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

Autor:	Keith N; School of Public and Environmental Affairs, Indiana University, Bloomington, Indiana 47405, USA;, Tucker AE; Biology Department, Southern Arkansas University, Magnolia, Arkansas 71753, USA;, Jackson CE; School of Public and Environmental Affairs, Indiana University, Bloomington, Indiana 47405, USA;, Sung W; Department of Biology, Indiana University, Bloomington, Indiana 47405, USA;, Lucas Lledó JI; Leibniz Institute of Freshwater Ecology and Inland Fisheries, Stechlin, 16775 Germany;, Schrider DR; Department of Genetics, Rutgers University, Piscataway, New Jersey 08854, USA;, Schaack S; Biology Department, Reed College, Portland, Oregon 97202, USA;, Dudycha JL; Department of Biological Sciences, University of South Carolina, Columbia, South Carolina 29208, USA;, Ackerman M; Department of Biology, Indiana University, Bloomington, Indiana 47405, USA;, Younge AJ; School of Informatics and Computing, Indiana University, Bloomington, Indiana 47405, USA;, Shaw JR; School of Public and Environmental Affairs, Indiana University, Bloomington, Indiana 47405, USA; School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom., Lynch M; Department of Biology, Indiana University, Bloomington, Indiana 47405, USA;
Jazyk:	angličtina
Zdroj:	Genome research [Genome Res] 2016 Jan; Vol. 26 (1), pp. 60-9. Date of Electronic Publication: 2015 Oct 30.
DOI:	10.1101/gr.191338.115
Abstrakt:	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. (© 2016 Keith et al.; Published by Cold Spring Harbor Laboratory Press.)
Databáze:	MEDLINE
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