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

Dee R. Denver (), Krystalynne Morris, Michael Lynch and W. Kelley Thomas
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Dee R. Denver: Indiana University
Krystalynne Morris: University of New Hampshire
Michael Lynch: Indiana University
W. Kelley Thomas: University of New Hampshire

Nature, 2004, vol. 430, issue 7000, 679-682

Abstract: 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.

Date: 2004
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DOI: 10.1038/nature02697

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