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MBE Advance Access published online on February 2, 2005
Molecular Biology and Evolution, doi:10.1093/molbev/msi092
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Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2005; all rights reserved.
Accepted January 7, 2005

Research Article

Evolution of the trnF(GAA) Gene in Arabidopsis Relatives and the Brassicaceae Family: Monophyletic Origin and subsequent Diversification of a Plastidic Pseudogene

Marcus A. Koch 1*, Christoph Dobes 1, Michaela Matschinger 1, Walter Bleeker 2, Johannes Vogel 3, Markus Kiefer 1, and Thomas Mitchell-Olds 4

1 Heidelberg Institute of Plant Science, Heidelberg University, Heidelberg, Germany
2 Department of Systematic Botany, University of Osnabrück, Germany
3 National History Museum, Botany Department, London, UK
4 Max Planck Institute for Chemical Ecology, Jena, Germany

* To whom correspondence should be addressed.
Marcus A. Koch, E-mail: marcus.koch{at}urz.uni-heidelberg.de


  Abstract

Recently we used the 5'-trnL(UAA)-trnF(GAA) region of the chloroplast DNA for phylogeographic reconstructions and phylogenetic analysis among the genera Arabidopsis, Boechera, Rorippa, Nasturtium and Cardamine. Despite the fact that extensive gene duplications are rare among the chloroplast genome of higher plants, within these taxa the anticodon domain of the trnF(GAA) gene exhibit extensive gene duplications with one to eight tandemly repeated copies in close 5'-proximity of the functional gene. Interestingly, even in Arabidopsis thaliana we found six putative pseudogenic copies of the functional trnF gene within the 5'-intergenic trnL-trnF spacer. A re-examination of trnL(UAA)-trnF(GAA) regions from numerous published phylogenetic studies among halimolobine, cardaminoid and other cruciferous taxa revealed not only extensive trnF gene duplications, but also favour the hypothesis about a single origin of trnF pseudogene formation during evolution of the Brassicaceae family 16-21 mya. Conserved sequence motifs from this tandemly repeated region are co-distributed non-randomly throughout the plastome, and we found some similarities with a DNA sequence duplication in the rps7 gene and its adjacent spacer. Our results demonstrate the potential evolutionary dynamics of a plastidic region generally regarded as highly conserved and probably co-transcribed, and, as shown here for several genera among cruciferous plants, greatly characterized by parallel gains and losses of duplicated trnF copies.

Keywords: Brassicaceae; trnF(GAA); pseudogenes; phylogeny; gene duplication.
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