Estimate of the spontaneous mutation rate in Chlamydomonas reinhardtii
The nature of spontaneous mutations, including their rate, distribution across the genome, and fitness consequences, is of central importance to biology. However, the low rate of mutation has made it difficult to study spontaneous mutagenesis, and few studies have directly addressed these questions....
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| Published in | Genetics (Austin) Vol. 192; no. 4; pp. 1447 - 1454 |
|---|---|
| Main Authors | , , , |
| Format | Journal Article |
| Language | English |
| Published |
United States
Genetics Society of America
01.12.2012
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| Subjects | |
| Online Access | Get full text |
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| Abstract | The nature of spontaneous mutations, including their rate, distribution across the genome, and fitness consequences, is of central importance to biology. However, the low rate of mutation has made it difficult to study spontaneous mutagenesis, and few studies have directly addressed these questions. Here, we present a direct estimate of the mutation rate and a description of the properties of new spontaneous mutations in the unicellular green alga Chlamydomonas reinhardtii. We conducted a mutation accumulation experiment for ∼350 generations followed by whole-genome resequencing of two replicate lines. Our analysis identified a total of 14 mutations, including 5 short indels and 9 single base mutations, and no evidence of larger structural mutations. From this, we estimate a total mutation rate of 3.23 × 10(-10)/site/generation (95% C.I. 1.82 × 10(-10) to 5.23 × 10(-10)) and a single base mutation rate of 2.08 × 10(-10)/site/generation (95% C.I., 1.09 × 10(-10) to 3.74 × 10(-10)). We observed no mutations from A/T → G/C, suggesting a strong mutational bias toward A/T, although paradoxically, the GC content of the C. reinhardtii genome is very high. Our estimate is only the second direct estimate of the mutation rate from plants and among the lowest spontaneous base-substitution rates known in eukaryotes. |
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| AbstractList | The nature of spontaneous mutations, including their rate, distribution across the genome, and fitness consequences, is of central importance to biology. However, the low rate of mutation has made it difficult to study spontaneous mutagenesis, and few studies have directly addressed these questions. Here, we present a direct estimate of the mutation rate and a description of the properties of new spontaneous mutations in the unicellular green alga
Chlamydomonas reinhardtii
. We conducted a mutation accumulation experiment for ∼350 generations followed by whole-genome resequencing of two replicate lines. Our analysis identified a total of 14 mutations, including 5 short indels and 9 single base mutations, and no evidence of larger structural mutations. From this, we estimate a total mutation rate of 3.23 × 10
−10
/site/generation (95% C.I. 1.82 × 10
−10
to 5.23 × 10
−10
) and a single base mutation rate of 2.08 × 10
−10
/site/generation (95% C.I., 1.09 × 10
−10
to 3.74 × 10
−10
). We observed no mutations from A/T → G/C, suggesting a strong mutational bias toward A/T, although paradoxically, the GC content of the
C. reinhardtii
genome is very high. Our estimate is only the second direct estimate of the mutation rate from plants and among the lowest spontaneous base-substitution rates known in eukaryotes. The nature of spontaneous mutations, including their rate, distribution across the genome, and fitness consequences, is of central importance to biology. However, the low rate of mutation has made it difficult to study spontaneous mutagenesis, and few studies have directly addressed these questions. Here, we present a direct estimate of the mutation rate and a description of the properties of new spontaneous mutations in the unicellular green alga Chlamydomonas reinhardtii. We conducted a mutation accumulation experiment for ∼350 generations followed by whole-genome resequencing of two replicate lines. Our analysis identified a total of 14 mutations, including 5 short indels and 9 single base mutations, and no evidence of larger structural mutations. From this, we estimate a total mutation rate of 3.23 × 10(-10)/site/generation (95% C.I. 1.82 × 10(-10) to 5.23 × 10(-10)) and a single base mutation rate of 2.08 × 10(-10)/site/generation (95% C.I., 1.09 × 10(-10) to 3.74 × 10(-10)). We