The Rate and Molecular Spectrum of Spontaneous Mutations in Arabidopsis thaliana

By Stephan Ossowski, Korbinian Schneeberger, J. I. Lucas-Lledó, Norman Warthmann, Richard M. Clark, R. Shaw, Detlef Weigel, Michael Lynch. Science, 2010

1,123 citations recorded by the source corpus.

Evolution in Action Rates of evolution in gene and genome sequences have been estimated, but these estimates are subject to error because many of the steps of evolution over the ages are not directly measurable or are hidden under subsequent changes. Ossowski et al. (p. 92) now provide a more accurate measurement of how often spontaneous mutations arise in a nuclear genome. Mutations arising over 30 generations were compared by sequencing DNA from individual Arabidopsis thaliana plants. UV- and deamination-induced mutagenesis appeared to bias the type of mutations found. Rapid sequencing technologies allow a more accurate calculation of the mutation rate for plants. To take complete advantage of information on within-species polymorphism and divergence from close relatives, one needs to know the rate and the molecular spectrum of spontaneous mutations. To this end, we have searched for de novo spontaneous mutations in the complete nuclear genomes of five Arabidopsis thaliana mutation accumulation lines that had been maintained by single-seed descent for 30 generations. We identified and validated 99 base substitutions and 17 small and large insertions and deletions. Our results imply a spontaneous mutation rate of 7 × 10−9 base substitutions per site per generation, the majority of which are G:C→A:T transitions. We explain this very biased spectrum of base substitution mutations as a result of two main processes: deamination of methylated cytosines and ultraviolet light–induced mutagenesis.

Subfields: Genetics, Plant Science

View Paper: https://www.semanticscholar.org/paper/0c33ff931947022c5aa9076a4c85ebd5f3b0d664

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Citations in the corpus

Evolution and Functional Diversification of MIRNA Genes (2011, background): “Although the majority of MIRNA families are conserved between the two species, 24 to 33% of the families were gained or lost by A. thaliana or A. lyrata since they diverged ;10 million years ago (Koch et al., 2000; Wright et al., 2002; Ossowski et al., 2010).”
Whole-genome sequencing of multiple Arabidopsis thaliana populations (2011, background): “Taking into account the experimentally determined mutation rat”
Spontaneous epigenetic variation in the Arabidopsis thaliana methylome (2011, background): “In contrast, larger regions of contiguous methylation were much more stable, and the frequency of changes was in the same low range as that of DNA mutation”
The Patterns and Causes of Variation in Plant Nucleotide Substitution Rates (2011, background): “The strength of the mutation bias is a function of sequence context Morton & Clegg 1995, Morton et al. 2006, Tian et al. 2008, Ossowski et al. 2010 Gene (G) Genes vary in rate as a function of many characteristics, but gene expression is a major predictor of KA Wright et al. 2004, Drummond & Wilke…”
Rate, molecular spectrum, and consequences of human mutation (2010, background): “although methylation alone does not completely explain the high rate ofG:C→A:T transition in this species, even at CpG sites (11).”
Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data (2013, background): “Thus, these two individuals may have accumulated mutations after multiple generations as described previously in Arabidopsis thaliana (Ossowski et al. 2010).”
1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana (2016, methodology): “Scaled times were converted to years assuming a generation time of one year and a mutation rate of 7*10^(-9) (Ossowski et al., 2010).”