Journal Article

Paleopolyploidy in the Brassicales: Analyses of the <i>Cleome</i> Transcriptome Elucidate the History of Genome Duplications in <i>Arabidopsis</i> and Other Brassicales

Michael S. Barker, Heiko Vogel and M. Eric Schranz

in Genome Biology and Evolution

Published on behalf of Society for Molecular Biology and Evolution

Volume 1, issue , pages 391-399
Published in print January 2009 |
Published online October 2009 | e-ISSN: 1759-6653 | DOI: http://dx.doi.org/10.1093/gbe/evp040

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The analysis of the Arabidopsis genome revealed evidence of three ancient polyploidy events in the evolution of the Brassicaceae, but the exact phylogenetic placement of these events is still not resolved. The most recent event is called the At-α (alpha) or 3R, the intermediate event is referred to as the At-β (beta) or 2R, and the oldest is the At-γ (gamma) or 1R. It has recently been established that At-γ is shared with other Rosids, including papaya (Carica), poplar (Populus), and grape (Vitis), whereas data to date suggest that At-α is Brassicaceae specific. To address more precisely when the At-α and At-β events occurred and which plant lineages share these paleopolyploidizations, we sequenced and analyzed over 4,700 normalized expressed sequence tag sequences from the Cleomaceae, the sister family to the Brassicaceae. Analysis of these Cleome data with homologous sequences from other Rosid genomes (Arabidopsis, Carica, Gossypium, Populus, and Vitis) yielded three major findings: 1) confirmation of a Cleome-specific paleopolyploidization (Cs-α) that is independent of the Brassicaceae At-α paleopolyploidization; 2) Cleome and Arabidopsis share the At-β duplication, which is lacking from papaya within the Brassicales; and 3) rates of molecular evolution are faster for the herbaceous annual taxa Arabidopsis and Cleome than the other predominantly woody perennial Rosid lineages. These findings contribute to our understanding of the dynamics of genome duplication and evolution within one of the most comprehensively surveyed clades of plants, the Rosids, and clarify the complex history of the At-α, At-β, and At-γ duplications of Arabidopsis.

Keywords: polyploidy; Brassicales; Cleome; Arabidopsis; transcriptome

Journal Article.  6100 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology ; Evolutionary Biology ; Genetics and Genomics

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