Mitogenomics of recombinant mitochondrial genomes of Baltic Sea Mytilus mussels

Recombination in the control region (CR)of Mytilus mitochondrial DNA (mtDNA) was originallyreported based on the relatively short, sequenced fragmentsof mitochondrial genomes. Recombination outside the CRhas been reported recently with the suggestion that suchprocesses are common in Mytilus. We have fully sequenceda set of 11 different mitochondrial haplotypes representingthe high diversity of paternally inherited mitochondrialgenomes of Baltic Sea Mytilus mussels, including the haplotypeclose to the native Mytilus trossulus mitochondrialgenome, which was thought to have been entirely eliminatedfrom this population. Phylogenetic and comparativeanalysis showed that the recombination is limited tothe vicinity of the CR in all sequenced genomes. Codingsequence comparison indicated that all paternally inheritedgenomes showed increased accumulation of nonsynonymoussubstitutions, including the genomes which switchedtheir transmission route very recently. The acquisition ofcertain CR sequences through recombination with highlydivergent paternally inherited genomes seems to precedeand favor the switch, but it is not a prerequisite for this process.Interspecies hybridization in the Baltic Sea during therecent 10,000 years created conditions for both structuraland evolutionary mitochondrial instability which resulted in the observed variation and dynamics of mtDNA in BalticSea Mytilus mussels. In conclusion, the data shows that theeffects of mitochondrial recombination are limited to theCR of few phylogenetic lineages.