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Open Access Highly Accessed Research article

Evidence and evolutionary analysis of ancient whole-genome duplication in barley predating the divergence from rice

Thomas Thiel1*, Andreas Graner1, Robbie Waugh2, Ivo Grosse3, Timothy J Close4 and Nils Stein1

Author Affiliations

1 IPK Gatersleben, Corrensstr. 3, 06466 Gatersleben, Germany

2 Scottish Crop Research Institute (SCRI), Invergowrie, Dundee DD2 5DA, UK

3 Institut für Informatik, Martin-Luther-Universität Halle-Wittenberg, Von-Seckendorff-Platz 1, 06120 Halle (Saale), Germany

4 Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521-0124, USA

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BMC Evolutionary Biology 2009, 9:209  doi:10.1186/1471-2148-9-209

Published: 22 August 2009

Abstract

Background

Well preserved genomic colinearity among agronomically important grass species such as rice, maize, Sorghum, wheat and barley provides access to whole-genome structure information even in species lacking a reference genome sequence. We investigated footprints of whole-genome duplication (WGD) in barley that shaped the cereal ancestor genome by analyzing shared synteny with rice using a ~2000 gene-based barley genetic map and the rice genome reference sequence.

Results

Based on a recent annotation of the rice genome, we reviewed the WGD in rice and identified 24 pairs of duplicated genomic segments involving 70% of the rice genome. Using 968 putative orthologous gene pairs, synteny covered 89% of the barley genetic map and 63% of the rice genome. We found strong evidence for seven shared segmental genome duplications, corresponding to more than 50% of the segmental genome duplications previously determined in rice. Analysis of synonymous substitution rates (Ks) suggested that shared duplications originated before the divergence of these two species. While major genome rearrangements affected the ancestral genome of both species, small paracentric inversions were found to be species specific.

Conclusion

We provide a thorough analysis of comparative genome evolution between barley and rice. A barley genetic map of approximately 2000 non-redundant EST sequences provided sufficient density to allow a detailed view of shared synteny with the rice genome. Using an indirect approach that included the localization of WGD-derived duplicated genome segments in the rice genome, we determined the current extent of shared WGD-derived genome duplications that occurred prior to species divergence.