Accelerated gene evolution and subfunctionalization in the pseudotetraploid frog <it>Xenopus laevis</it>
<p>Abstract</p> <p>Background</p> <p>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. Th...
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BMC
2007-07-01
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| Series: | BMC Biology |
| Online Access: | http://www.biomedcentral.com/1741-7007/5/31 |
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| author | Grammer Timothy C Khokha Mustafa K Hellsten Uffe Harland Richard M Richardson Paul Rokhsar Daniel S |
| author_facet | Grammer Timothy C Khokha Mustafa K Hellsten Uffe Harland Richard M Richardson Paul Rokhsar Daniel S |
| author_sort | Grammer Timothy C |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>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 <it>Xenopus laevis </it>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 <it>Xenopus tropicalis </it>provides a unique opportunity to study the genomic response to whole genome duplication.</p> <p>Results</p> <p>We identified 2218 gene triplets in which a single gene in <it>X. tropicalis </it>corresponds to precisely two co-orthologous genes in <it>X. laevis </it>– 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 <it>X. laevis </it>pairs compared with the orthologous sequences in <it>X. tropicalis </it>and other vertebrates. In contrast, single-copy <it>X. laevis </it>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.</p> <p>Conclusion</p> <p>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.</p> |
| first_indexed | 2024-12-10T05:07:52Z |
| format | Article |
| id | doaj.art-cc22d13db7804fd8acad53bdc927a597 |
| institution | Directory Open Access Journal |
| issn | 1741-7007 |
| language | English |
| last_indexed | 2024-12-10T05:07:52Z |
| publishDate | 2007-07-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Biology |
| spelling | doaj.art-cc22d13db7804fd8acad53bdc927a5972022-12-22T02:01:11ZengBMCBMC Biology1741-70072007-07-01513110.1186/1741-7007-5-31Accelerated gene evolution and subfunctionalization in the pseudotetraploid frog <it>Xenopus laevis</it>Grammer Timothy CKhokha Mustafa KHellsten UffeHarland Richard MRichardson PaulRokhsar Daniel S<p>Abstract</p> <p>Background</p> <p>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 <it>Xenopus laevis </it>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 <it>Xenopus tropicalis </it>provides a unique opportunity to study the genomic response to whole genome duplication.</p> <p>Results</p> <p>We identified 2218 gene triplets in which a single gene in <it>X. tropicalis </it>corresponds to precisely two co-orthologous genes in <it>X. laevis </it>– 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 <it>X. laevis </it>pairs compared with the orthologous sequences in <it>X. tropicalis </it>and other vertebrates. In contrast, single-copy <it>X. laevis </it>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.</p> <p>Conclusion</p> <p>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.</p>http://www.biomedcentral.com/1741-7007/5/31 |
| spellingShingle | Grammer Timothy C Khokha Mustafa K Hellsten Uffe Harland Richard M Richardson Paul Rokhsar Daniel S Accelerated gene evolution and subfunctionalization in the pseudotetraploid frog <it>Xenopus laevis</it> BMC Biology |
| title | Accelerated gene evolution and subfunctionalization in the pseudotetraploid frog <it>Xenopus laevis</it> |
| title_full | Accelerated gene evolution and subfunctionalization in the pseudotetraploid frog <it>Xenopus laevis</it> |
| title_fullStr | Accelerated gene evolution and subfunctionalization in the pseudotetraploid frog <it>Xenopus laevis</it> |
| title_full_unstemmed | Accelerated gene evolution and subfunctionalization in the pseudotetraploid frog <it>Xenopus laevis</it> |
| title_short | Accelerated gene evolution and subfunctionalization in the pseudotetraploid frog <it>Xenopus laevis</it> |
| title_sort | accelerated gene evolution and subfunctionalization in the pseudotetraploid frog it xenopus laevis it |
| url | http://www.biomedcentral.com/1741-7007/5/31 |
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