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MBE Advance Access published online on September 20, 2006
Molecular Biology and Evolution, doi:10.1093/molbev/msl130
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© The Author 2006. 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
Accepted September 18, 2006

Research Article

Supernetwork Identifies Multiple Events of Plastid TRNF(GAA) Psuedogene Evolution in the Brassicaceae

Marcus A. Koch 1 *, Christoph Dobes 1, Christiane Kiefer 1, Roswitha Schmickl 1, Leos Klimes 2, and Martin A. Lysak 3

1 Heidelberg Institute for Plant Science, Biodiversity and Plant Systematics, Heidelberg University, Heidelberg, Germany
2 Institute of Botany, Academy of Sciences of the Czech Republic, Dukelská 135, CZ-379 01 Trebon, Czech Republic
3 Jodrell Laboratory, Royal Botanic Gardens, Kew, UK & Department of Functional Genomics and Proteomics, Masaryk University, Brno, Czech Republic

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


  Abstract

The occurrence of non-functional trnF pseudogenes has been rarely described in flowering plants. However, we describe the first large scale supernetwork for the Brassiccaeae built from gene trees for 5 loci (adh, chs, matK, trnL-F and ITS) and report multiple independent origins for trnF pseudogenes in crucifers. The duplicated regions of the original trnF gene are comprised of its anticodon domain and several other highly structured motifs not related to the original gene. Length variation of the trnL-F intergenic spacer region in different taxa ranges from 219 - 900 bps as a result of differences in pseudocopy number (1-14). It is speculated that functional constraints favour 2-3 or 5-6 copies, as found in Arabidopsis and Boechera. The phylogenetic distribution of micro structural changes for the trnL-F region supports ancient patterns of divergence in crucifer evolution for some but not all gene loci.

Keywords: Brassicaceae; plastome; pseudogene evolution; trnF gene; supernetwork.
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