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

Journal of Molecular Evolution volume 65, pages124–136(2007)Cite this article

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 (OH) 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 (OL) suggested that the most probable site lies within the ND3 gene. By adopting this OL position we calculated times of exposure for 0FD (nondegenerate), 2FD (twofold degenerate), and 4FD (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 4FD sites was highly correlated with the presumed time of exposure. Such an effect was not found for the 2FD sites, the rRNA, the tRNA, or the noncoding parts. There was a trend for a small increase in cytosine at 0FD sites with exposure time, which is explicable as the result of biased usage of 4FD 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.

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Acknowledgments

This work was supported by the Greek General Secretariat for Research and Technology (Grant PENED-01ED42 to G.C.R., A.M., and E.Z.), by the Marine Genomics Europe Network of Excellence (to E.Z.), by the Natural Sciences and Engineering Research Council of Canada (to E.K.), by Dalhousie University and Patrick Lett Scholarships and Fisheries and Oceans, Canada (to L.C.), and by the University of Athens, Greece (to G.C.R.). We thank S. J. Smith, Bedford Institute of Oceanography, Dartmouth, NS, Canada, for statistical advice. We also thank two anonymous referees for constructive comments.

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  1. Liqin Cao

    Present address: Department of Laboratory Animal Science, Tokyo Metropolitan Institute of Medical Science, Tokyo, 113-8613, Japan

Affiliations

  1. Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Panepistimioupolis, 15701, Athens, Greece

    George C. Rodakis & Athanasia Mizi

  2. Department of Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4J1, Canada

    Liqin Cao & Ellen L. R. Kenchington

  3. Department of Fisheries and Oceans, Bedford Institute of Oceanography, Dartmouth, Nova Scotia, B2Y 4A2, Canada

    Ellen L. R. Kenchington

  4. Department of Biology, University of Crete, 71409, Heraklion, Crete, Greece

    Eleftherios Zouros

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  1. George C. Rodakis
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Correspondence to Eleftherios Zouros.

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Rodakis, G.C., Cao, L., Mizi, A. et al. Nucleotide Content Gradients in Maternally and Paternally Inherited Mitochondrial Genomes of the Mussel Mytilus . J Mol Evol 65, 124–136 (2007). https://doi.org/10.1007/s00239-005-0298-6

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Keywords

  • Mytilus
  • Mitochondrial genome
  • Maternally/paternally inherited mtDNA
  • Mutational strand asymmetry