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High mutation rate and predominance of insertions in the Caenorhabditis elegans nuclear genome

Abstract

Mutations have pivotal functions in the onset of genetic diseases and are the fundamental substrate for evolution. However, present estimates of the spontaneous mutation rate and spectrum are derived from indirect and biased measurements. For instance, mutation rate estimates for Caenorhabditis elegans are extrapolated from observations on a few genetic loci with visible phenotypes and vary over an order of magnitude1. Alternative approaches in mammals, relying on phylogenetic comparisons of pseudogene loci2 and fourfold degenerate codon positions3, suffer from uncertainties in the actual number of generations separating the compared species and the inability to exclude biases associated with natural selection. Here we provide a direct and unbiased estimate of the nuclear mutation rate and its molecular spectrum with a set of C. elegans mutation-accumulation lines that reveal a mutation rate about tenfold higher than previous indirect estimates and an excess of insertions over deletions. Because deletions dominate patterns of C. elegans pseudogene variation4,5, our observations indicate that natural selection might be significant in promoting small genome size, and challenge the prevalent assumption that pseudogene divergence accurately reflects the spontaneous mutation spectrum.

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Acknowledgements

We thank L. L. Vassilieva, S. Estes, V. Katju and C. Steding for their respective roles in propagating and maintaining the MA lines over the past 5 years; D. Ash for help with primer sequence design and DNA sequencing; and the Caenorhabditis Genetics Center for providing the C. elegans natural isolates. This work was supported by a University of Missouri Research Board grant to W.K.T., and an NIH grant to M.L. and W.K.T.

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Correspondence to Dee R. Denver.

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Denver, D., Morris, K., Lynch, M. et al. High mutation rate and predominance of insertions in the Caenorhabditis elegans nuclear genome. Nature 430, 679–682 (2004). https://doi.org/10.1038/nature02697

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