that shows considerable levels of both GRr and PGD. After observing a significant correlation between AT and GC skew with D (ssH) at fourfold redundant sites, we ran our analysis and detected 31.3% of the species with GRr and/or PGD. By comparing the nucleotide composition at fourfold redundant sites in normal and "abnormal" species, we found that A/C variation occurs and is associated with GRr/PGD. These results show that by analyzing the nucleotide skews of only three genes, it may be possible to predict some mitochondrial GRr and/or PGD without knowing the complete mtDNA genome sequence.