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Science 19 November 2004:
Vol. 306. no. 5700, pp. 1367 - 1370
DOI: 10.1126/science.1102033
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Reports

Very Low Gene Duplication Rate in the Yeast Genome

Li-zhi Gao and Hideki Innan1*

The gene duplication rate in the yeast genome is estimated without assuming the molecular clock model to be ~0.01 to 0.06 per gene per billion years; this rate is two orders of magnitude lower than a previous estimate based on the molecular clock model. This difference is explained by extensive concerted evolution via gene conversion between duplicated genes, which violates the assumption of the molecular clock in the analyses of duplicated genes. The average length of the period of concerted evolution and the gene conversion rate are estimated to be ~25 million years and ~28 times the mutation rate, respectively.

1 Human Genetics Center, School of Public Health, University of Texas Health Science Center, 1200 Hermann Pressler, Houston, TX 77030, USA.

* To whom correspondence should be addressed. E-mail: hideki.innan{at}uth.tmc.edu

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THIS ARTICLE HAS BEEN CITED BY OTHER ARTICLES:
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Inferring Natural Selection on Fine-Scale Chromatin Organization in Yeast.
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Neofunctionalization of Duplicated Genes Under the Pressure of Gene Conversion.
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The Neutral Coalescent Process for Recent Gene Duplications and Copy-Number Variants.
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Genetics 177, 987-1000
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Evolutionary Strata on the X Chromosomes of the Dioecious Plant Silene latifolia: Evidence From New Sex-Linked Genes.
R. Bergero, A. Forrest, E. Kamau, and D. Charlesworth (2007)
Genetics 175, 1945-1954
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The Conversion of 3' UTRs into Coding Regions.
M. G. Giacomelli, A. S. Hancock, and J. Masel (2007)
Mol. Biol. Evol. 24, 457-464
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Preferential Duplication in the Sparse Part of Yeast Protein Interaction Network.
L. Li, Y. Huang, X. Xia, and Z. Sun (2006)
Mol. Biol. Evol. 23, 2467-2473
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Codon-usage bias versus gene conversion in the evolution of yeast duplicate genes.
Y.-S. Lin, J. K. Byrnes, J.-K. Hwang, and W.-H. Li (2006)
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Gene-balanced duplications, like tetraploidy, provide predictable drive to increase morphological complexity.
M. Freeling and B. C. Thomas (2006)
Genome Res. 16, 805-814
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Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes.
B. C. Thomas, B. Pedersen, and M. Freeling (2006)
Genome Res. 16, 934-946
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Linkage Disequilibrium Between Incompatibility Locus Region Genes in the Plant Arabidopsis lyrata.
J. Hagenblad, J. Bechsgaard, and D. Charlesworth (2006)
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Genome-Wide Search of Gene Conversions in Duplicated Genes of Mouse and Rat.
K. Ezawa, S. OOta, and N. Saitou (2006)
Mol. Biol. Evol. 23, 927-940
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Comparative and evolutionary analysis of genes encoding small GTPases and their activating proteins in eukaryotic genomes.
S.-Y. Jiang and S. Ramachandran (2006)
Physiol Genomics 24, 235-251
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Buffering of crucial functions by paleologous duplicated genes may contribute cyclicality to angiosperm genome duplication.
B. A. Chapman, J. E. Bowers, F. A. Feltus, and A. H. Paterson (2006)
PNAS 103, 2730-2735
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Role of positive selection in the retention of duplicate genes in mammalian genomes.
S.-H. Shiu, J. K. Byrnes, R. Pan, P. Zhang, and W.-H. Li (2006)
PNAS 103, 2232-2236
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Gene Conversion and the Evolution of Three Leucine-Rich Repeat Gene Families in Arabidopsis thaliana.
M. Mondragon-Palomino and B. S. Gaut (2005)
Mol. Biol. Evol. 22, 2444-2456
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The Yeast Gene Order Browser: Combining curated homology and syntenic context reveals gene fate in polyploid species.
K. P. Byrne and K. H. Wolfe (2005)
Genome Res. 15, 1456-1461
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A response to Michael Lynch.
M. J. Behe and D. W. Snoke (2005)
Protein Sci. 14, 2226-2227
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Estimating the Time to the Whole-Genome Duplication and the Duration of Concerted Evolution via Gene Conversion in Yeast.
R. P. Sugino and H. Innan (2005)
Genetics 171, 63-69
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Ectopic Gene Conversions Increase the G + C Content of Duplicated Yeast and Arabidopsis Genes.
D. Benovoy, R. T. Morris, A. Morin, and G. Drouin (2005)
Mol. Biol. Evol. 22, 1865-1868
   Abstract »    Full Text »    PDF »


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Science. ISSN 0036-8075 (print), 1095-9203 (online)