Cargando…
Low Base-Substitution Mutation Rate in the Germline Genome of the Ciliate Tetrahymena thermophila
Mutation is the ultimate source of all genetic variation and is, therefore, central to evolutionary change. Previous work on Paramecium tetraurelia found an unusually low germline base-substitution mutation rate in this ciliate. Here, we tested the generality of this result among ciliates using Tetr...
Autores principales: | , , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2016
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5585995/ https://www.ncbi.nlm.nih.gov/pubmed/27635054 http://dx.doi.org/10.1093/gbe/evw223 |
_version_ | 1783261733830262784 |
---|---|
author | Long, Hongan Winter, David J Chang, Allan Y.-C Sung, Way Wu, Steven H Balboa, Mariel Azevedo, Ricardo B R Cartwright, Reed A Lynch, Michael Zufall, Rebecca A |
author_facet | Long, Hongan Winter, David J Chang, Allan Y.-C Sung, Way Wu, Steven H Balboa, Mariel Azevedo, Ricardo B R Cartwright, Reed A Lynch, Michael Zufall, Rebecca A |
author_sort | Long, Hongan |
collection | PubMed |
description | Mutation is the ultimate source of all genetic variation and is, therefore, central to evolutionary change. Previous work on Paramecium tetraurelia found an unusually low germline base-substitution mutation rate in this ciliate. Here, we tested the generality of this result among ciliates using Tetrahymena thermophila. We sequenced the genomes of 10 lines of T. thermophila that had each undergone approximately 1,000 generations of mutation accumulation (MA). We applied an existing mutation-calling pipeline and developed a new probabilistic mutation detection approach that directly models the design of an MA experiment and accommodates the noise introduced by mismapped reads. Our probabilistic mutation-calling method provides a straightforward way of estimating the number of sites at which a mutation could have been called if one was present, providing the denominator for our mutation rate calculations. From these methods, we find that T. thermophila has a germline base-substitution mutation rate of 7.61 × 10 (−) (12) per-site, per cell division, which is consistent with the low base-substitution mutation rate in P. tetraurelia. Over the course of the evolution experiment, genomic exclusion lines derived from the MA lines experienced a fitness decline that cannot be accounted for by germline base-substitution mutations alone, suggesting that other genetic or epigenetic factors must be involved. Because selection can only operate to reduce mutation rates based upon the "visible" mutational load, asexual reproduction with a transcriptionally silent germline may allow ciliates to evolve extremely low germline mutation rates. |
format | Online Article Text |
id | pubmed-5585995 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-55859952017-09-11 Low Base-Substitution Mutation Rate in the Germline Genome of the Ciliate Tetrahymena thermophila Long, Hongan Winter, David J Chang, Allan Y.-C Sung, Way Wu, Steven H Balboa, Mariel Azevedo, Ricardo B R Cartwright, Reed A Lynch, Michael Zufall, Rebecca A Genome Biol Evol Research Article Mutation is the ultimate source of all genetic variation and is, therefore, central to evolutionary change. Previous work on Paramecium tetraurelia found an unusually low germline base-substitution mutation rate in this ciliate. Here, we tested the generality of this result among ciliates using Tetrahymena thermophila. We sequenced the genomes of 10 lines of T. thermophila that had each undergone approximately 1,000 generations of mutation accumulation (MA). We applied an existing mutation-calling pipeline and developed a new probabilistic mutation detection approach that directly models the design of an MA experiment and accommodates the noise introduced by mismapped reads. Our probabilistic mutation-calling method provides a straightforward way of estimating the number of sites at which a mutation could have been called if one was present, providing the denominator for our mutation rate calculations. From these methods, we find that T. thermophila has a germline base-substitution mutation rate of 7.61 × 10 (−) (12) per-site, per cell division, which is consistent with the low base-substitution mutation rate in P. tetraurelia. Over the course of the evolution experiment, genomic exclusion lines derived from the MA lines experienced a fitness decline that cannot be accounted for by germline base-substitution mutations alone, suggesting that other genetic or epigenetic factors must be involved. Because selection can only operate to reduce mutation rates based upon the "visible" mutational load, asexual reproduction with a transcriptionally silent germline may allow ciliates to evolve extremely low germline mutation rates. Oxford University Press 2016-09-15 /pmc/articles/PMC5585995/ /pubmed/27635054 http://dx.doi.org/10.1093/gbe/evw223 Text en © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Long, Hongan Winter, David J Chang, Allan Y.-C Sung, Way Wu, Steven H Balboa, Mariel Azevedo, Ricardo B R Cartwright, Reed A Lynch, Michael Zufall, Rebecca A Low Base-Substitution Mutation Rate in the Germline Genome of the Ciliate Tetrahymena thermophila |
title | Low Base-Substitution Mutation Rate in the Germline Genome of the Ciliate Tetrahymena thermophila |
title_full | Low Base-Substitution Mutation Rate in the Germline Genome of the Ciliate Tetrahymena thermophila |
title_fullStr | Low Base-Substitution Mutation Rate in the Germline Genome of the Ciliate Tetrahymena thermophila |
title_full_unstemmed | Low Base-Substitution Mutation Rate in the Germline Genome of the Ciliate Tetrahymena thermophila |
title_short | Low Base-Substitution Mutation Rate in the Germline Genome of the Ciliate Tetrahymena thermophila |
title_sort | low base-substitution mutation rate in the germline genome of the ciliate tetrahymena thermophila |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5585995/ https://www.ncbi.nlm.nih.gov/pubmed/27635054 http://dx.doi.org/10.1093/gbe/evw223 |
work_keys_str_mv | AT longhongan lowbasesubstitutionmutationrateinthegermlinegenomeoftheciliatetetrahymenathermophila AT winterdavidj lowbasesubstitutionmutationrateinthegermlinegenomeoftheciliatetetrahymenathermophila AT changallanyc lowbasesubstitutionmutationrateinthegermlinegenomeoftheciliatetetrahymenathermophila AT sungway lowbasesubstitutionmutationrateinthegermlinegenomeoftheciliatetetrahymenathermophila AT wustevenh lowbasesubstitutionmutationrateinthegermlinegenomeoftheciliatetetrahymenathermophila AT balboamariel lowbasesubstitutionmutationrateinthegermlinegenomeoftheciliatetetrahymenathermophila AT azevedoricardobr lowbasesubstitutionmutationrateinthegermlinegenomeoftheciliatetetrahymenathermophila AT cartwrightreeda lowbasesubstitutionmutationrateinthegermlinegenomeoftheciliatetetrahymenathermophila AT lynchmichael lowbasesubstitutionmutationrateinthegermlinegenomeoftheciliatetetrahymenathermophila AT zufallrebeccaa lowbasesubstitutionmutationrateinthegermlinegenomeoftheciliatetetrahymenathermophila |