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Accelerated gene evolution and subfunctionalization in the pseudotetraploid frog Xenopus laevis
Uffe Hellsten1, Mustafa K Khokha, Timothy C Grammer
1Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA. uhellsten@lbl.gov
BMC Biology
|July 27, 2007
Summary
The African clawed frog (Xenopus laevis) retained duplicated genes after whole genome duplication, showing accelerated evolution or relaxed constraint in these genes. This suggests subfunctionalization or relaxed constraint drives duplicate gene retention in animals.
Area of Science:
- Evolutionary genomics
- Comparative genomics
Background:
- Whole genome duplication (WGD) events significantly impact vertebrate and angiosperm evolution.
- The African clawed frog (Xenopus laevis) underwent a recent tetraploidization event approximately 40 million years ago.
- Studying Xenopus laevis offers a unique window into the genomic consequences of WGD.
Purpose of the Study:
- To investigate the evolutionary fate of genes following a whole genome duplication event.
- To analyze the genomic and expression patterns of duplicated genes in Xenopus laevis.
- To understand the mechanisms of duplicate gene retention after WGD.
Main Methods:
- Comparative analysis of Xenopus laevis EST sequences and Xenopus tropicalis genome sequence.
- Identification and analysis of gene triplets (one X. tropicalis gene, two X. laevis co-orthologs).
- Sequence evolution analysis comparing duplicated and single-copy genes.
Main Results:
- Identified 2218 gene triplets, the largest set from any animal duplication.
- Observed accelerated evolution or relaxed constraint in duplicated X. laevis genes compared to X. tropicalis and other vertebrates.
- Found significant differences in expression levels and patterns between duplicated genes, but no significant difference in gene content ontology.
Conclusions:
- Duplicate genes are retained via subfunctionalization and/or relaxation of constraint.
- The evolutionary trajectory of duplicated genes involves changes in sequence evolution and expression.
- WGD provides raw material for evolutionary innovation, with duplicate genes diverging in function and regulation.
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