Rapid Evolution of Expression and Regulatory Divergences after Yeast Gene Duplication
Although gene duplication is widely believed to be the major source of genetic novelty, how the expression or regulatory network of duplicate genes evolves remains poorly understood. In this article, we propose an additive expression distance between duplicate genes, so that the evolutionary rate of...
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| Veröffentlicht in: | Proceedings of the National Academy of Sciences - PNAS 2005-01, Vol.102 (3), p.707-712 |
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| creator | Gu, Xun Zhang, Zhongqi Huang, Wei Tan, Jiazhen |
| description | Although gene duplication is widely believed to be the major source of genetic novelty, how the expression or regulatory network of duplicate genes evolves remains poorly understood. In this article, we propose an additive expression distance between duplicate genes, so that the evolutionary rate of expression divergence after gene duplication can be estimated through phylogenomic analysis. We have analyzed yeast genome sequences, microarrays, and transcriptional regulatory networks, showing a >10-fold increase in the initial rate for both expression and regulatory network evolution after gene duplication but only an ≈20% rate increase in the early stage for protein sequences. Based on the estimated age distribution of yeast duplicate genes, we roughly estimate that the initial rate of expression divergence shortly after gene duplication is 2.9× 10-9per year, whereas the baseline rate for very ancient gene duplication is 0.14× 10-9per year. Relative expression rate tests suggest that the expression of duplicate genes tends to evolve asymmetrically, that is, the expression of one copy evolves rapidly, whereas the other one largely maintains the ancestral expression profile. Our study highlights the crucial role of early rapid evolution after gene/genome duplication for continuously increasing the complexity of the yeast regulatory network. |
| doi_str_mv | 10.1073/pnas.0409186102 |
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In this article, we propose an additive expression distance between duplicate genes, so that the evolutionary rate of expression divergence after gene duplication can be estimated through phylogenomic analysis. We have analyzed yeast genome sequences, microarrays, and transcriptional regulatory networks, showing a >10-fold increase in the initial rate for both expression and regulatory network evolution after gene duplication but only an ≈20% rate increase in the early stage for protein sequences. Based on the estimated age distribution of yeast duplicate genes, we roughly estimate that the initial rate of expression divergence shortly after gene duplication is 2.9× 10-9per year, whereas the baseline rate for very ancient gene duplication is 0.14× 10-9per year. Relative expression rate tests suggest that the expression of duplicate genes tends to evolve asymmetrically, that is, the expression of one copy evolves rapidly, whereas the other one largely maintains the ancestral expression profile. 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In this article, we propose an additive expression distance between duplicate genes, so that the evolutionary rate of expression divergence after gene duplication can be estimated through phylogenomic analysis. We have analyzed yeast genome sequences, microarrays, and transcriptional regulatory networks, showing a >10-fold increase in the initial rate for both expression and regulatory network evolution after gene duplication but only an ≈20% rate increase in the early stage for protein sequences. Based on the estimated age distribution of yeast duplicate genes, we roughly estimate that the initial rate of expression divergence shortly after gene duplication is 2.9× 10-9per year, whereas the baseline rate for very ancient gene duplication is 0.14× 10-9per year. Relative expression rate tests suggest that the expression of duplicate genes tends to evolve asymmetrically, that is, the expression of one copy evolves rapidly, whereas the other one largely maintains the ancestral expression profile. Our study highlights the crucial role of early rapid evolution after gene/genome duplication for continuously increasing the complexity of the yeast regulatory network.</description><subject>Age distribution</subject><subject>Arrays</subject><subject>Biological Sciences</subject><subject>Divergent evolution</subject><subject>Duplicate genes</subject><subject>Evolution</subject><subject>Evolution, Molecular</subject><subject>Gene Duplication</subject><subject>Gene expression</subject><subject>Gene Expression Regulation - genetics</subject><subject>Genes</subject><subject>Genetics</subject><subject>Kinetics</subject><subject>Models, Genetic</subject><subject>P values</subject><subject>Phylogenetics</subject><subject>Phylogeny</subject><subject>Statistical variance</subject><subject>Yeast</subject><subject>Yeasts</subject><subject>Yeasts - cytology</subject><subject>Yeasts - genetics</subject><issn>0027-8424</issn><issn>1091-6490</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2005</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkc1v1DAQxS0EokvhzAWQ1QO3tP6M7QMH1C4FqRJS1R56spxksmSVjYPtrNr_vo521S0IiZPHmt97mpmH0HtKTilR_GwcXDwlghiqS0rYC7SguS5KYchLtCCEqUILJo7QmxjXhBAjNXmNjqgsheJCL9DttRu7Bi-3vp9S5wfsW7y8HwPEOP_c0OBrWE29Sz484ItuC2EFQw0RuzZBwHfgYsKXMAC-mMa-q93s8ha9al0f4d3-PUa335Y359-Lq5-XP86_XhW11DoVBhpX6ZJR7gwDyjhvy4o2nEBLaUkYiKqqiaJGVjVrKsmVAC5LqblpQRrHj9GXne84VRtoahhScL0dQ7dx4cF619k_O0P3y6781kohpWJZ_3mvD_73BDHZTRdr6Hs3gJ-iLRVXmkvxX5CqfH8jZ8eTv8C1n8KQj2AZoSxPrlWGznZQHXyMAdqniSmxc652ztUecs2KT88XPfD7IDPwcQ_MyoMds9wqop4t8M--bae-T3CfMvhhB65jjvyJ5Pn2nHL-CL3ev-k</recordid><startdate>20050118</startdate><enddate>20050118</enddate><creator>Gu, Xun</creator><creator>Zhang, Zhongqi</creator><creator>Huang, Wei</creator><creator>Tan, Jiazhen</creator><general>National Academy of Sciences</general><general>National Acad Sciences</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QG</scope><scope>7QL</scope><scope>7QP</scope><scope>7QR</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TK</scope><scope>7TM</scope><scope>7TO</scope><scope>7U9</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>H94</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20050118</creationdate><title>Rapid Evolution of Expression and Regulatory Divergences after Yeast Gene Duplication</title><author>Gu, Xun ; 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| subjects | Age distribution Arrays Biological Sciences Divergent evolution Duplicate genes Evolution Evolution, Molecular Gene Duplication Gene expression Gene Expression Regulation - genetics Genes Genetics Kinetics Models, Genetic P values Phylogenetics Phylogeny Statistical variance Yeast Yeasts Yeasts - cytology Yeasts - genetics |
| title | Rapid Evolution of Expression and Regulatory Divergences after Yeast Gene Duplication |
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