High mutational rates of large-scale duplication and deletion in Daphnia pulex

Nathan Keith, Abraham E. Tucker, Craig E. Jackson, Way Sung, José Ignacio Lucas Lledó, Daniel R. Schrider, Sarah Schaack, Jeffry L. Dudycha, Matthew Ackerman, Andrew J. Younge, Joseph R. Shaw, Michael Lynch

Research output: Contribution to journalArticle

24 Citations (Scopus)

Abstract

Knowledge of the genome-wide rate and spectrum of mutations is necessary to understand the origin of disease and the genetic variation driving all evolutionary processes. Here, we provide a genome-wide analysis of the rate and spectrum of mutations obtained in two Daphnia pulex genotypes via separate mutation-accumulation (MA) experiments. Unlike most MA studies that utilize haploid, homozygous, or self-fertilizing lines, D. pulex can be propagated ameiotically while maintaining a naturally heterozygous, diploid genome, allowing the capture of the full spectrum of genomic changes that arise in a heterozygous state. While base-substitution mutation rates are similar to those in other multicellular eukaryotes (about 4 × 10-9 per site per generation), we find that the rates of large-scale (>100 kb) de novo copy-number variants (CNVs) are significantly elevated relative to those seen in previous MA studies. The heterozygosity maintained in this experiment allowed for estimates of gene-conversion processes. While most of the conversion tract lengths we report are similar to those generated by meiotic processes, we also find larger tract lengths that are indicative of mitotic processes. Comparison of MA lines to natural isolates reveals that a majority of large-scale CNVs in natural populations are removed by purifying selection. The mutations observed here share similarities with disease-causing, complex, large-scale CNVs, thereby demonstrating that MA studies in D. pulex serve as a system for studying the processes leading to such alterations.

Original languageEnglish (US)
Pages (from-to)60-69
Number of pages10
JournalGenome Research
Volume26
Issue number1
DOIs
StatePublished - Jan 1 2016
Externally publishedYes

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Daphnia
Mutation Rate
Genome
Gene Conversion
Haploidy
Eukaryota
Diploidy
Spectrum Analysis
Genotype
Mutation Accumulation
Mutation
Population

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

Keith, N., Tucker, A. E., Jackson, C. E., Sung, W., Lledó, J. I. L., Schrider, D. R., ... Lynch, M. (2016). High mutational rates of large-scale duplication and deletion in Daphnia pulex. Genome Research, 26(1), 60-69. https://doi.org/10.1101/gr.191338.115

High mutational rates of large-scale duplication and deletion in Daphnia pulex. / Keith, Nathan; Tucker, Abraham E.; Jackson, Craig E.; Sung, Way; Lledó, José Ignacio Lucas; Schrider, Daniel R.; Schaack, Sarah; Dudycha, Jeffry L.; Ackerman, Matthew; Younge, Andrew J.; Shaw, Joseph R.; Lynch, Michael.

In: Genome Research, Vol. 26, No. 1, 01.01.2016, p. 60-69.

Research output: Contribution to journalArticle

Keith, N, Tucker, AE, Jackson, CE, Sung, W, Lledó, JIL, Schrider, DR, Schaack, S, Dudycha, JL, Ackerman, M, Younge, AJ, Shaw, JR & Lynch, M 2016, 'High mutational rates of large-scale duplication and deletion in Daphnia pulex', Genome Research, vol. 26, no. 1, pp. 60-69. https://doi.org/10.1101/gr.191338.115
Keith N, Tucker AE, Jackson CE, Sung W, Lledó JIL, Schrider DR et al. High mutational rates of large-scale duplication and deletion in Daphnia pulex. Genome Research. 2016 Jan 1;26(1):60-69. https://doi.org/10.1101/gr.191338.115
Keith, Nathan ; Tucker, Abraham E. ; Jackson, Craig E. ; Sung, Way ; Lledó, José Ignacio Lucas ; Schrider, Daniel R. ; Schaack, Sarah ; Dudycha, Jeffry L. ; Ackerman, Matthew ; Younge, Andrew J. ; Shaw, Joseph R. ; Lynch, Michael. / High mutational rates of large-scale duplication and deletion in Daphnia pulex. In: Genome Research. 2016 ; Vol. 26, No. 1. pp. 60-69.
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