Rate and Molecular Spectrum of Spontaneous Mutations in Arabidopsis thaliana
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 Arabid...
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Published in | Science (American Association for the Advancement of Science) Vol. 327; no. 5961; pp. 92 - 94 |
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Main Authors | , , , , , , , |
Format | Journal Article |
Language | English |
Published |
Washington, DC
American Association for the Advancement of Science
2010
The American Association for the Advancement of Science |
Subjects | |
Online Access | Get full text |
ISSN | 0036-8075 1095-9203 1095-9203 |
DOI | 10.1126/science.1180677 |
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Abstract | 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 x 10⁻⁹ base substitutions per site per generation, the majority of which are G:C[rightward arrow]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. |
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AbstractList | 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 x 10⁻⁹ base substitutions per site per generation, the majority of which are G:C[rightward arrow]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. 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. 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. 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 x 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. 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 x 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.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 x 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. 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[arrow right]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. [PUBLICATION ABSTRACT] 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 x 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. |
Author | Lucas-Lledó, José Ignacio Schneeberger, Korbinian Weigel, Detlef Lynch, Michael Ossowski, Stephan Shaw, Ruth G Warthmann, Norman Clark, Richard M |
AuthorAffiliation | 3 Department of Biology, University of Utah, Salt Lake City, UT 84112, USA 4 Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN 55108, USA 1 Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany 2 Department of Biology, Indiana University, Bloomington, IN 47405, USA |
AuthorAffiliation_xml | – name: 1 Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany – name: 2 Department of Biology, Indiana University, Bloomington, IN 47405, USA – name: 3 Department of Biology, University of Utah, Salt Lake City, UT 84112, USA – name: 4 Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN 55108, USA |
Author_xml | – sequence: 1 fullname: Ossowski, Stephan – sequence: 2 fullname: Schneeberger, Korbinian – sequence: 3 fullname: Lucas-Lledó, José Ignacio – sequence: 4 fullname: Warthmann, Norman – sequence: 5 fullname: Clark, Richard M – sequence: 6 fullname: Shaw, Ruth G – sequence: 7 fullname: Weigel, Detlef – sequence: 8 fullname: Lynch, Michael |
BackLink | http://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=22280699$$DView record in Pascal Francis https://www.ncbi.nlm.nih.gov/pubmed/20044577$$D View this record in MEDLINE/PubMed |
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Keywords | Single seed descent Divergence Spontaneous Arabidopsis thaliana Ultraviolet radiation Mutagenesis Substitution Cruciferae Dicotyledones Angiospermae Deletion Chromosome DNA Spermatophyta Cytosine Mutation Experimental plant Genome Methylation Polymorphism |
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References | e_1_3_2_8_2 e_1_3_2_7_2 e_1_3_2_17_2 e_1_3_2_6_2 Wright S. I. (e_1_3_2_16_2) 2002; 19 e_1_3_2_18_2 e_1_3_2_19_2 e_1_3_2_20_2 e_1_3_2_10_2 e_1_3_2_21_2 e_1_3_2_11_2 e_1_3_2_22_2 e_1_3_2_4_2 e_1_3_2_12_2 e_1_3_2_23_2 e_1_3_2_3_2 e_1_3_2_13_2 e_1_3_2_24_2 e_1_3_2_2_2 e_1_3_2_14_2 Shaw F. H. (e_1_3_2_15_2) 2002; 56 Shaw R. G. (e_1_3_2_5_2) 2000; 155 |
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Snippet | To take complete advantage of information on within-species polymorphism and divergence from close relatives, one needs to know the rate and the molecular... 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... |
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SubjectTerms | Agronomy. Soil science and plant productions Arabidopsis - genetics Arabidopsis - radiation effects Arabidopsis thaliana Biological and medical sciences Cytosine - metabolism Deamination DNA Methylation DNA, Intergenic DNA, Plant - genetics Flowers & plants Fundamental and applied biological sciences. Psychology Genetic mutation Genetics and breeding of economic plants genome Genome, Plant Genomes Genomics INDEL Mutation Intergenic DNA Introns Methylation Molecular biology Molecular spectra Mutagenesis Mutation Natural selection Plant biology Plant breeding: fundamental aspects and methodology Polymorphism Sequence Analysis, DNA Sequence Deletion Sequencing Ultraviolet radiation Ultraviolet Rays Untranslated regions |
Title | Rate and Molecular Spectrum of Spontaneous Mutations in Arabidopsis thaliana |
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