Nucleotide Content Gradients in Maternally and Paternally Inherited Mitochondrial Genomes of the Mussel Mytilus

Abstract

Several studies have shown that in vertebrate mtDNAs the nucleotide content at fourfold degenerate sites is well correlated with the site's time of exposure to the single-strand state, as predicted from the asymmetrical model of mtDNA replication. Here we examine whether the same explanation may hold for the regional variation in nucleotide content in the maternal and paternal mtDNAs of the mussel Mytilus galloprovincialis. The origin of replication of the heavy strand (O(H)) of these genomes has been previously established. A systematic search of the two genomes for sequences that are likely to act as the origin of replication of the light strand (O(L)) suggested that the most probable site lies within the ND3 gene. By adopting this O(L) position we calculated times of exposure for 0(FD) (nondegenerate), 2(FD) (twofold degenerate), and 4(FD) (fourfold degenerate) sites of the protein-coding part of the genome and for the rRNA, tRNA and noncoding parts. The presence of thymine and absence of guanine at 4(FD) sites was highly correlated with the presumed time of exposure. Such an effect was not found for the 2(FD) sites, the rRNA, the tRNA, or the noncoding parts. There was a trend for a small increase in cytosine at 0(FD) sites with exposure time, which is explicable as the result of biased usage of 4(FD) codons. The same analysis was applied to a recently sequenced mitochondrial genome of Mytilus trossulus and produced similar results. These results are consistent with the asymmetrical model of replication and suggest that guanine oxidation due to single-strand exposure is the main cause of regional variation of nucleotide content in Mytilus mitochondrial genomes.