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MBE Advance Access originally published online on September 20, 2006
Molecular Biology and Evolution 2007 24(1):63-73; 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

Research Articles

Supernetwork Identifies Multiple Events of Plastid trnF(GAA) Pseudogene Evolution in the Brassicaceae

Marcus A. Koch*, Christoph Dobes*, Christiane Kiefer*, Roswitha Schmickl*, Leos Klimes{dagger} and Martin A. Lysak{ddagger},§

* Heidelberg Institute for Plant Science, Biodiversity and Plant Systematics, Heidelberg University, Heidelberg, Germany
{dagger} Institute of Botany, Academy of Sciences of the Czech Republic, Trebon, Czech Republic
{ddagger} Jodrell Laboratory, Royal Botanic Gardens, Kew, UK
§ Department of Functional Genomics and Proteomics, Masaryk University, Brno, Czech Republic

E-mail: marcus.koch{at}urz.uni-heidelberg.de.

Accepted for publication September 18, 2006.

The occurrence of nonfunctional 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 to 900 bp as a result of differences in pseudocopy number (1–14). It is speculated that functional constraints favor 2–3 or 5–6 copies, as found in Arabidopsis and Boechera. The phylogenetic distribution of microstructural changes for the trnL-F region supports ancient patterns of divergence in crucifer evolution for some but not all gene loci.

Key Words: Brassicaceae • plastome • pseudogene evolution • trnF gene • supernetwork

Peter Lockhart, Associate Editor


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