The insect-killing bacterium Photorhabdus luminescens has the lowest mutation rate among bacteria
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RESEARCH PAPER
The insect‑killing bacterium Photorhabdus luminescens has the lowest mutation rate among bacteria Jiao Pan1 · Emily Williams2 · Way Sung3 · Michael Lynch2 · Hongan Long1 Received: 26 March 2020 / Accepted: 3 July 2020 © The Author(s) 2020
Abstract Mutation is a primary source of genetic variation that is used to power evolution. Many studies, however, have shown that most mutations are deleterious and, as a result, extremely low mutation rates might be beneficial for survival. Using a mutation accumulation experiment, an unbiased method for mutation study, we found an extremely low base-substitution mutation rate of 5.94 × 10–11 per nucleotide site per cell division (95% Poisson confidence intervals: 4.65 × 10–11, 7.48 × 10–11) and indel mutation rate of 8.25 × 10–12 per site per cell division (95% confidence intervals: 3.96 × 10–12, 1.52 × 10–11) in the bacterium Photorhabdus luminescens ATCC29999. The mutations are strongly A/T-biased with a mutation bias of 10.28 in the A/T direction. It has been hypothesized that the ability for selection to lower mutation rates is inversely proportional to the effective population size (drift-barrier hypothesis) and we found that the effective population size of this bacterium is significantly greater than most other bacteria. This finding further decreases the lower-bounds of bacterial mutation rates and provides evidence that extreme levels of replication fidelity can evolve within organisms that maintain large effective population sizes. Keywords Neutral evolution · Mutation accumulation · Mutation spectrum · Drift-barrier hypothesis · Lower-limit of mutation rate
Introduction Mutations are the ultimate source for genetic variation and also contribute to diseases, cell senescence, and cancer (Alfred and Knudson 1971; Davies et al. 2002). Although mutations provide the primary source for evolutionary processes, the mostly deleterious nature of mutations requires that the ability for selection to refine the mechanisms driving Edited by Jiamei Li. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s42995-020-00060-0) contains supplementary material, which is available to authorized users. * Hongan Long [email protected] 1
Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao 266003, China
2
Center for Mechanisms of Evolution, The Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA
3
Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, NC 28223, USA
replication fidelity is limited by random genetic drift (Eyrewalker and Keightley 2007; Lynch et al. 2016; Sung et al. 2012a). Until now, the drift-barrier hypothesis provided the only universal explanation for mutation rate determination (Sung et al. 2016, 2012a, b). Mutation accumulation (MA) technique combined with deep whole-genome sequencing is one of the most accurate and unbiased methods for estimating the rate and spectrum of spontaneous mutations (Halligan an
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