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MBE Advance Access published online on April 15, 2008
Molecular Biology and Evolution, doi:10.1093/molbev/msn088
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© The Author 2008. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

Research Article

Mitochondrial Genome Evolution in the Social Amoebae

Andrew J. Heidel and Gernot Glöckner

Genome Analysis Group, Leibniz Institute for Age Research – Fritz Lipmann Institute, 07745 Jena, Germany

Corresponding author: Andrew Heidel, Genome Analysis Group, Leibniz Institute for Age Research – Fritz Lipmann Institute, 07745 Jena, Germany, phone +49-(0)3641-656441, fax +49-(0)3641-656255 aheidel{at}fli-leibniz.de

Received for publication December 18, 2007. Revision received April 4, 2008. Accepted for publication April 7, 2008.

Most mitochondria contain a core set of genes required for mitochondrial function, but beyond this base there are variable genomic features. The mitochondrial genome of the model species Dictyostelium discoideum demonstrated that the social amoebae mitochondrial genomes have a size between those of metazoans and plants, but no comparative study of social amoebae mitochondria has been performed. Here, we present a comparative analysis of social amoebae mitochondrial genomes using D. discoideum, D. citrinum, D. fasciculatum and Polysphondylium pallidum. The social amoebae mitochondria have similar sizes, AT content, gene content and have a high level of synteny except for one segmental rearrangement and extensive displacement of tRNAs. From the species that contain the rearrangement, it can be concluded that the event occurred late in the evolution of social amoebas. A phylogeny using 36 mitochondrial genes produced a well-supported tree suggesting that the pairs of D. discoideum/D. citrinum and D. fasciculatum/P. pallidum are sister species although the position of the root is not certain. Group I introns and endonucleases are variable in number and location in the social amoebae. Phylogenies of the introns and endonucleases suggest that there have been multiple recent duplications or extinctions and confirms that endonucleases have the ability to insert into new areas. An analysis of dN/dS ratios in mitochondrial genes revealed that among groups of genes, ATP synthase complex genes have the highest ratio while cytochrome oxidase and NADH dehydrogenase genes had the lowest ratio. The genetic codes of D. citrinum, P. pallidum and D. fasciculatum are the universal code although D. fasciculatum does not use the TGA stop codon. In D. fasciculatum, we demonstrate for the first time that a mitochondrial genome without the TGA stop codon still uses the release factor RF2 that recognizes TGA. Theories of how the genetic code can change and why RF2 may be a constraint against switching codes are discussed.

Key Words: Dictyostelium discoideum • social amoebae • mitochondrial genomes • genetic codes


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