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Nucleic Acids Research Advance Access first published online on January 9, 2009
This version published online on January 28, 2009
Nucleic Acids Research, doi:10.1093/nar/gkn1048
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Genomics

Structure and expression analysis of rice paleo duplications

Mickael Throude1, Stéphanie Bolot1, Mickael Bosio2, Caroline Pont1, Xavier Sarda2, Umar Masood Quraishi1, Fabienne Bourgis3, Philippe Lessard2, Peter Rogowsky4, Alain Ghesquiere3, Alain Murigneux2, Gilles Charmet1, Pascual Perez2 and Jérôme Salse1,*

1UMR 1095 INRA/UBP, Génétique, Diversité et Ecophysiologie des Céréales (GDEC), Domaine de Crouelle, 234, 63100 Clermont Ferrand, 2Biogemma, Z.I. Du Brézet, 63028 Clermont Ferrand Cedex 2, 3IRD, Avenue Agropolis, 34394 Montpellier Cedex 05 and 4Ecole Normale Superieure de Lyon, 69364 Lyon Cedex 07, France

*To whom correspondence should be addressed. Tel: +33 4 73 62 43 80; Fax: +33 4 73 62 44 53; Email: jsalse{at}clermont.inra.fr

Received November 7, 2008. Revised December 15, 2008. Accepted December 15, 2008.

Having a well-known history of genome duplication, rice is a good model for studying structural and functional evolution of paleo duplications. Improved sequence alignment criteria were used to characterize 10 major chromosome-to-chromosome duplication relationships associated with 1440 paralogous pairs, covering 47.8% of the rice genome, with 12.6% of genes that are conserved within sister blocks. Using a micro-array experiment, a genome-wide expression map has been produced, in which 2382 genes show significant differences of expression in root, leaf and grain. By integrating both structural (1440 paralogous pairs) and functional information (2382 differentially expressed genes), we identified 115 paralogous gene pairs for which at least one copy is differentially expressed in one of the three tissues. A vast majority of the 115 paralogous gene pairs have been neofunctionalized or subfunctionalized as 88%, 89% and 96% of duplicates, respectively, expressed in grain, leaf and root show distinct expression patterns. On the basis of a Gene Ontology analysis, we have identified and characterized the gene families that have been structurally and functionally preferentially retained in the duplication showing that the vast majority (>85%) of duplicated have been either lost or have been subfunctionalized or neofunctionalized during 50–70 million years of evolution.

The authors wish it to be known that, in their opinion, the first three authors should be regarded as joint First Authors.


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