Originally published as Genetics Published Articles Ahead of Print on September 9, 2008.

Genetics, Vol. 180, 1071-1086, October 2008, Copyright © 2008
doi:10.1534/genetics.108.092304

Dynamics and Differential Proliferation of Transposable Elements During the Evolution of the B and A Genomes of Wheat

Mathieu Charles^*, Harry Belcram^*, Jérémy Just^*, Cécile Huneau^*, Agnès Viollet, Arnaud Couloux, Béatrice Segurens, Meredith Carter, Virginie Huteau, Olivier Coriton, Rudi Appels, Sylvie Samain and Boulos Chalhoub^*,1

^* Organization and Evolution of Plant Genomes, Unité de Recherche en Génomique Végétale, UMR: INRA-1165, CNR-S8114, 91057 Evry Cedex, France, CEA: Institut de Génomique GENOSCOPE, 91057 Evry Cedex, France, State Agricultural Biotechnology Centre and Centre for Comparative Genomics, Murdoch University, Perth, Western Australia 6150, Australia and Unité Mixte de Recherches INRA, Agrocampus Rennes Amélioration des Plantes et Biotechnologies Végétales, 35653 Le Rheu, France

¹ Corresponding author: Organization and Evolution of Plant Genomes, Unité de Recherche en Génomique Végétale, UMR: INRA-1165, CNR-S8114, 2 rue Gaston Crémieux, 91057 Evry Cedex, France.
E-mail: chalhoub{at}evry.inra.fr

Transposable elements (TEs) constitute >80% of the wheat genome but their dynamics and contribution to size variation and evolution of wheat genomes (Triticum and Aegilops species) remain unexplored. In this study, 10 genomic regions have been sequenced from wheat chromosome 3B and used to constitute, along with all publicly available genomic sequences of wheat, 1.98 Mb of sequence (from 13 BAC clones) of the wheat B genome and 3.63 Mb of sequence (from 19 BAC clones) of the wheat A genome. Analysis of TE sequence proportions (as percentages), ratios of complete to truncated copies, and estimation of insertion dates of class I retrotransposons showed that specific types of TEs have undergone waves of differential proliferation in the B and A genomes of wheat. While both genomes show similar rates and relatively ancient proliferation periods for the Athila retrotransposons, the Copia retrotransposons proliferated more recently in the A genome whereas Gypsy retrotransposon proliferation is more recent in the B genome. It was possible to estimate for the first time the proliferation periods of the abundant CACTA class II DNA transposons, relative to that of the three main retrotransposon superfamilies. Proliferation of these TEs started prior to and overlapped with that of the Athila retrotransposons in both genomes. However, they also proliferated during the same periods as Gypsy and Copia retrotransposons in the A genome, but not in the B genome. As estimated from their insertion dates and confirmed by PCR-based tracing analysis, the majority of differential proliferation of TEs in B and A genomes of wheat (87 and 83%, respectively), leading to rapid sequence divergence, occurred prior to the allotetraploidization event that brought them together in Triticum turgidum and Triticum aestivum, <0.5 million years ago. More importantly, the allotetraploidization event appears to have neither enhanced nor repressed retrotranspositions. We discuss the apparent proliferation of TEs as resulting from their insertion, removal, and/or combinations of both evolutionary forces.

This article has been cited by other articles:

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