observed no mutations from A/T → G/C, suggesting a strong mutational bias toward A/T, although paradoxically, the GC content of the C. reinhardtii genome is very high. Our estimate is only the second direct estimate of the mutation rate from plants and among the lowest spontaneous base-substitution rates known in eukaryotes. Abstract The nature of spontaneous mutations, including their rate, distribution across the genome, and fitness consequences, is of central importance to biology. However, the low rate of mutation has made it difficult to study spontaneous mutagenesis, and few studies have directly addressed these questions. Here, we present a direct estimate of the mutation rate and a description of the properties of new spontaneous mutations in the unicellular green alga Chlamydomonas reinhardtii. We conducted a mutation accumulation experiment for ∼350 generations followed by whole-genome resequencing of two replicate lines. Our analysis identified a total of 14 mutations, including 5 short indels and 9 single base mutations, and no evidence of larger structural mutations. From this, we estimate a total mutation rate of 3.23 × 10−10/site/generation (95% C.I. 1.82 × 10−10 to 5.23 × 10−10) and a single base mutation rate of 2.08 × 10−10/site/generation (95% C.I., 1.09 × 10−10 to 3.74 × 10−10). We observed no mutations from A/T → G/C, suggesting a strong mutational bias toward A/T, although paradoxically, the GC content of the C. reinhardtii genome is very high. Our estimate is only the second direct estimate of the mutation rate from plants and among the lowest spontaneous base-substitution rates known in eukaryotes. The nature of spontaneous mutations, including their rate, distribution across the genome, and fitness consequences, is of central importance to biology. However, the low rate of mutation has made it difficult to study spontaneous mutagenesis, and few studies have directly addressed these questions. Here, we present a direct estimate of the mutation rate and a description of the properties of new spontaneous mutations in the unicellular green alga Chlamydomonas reinhardtii. We conducted a mutation accumulation experiment for ~350 generations followed by whole-genome resequencing of two replicate lines. Our analysis identified a total of 14 mutations, including 5 short indels and 9 single base mutations, and no evidence of larger structural mutations. From this, we estimate a total mutation rate of 3.23 × 10^sup -10^/site/generation (95% C.I. 1.82 × 10^sup -10^ to 5.23 × 10^sup -10^) and a single base mutation rate of 2.08 × 10^sup -10^/site/generation (95% C.I., 1.09 × 10^sup -10^ to 3.74 × 10^sup -10^). We observed no mutations from A/T [arrow right] G/C, suggesting a strong mutational bias toward A/T, although paradoxically, the GC content of the C. reinhardtii genome is very high. Our estimate is only the second direct estimate of the mutation rate from plants and among the lowest spontaneous base-substitution rates known in eukaryotes. [PUBLICATION ABSTRACT] |
| Author | Ness, Rob W Colegrave, Nick Keightley, Peter D Morgan, Andrew D |
| Author_xml | – sequence: 1 givenname: Rob W surname: Ness fullname: Ness, Rob W email: ness.eeb@gmail.com organization: Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom. ness.eeb@gmail.com – sequence: 2 givenname: Andrew D surname: Morgan fullname: Morgan, Andrew D – sequence: 3 givenname: Nick surname: Colegrave fullname: Colegrave, Nick – sequence: 4 givenname: Peter D surname: Keightley fullname: Keightley, Peter D |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/23051642$$D View this record in MEDLINE/PubMed |
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| Copyright | Copyright Genetics Society of America Dec 2012 Copyright © 2012 by the Genetics Society of America 2012 |
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| DOI | 10.1534/genetics.112.145078 |
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| Notes | Supporting information is available online at http://www.genetics.org/lookup/suppl/doi:10.1534/genetics.112.145078/-/DC1/. These authors contributed equally to this work. |
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| SubjectTerms | Algae Base Composition Chlamydomonas reinhardtii - genetics Eukaryotes Genome, Plant Genomes INDEL Mutation Investigations Models, Genetic Mutation Mutation Rate Sequence Analysis, DNA - methods |
| Title | Estimate of the spontaneous mutation rate in Chlamydomonas reinhardtii |
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