Whole Genome Sequencing of Mutation Accumulation Lines Reveals a Low Mutation Rate in the Social Amoeba Dictyostelium discoideum

Gerda Saxer, Paul Havlak, Sara A. Fox, Michael A. Quance, Sharu Gupta, Yuriy Fofanov, Joan E. Strassmann, David C. Queller

Research output: Contribution to journalArticle

27 Citations (Scopus)

Abstract

Spontaneous mutations play a central role in evolution. Despite their importance, mutation rates are some of the most elusive parameters to measure in evolutionary biology. The combination of mutation accumulation (MA) experiments and whole-genome sequencing now makes it possible to estimate mutation rates by directly observing new mutations at the molecular level across the whole genome. We performed an MA experiment with the social amoeba Dictyostelium discoideum and sequenced the genomes of three randomly chosen lines using high-throughput sequencing to estimate the spontaneous mutation rate in this model organism. The mitochondrial mutation rate of 6.76×10-9, with a Poisson confidence interval of 4.1×10-9 - 9.5×10-9, per nucleotide per generation is slightly lower than estimates for other taxa. The mutation rate estimate for the nuclear DNA of 2.9×10-11, with a Poisson confidence interval ranging from 7.4×10-13 to 1.6×10-10, is the lowest reported for any eukaryote. These results are consistent with low microsatellite mutation rates previously observed in D. discoideum and low levels of genetic variation observed in wild D. discoideum populations. In addition, D. discoideum has been shown to be quite resistant to DNA damage, which suggests an efficient DNA-repair mechanism that could be an adaptation to life in soil and frequent exposure to intracellular and extracellular mutagenic compounds. The social aspect of the life cycle of D. discoideum and a large portion of the genome under relaxed selection during vegetative growth could also select for a low mutation rate. This hypothesis is supported by a significantly lower mutation rate per cell division in multicellular eukaryotes compared with unicellular eukaryotes.

Original languageEnglish (US)
Article numbere46759
JournalPLoS One
Volume7
Issue number10
DOIs
StatePublished - Oct 8 2012
Externally publishedYes

Fingerprint

Dictyostelium discoideum
Amoeba
Dictyostelium
Mutation Rate
Genes
Genome
mutation
genome
DNA
Eukaryota
Social aspects
Microsatellite Repeats
eukaryotic cells
Life cycle
Repair
Nucleotides
Experiments
Cells
Throughput
Confidence Intervals

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Whole Genome Sequencing of Mutation Accumulation Lines Reveals a Low Mutation Rate in the Social Amoeba Dictyostelium discoideum. / Saxer, Gerda; Havlak, Paul; Fox, Sara A.; Quance, Michael A.; Gupta, Sharu; Fofanov, Yuriy; Strassmann, Joan E.; Queller, David C.

In: PLoS One, Vol. 7, No. 10, e46759, 08.10.2012.

Research output: Contribution to journalArticle

Saxer, Gerda ; Havlak, Paul ; Fox, Sara A. ; Quance, Michael A. ; Gupta, Sharu ; Fofanov, Yuriy ; Strassmann, Joan E. ; Queller, David C. / Whole Genome Sequencing of Mutation Accumulation Lines Reveals a Low Mutation Rate in the Social Amoeba Dictyostelium discoideum. In: PLoS One. 2012 ; Vol. 7, No. 10.
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