Accelerated gene evolution and subfunctionalization in the pseudotetraploid frog Xenopus laevis

Uffe Hellsten¹ , Mustafa K Khokha¹^,2 , Timothy C Grammer¹^,2 , Richard M Harland¹^,2 , Paul Richardson¹ and Daniel S Rokhsar¹^,2

¹Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA

²Center for Integrative Genomics and Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA

author email corresponding author email

BMC Biology 2007, 5:31doi:10.1186/1741-7007-5-31


Published:	25 July 2007

Abstract

Background

Ancient whole genome duplications have been implicated in the vertebrate and teleost radiations, and in the emergence of diverse angiosperm lineages, but the evolutionary response to such a perturbation is still poorly understood. The African clawed frog Xenopus laevis experienced a relatively recent tetraploidization ~40 million years ago. Analysis of the considerable amount of EST sequence available for this species together with the genome sequence of the related diploid Xenopus tropicalis provides a unique opportunity to study the genomic response to whole genome duplication.

Results

We identified 2218 gene triplets in which a single gene in X. tropicalis corresponds to precisely two co-orthologous genes in X. laevis – the largest such collection published from any duplication event in animals. Analysis of these triplets reveals accelerated evolution or relaxation of constraint in the peptides of the X. laevis pairs compared with the orthologous sequences in X. tropicalis and other vertebrates. In contrast, single-copy X. laevis genes do not show this acceleration. Duplicated genes can differ substantially in expression levels and patterns. We find no significant difference in gene content in the duplicated set, versus the single-copy set based on molecular and biological function ontologies.

Conclusion

These results support a scenario in which duplicate genes are retained through a process of subfunctionalization and/or relaxation of constraint on both copies of an ancestral gene.