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Predicting the Proportion of Essential Genes in Mouse Duplicates Based on Biased Mouse Knockout Genes

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Abstract

In the yeast or nematode, the proportion of essential genes in duplicates is lower than in singletons (single-copy genes), due to the functional redundancy. One may expect that it should be the same in the mouse genome. However, based on the publicly available mouse knockout data, it was observed that the proportion of essential genes in duplicates is similar to that in singletons. The most straightforward interpretation, as claimed in a recent study, is that duplicate genes may have a negligible role in the mouse genetic robustness. Here we show that in the current mouse knockout dataset, recently duplicated genes have been highly underrepresented, leading to an overestimation of the proportion of essential genes in duplicates. After estimating the duplication time of mouse duplication events, we have developed a simple bias-correcting procedure and shown that the bias-corrected proportion of essential genes in mouse duplicates is significantly lower than that in singletons.

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Acknowledgments

This work was supported in part by grants (30428003 to X.G., 30700140 to Z.S.) from the National Natural Science Foundation of China, and grants from Iowa State University and Fudan University (to X.G.), and supported by the Shanghai Leading Academic Discipline Project (Project No. B111). We are grateful to Wen-Hsiung Li, Han Liang, and Jianzhi Zhang for critical comments on the early version of the manuscript.

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Authors and Affiliations

  1. Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China

    Zhixi Su & Xun Gu

  2. School of Life Sciences, Center for Evolutionary Biology, Fudan University, Shanghai, 200433, China

    Xun Gu

  3. Department of Genetics, Development and Cell Biology, Center for Bioinformatics and Biological Statistics, Iowa State University, 536 Science II, Ames, IA, 50011, USA

    Xun Gu

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  1. Zhixi Su
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  2. Xun Gu
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Correspondence to Xun Gu.

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Su, Z., Gu, X. Predicting the Proportion of Essential Genes in Mouse Duplicates Based on Biased Mouse Knockout Genes. J Mol Evol 67, 705–709 (2008). https://doi.org/10.1007/s00239-008-9170-9

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  • DOI: https://doi.org/10.1007/s00239-008-9170-9

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