Work

Estimating somatic mutation rates by Duplex Sequencing in non-model organisms: Daphnia magna as a case study

Year: 2022

Type: preprint

Abstract: Somatic mutations are evolutionarily important as determinants of individual organismal fitness, as well as being a focus of clinical research on age-related disease, such as cancer. Identifying somatic mutations and quantifying mutation rates, however, is extremely challenging and genome-wide somatic mutation rates have only been reported for a few model organisms. Here, we describe the application of Duplex Sequencing on bottlenecked WGS libraries to quantify genome-wide somatic base substitution rates in Daphnia magna. Daphnia , historically an ecological model system, has more recently been the focus of mutation studies, in part because of its high germline mutation rates. Using our protocol and pipeline, we estimate a somatic mutation rate of 2.14 × 10 −7 substitutions per site (in a genotype where the germline rate is 3.60 × 10 −9 substitutions per site per generation). To obtain this estimate, we tested multiple dilution levels to maximize sequencing efficiency, and developed bioinformatic filters needed to minimize false positives when a high quality reference genome is not available. In addition to laying the groundwork for estimating genotypic variation in rates of somatic mutations within D. magna , we provide a framework for quantifying somatic mutations in other non-model systems, and also highlight recent innovations to single molecule sequencing that will help to further refine such estimates.

Source: bioRxiv (Cold Spring Harbor Laboratory)

DOI: 10.1101/2022.05.31.494242

Authors: Eli Sobel, Jeremy E. Coate, Sarah Schaack

Institution: Reed College

Language: English

Topic: Genomics and Phylogenetic Studies

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: green

Funders: National Science Foundation, Reed College, National Institutes of Health, National Institute of General Medical Sciences

Awards: G371925785, CAREER: Upon Which Selection Can Act: Quantifying How Mutation and Environment Generate Genotypic & Phenotypic Variation in an Emerging Ecological & Evolutionary Genomic Model, Tissue, Time, and Genotype: Investigating the Effects of Cellular Environment, Age, and Germline Mutation Rate on the Genome-Wide Rate and Spectrum of Somatic Mutation