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Evolution of trnF(GAA) pseudogenes in cruciferous plants

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Abstract

In several studies we used the 5′-trnL(UAA)–trnF(GAA) region of the chloroplast DNA for phylogeographic reconstructions, gene diversity calculations and phylogenetic analyses among the genera Arabidopsis and Boechera. Despite the fact that extensive gene duplications are rare within the chloroplast genome of higher plants, within several genera of the Brassicaceae the anticodon domain of the trnF(GAA) gene exhibit extensive gene duplications with 1–12 tandemly repeated copies in close 5′-proximity of the functional gene. A recent re-examination and additional analysis of trnL(UAA)–trnF(GAA) regions from numerous cruciferous taxa not only reveal extensive trnF gene duplications, but also favour the hypothesis that in cruciferous taxa at least four independent phylogenetic lineages are characterized by these pseudogenes. Among these lineages there is one major clade of taxa carrying pseudogenes indicating an ancient split in crucifer evolution. In two case studies, Boechera and Arabidopsis, intra- and inter-molecular recombinations have been shown to be the reason for the reciprocal exchange of several similar motifs. However, functional constraints might favour two to three or five to six copies as shown for Arabidopsis and Boechera. Herein, we compare the occurrence and distribution of pseudogene copy number in the framework of a comprehensive survey of cpDNA haplotype variation in Boechera, the former genus Cardaminopsis and Arabidopsis thaliana and comment on the value of such kind of mutations in phylogenetic and evolutionary reconstructions.

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Acknowledgments

This work was supported by grants from the Austrian Science Foundation—FWF (GEN-15609 and GEN-14463) and the German Science Foundation—DFG (Ko-2302/4-1 and Ko-2302/5-1) to M. Koch. We also thank James Beck and Steve Ansell providing us with their original DNA sequence alignments.

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  1. Heidelberg Institute of Plant Science, University of Heidelberg, Im Neuenheimer Feld 345, 69120, Heidelberg, Germany

    Roswitha Schmickl, Christiane Kiefer, Christoph Dobeš & Marcus A. Koch

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  1. Roswitha Schmickl
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  2. Christiane Kiefer
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Correspondence to Marcus A. Koch.

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Schmickl, R., Kiefer, C., Dobeš, C. et al. Evolution of trnF(GAA) pseudogenes in cruciferous plants. Plant Syst Evol 282, 229–240 (2009). https://doi.org/10.1007/s00606-008-0030-2

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