TY - JOUR
T1 - Low base-substitution mutation rate and predominance of insertion-deletion events in the acidophilic bacterium Acidobacterium capsulatum
AU - Kucukyildirim, Sibel
AU - Miller, Samuel F.
AU - Lynch, Michael
N1 - Funding Information:
This study is funded by a Multidisciplinary University Research Initiative award (W911NF‐09‐1‐0444) from the US Army Research Office and National Institutes of Health awards (R01GM036827 and R35‐GM122566). This research was supported in part by Lilly Endowment, Inc., through its support for the Indiana University Pervasive Technology Institute, and in part by the Indiana METACyt Initiative. The Indiana METACyt Initiative at IU was also supported in part by Lilly Endowment, Inc. We thank Emily M. Williams for technical support.
Publisher Copyright:
© 2021 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.
PY - 2021/12
Y1 - 2021/12
N2 - Analyses of spontaneous mutation have shown that total genome-wide mutation rates are quantitatively similar for most prokaryotic organisms. However, this view is mainly based on organisms that grow best around neutral pH values (6.0–8.0). In particular, the whole-genome mutation rate has not been determined for an acidophilic organism. Here, we have determined the genome-wide rate of spontaneous mutation in the acidophilic Acidobacterium capsulatum using a direct and unbiased method: a mutation-accumulation experiment followed by whole-genome sequencing. Evaluation of 69 mutation accumulation lines of A. capsulatum after an average of ~2900 cell divisions yielded a base-substitution mutation rate of 1.22 × 10−10 per site per generation or 4 × 10−4 per genome per generation, which is significantly lower than the consensus value (2.5−4.6 × 10−3) of mesothermophilic (~15–40°C) and neutrophilic (pH 6–8) prokaryotic organisms. However, the insertion-deletion rate (0.43 × 10−10 per site per generation) is high relative to the base-substitution mutation rate. Organisms with a similar effective population size and a similar expected effect of genetic drift should have similar mutation rates. Because selection operates on the total mutation rate, it is suggested that the relatively high insertion-deletion rate may be balanced by a low base-substitution rate in A. capsulatum, with selection operating on the total mutation rate.
AB - Analyses of spontaneous mutation have shown that total genome-wide mutation rates are quantitatively similar for most prokaryotic organisms. However, this view is mainly based on organisms that grow best around neutral pH values (6.0–8.0). In particular, the whole-genome mutation rate has not been determined for an acidophilic organism. Here, we have determined the genome-wide rate of spontaneous mutation in the acidophilic Acidobacterium capsulatum using a direct and unbiased method: a mutation-accumulation experiment followed by whole-genome sequencing. Evaluation of 69 mutation accumulation lines of A. capsulatum after an average of ~2900 cell divisions yielded a base-substitution mutation rate of 1.22 × 10−10 per site per generation or 4 × 10−4 per genome per generation, which is significantly lower than the consensus value (2.5−4.6 × 10−3) of mesothermophilic (~15–40°C) and neutrophilic (pH 6–8) prokaryotic organisms. However, the insertion-deletion rate (0.43 × 10−10 per site per generation) is high relative to the base-substitution mutation rate. Organisms with a similar effective population size and a similar expected effect of genetic drift should have similar mutation rates. Because selection operates on the total mutation rate, it is suggested that the relatively high insertion-deletion rate may be balanced by a low base-substitution rate in A. capsulatum, with selection operating on the total mutation rate.
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U2 - 10.1002/ece3.8429
DO - 10.1002/ece3.8429
M3 - Article
AN - SCOPUS:85121432876
SN - 2045-7758
VL - 11
SP - 17609
EP - 17614
JO - Ecology and Evolution
JF - Ecology and Evolution
IS - 24
ER -