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Repeat-induced point mutation in Neurospora crassa causes the highest known mutation rate and mutational burden of any cellular life
BACKGROUND: Repeat-induced point (RIP) mutation in Neurospora crassa degrades transposable elements by targeting repeats with C→T mutations. Whether RIP affects core genomic sequence in important ways is unknown. RESULTS: By parent-offspring whole genome sequencing, we estimate a mutation rate (3.38...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7296669/ https://www.ncbi.nlm.nih.gov/pubmed/32546205 http://dx.doi.org/10.1186/s13059-020-02060-w |
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author | Wang, Long Sun, Yingying Sun, Xiaoguang Yu, Luyao Xue, Lan He, Zhen Huang, Ju Tian, Dacheng Hurst, Laurence D. Yang, Sihai |
author_facet | Wang, Long Sun, Yingying Sun, Xiaoguang Yu, Luyao Xue, Lan He, Zhen Huang, Ju Tian, Dacheng Hurst, Laurence D. Yang, Sihai |
author_sort | Wang, Long |
collection | PubMed |
description | BACKGROUND: Repeat-induced point (RIP) mutation in Neurospora crassa degrades transposable elements by targeting repeats with C→T mutations. Whether RIP affects core genomic sequence in important ways is unknown. RESULTS: By parent-offspring whole genome sequencing, we estimate a mutation rate (3.38 × 10(−6) per bp per generation) that is two orders of magnitude higher than reported for any non-viral organism, with 93–98% of mutations being RIP-associated. RIP mutations are, however, relatively rare in coding sequence, in part because RIP preferentially attacks GC-poor long duplicates that interact in three dimensional space, while coding sequence duplicates are rare, GC-rich, short, and tend not to interact. Despite this, with over 5 coding sequence mutations per genome per generation, the mutational burden is an order of magnitude higher than the previously highest observed. Unexpectedly, the majority of these coding sequence mutations appear not to be the direct product of RIP being mostly in non-duplicate sequence and predominantly not C→T mutations. Nonetheless, RIP-deficient strains have over an order of magnitude fewer coding sequence mutations outside of duplicated domains than RIP-proficient strains. CONCLUSIONS: Neurospora crassa has the highest mutation rate and mutational burden of any non-viral life. While the high rate is largely due to the action of RIP, the mutational burden appears to be RIP-associated but not directly caused by RIP. |
format | Online Article Text |
id | pubmed-7296669 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-72966692020-06-16 Repeat-induced point mutation in Neurospora crassa causes the highest known mutation rate and mutational burden of any cellular life Wang, Long Sun, Yingying Sun, Xiaoguang Yu, Luyao Xue, Lan He, Zhen Huang, Ju Tian, Dacheng Hurst, Laurence D. Yang, Sihai Genome Biol Research BACKGROUND: Repeat-induced point (RIP) mutation in Neurospora crassa degrades transposable elements by targeting repeats with C→T mutations. Whether RIP affects core genomic sequence in important ways is unknown. RESULTS: By parent-offspring whole genome sequencing, we estimate a mutation rate (3.38 × 10(−6) per bp per generation) that is two orders of magnitude higher than reported for any non-viral organism, with 93–98% of mutations being RIP-associated. RIP mutations are, however, relatively rare in coding sequence, in part because RIP preferentially attacks GC-poor long duplicates that interact in three dimensional space, while coding sequence duplicates are rare, GC-rich, short, and tend not to interact. Despite this, with over 5 coding sequence mutations per genome per generation, the mutational burden is an order of magnitude higher than the previously highest observed. Unexpectedly, the majority of these coding sequence mutations appear not to be the direct product of RIP being mostly in non-duplicate sequence and predominantly not C→T mutations. Nonetheless, RIP-deficient strains have over an order of magnitude fewer coding sequence mutations outside of duplicated domains than RIP-proficient strains. CONCLUSIONS: Neurospora crassa has the highest mutation rate and mutational burden of any non-viral life. While the high rate is largely due to the action of RIP, the mutational burden appears to be RIP-associated but not directly caused by RIP. BioMed Central 2020-06-16 /pmc/articles/PMC7296669/ /pubmed/32546205 http://dx.doi.org/10.1186/s13059-020-02060-w Text en © The Author(s) 2020 Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Research Wang, Long Sun, Yingying Sun, Xiaoguang Yu, Luyao Xue, Lan He, Zhen Huang, Ju Tian, Dacheng Hurst, Laurence D. Yang, Sihai Repeat-induced point mutation in Neurospora crassa causes the highest known mutation rate and mutational burden of any cellular life |
title | Repeat-induced point mutation in Neurospora crassa causes the highest known mutation rate and mutational burden of any cellular life |
title_full | Repeat-induced point mutation in Neurospora crassa causes the highest known mutation rate and mutational burden of any cellular life |
title_fullStr | Repeat-induced point mutation in Neurospora crassa causes the highest known mutation rate and mutational burden of any cellular life |
title_full_unstemmed | Repeat-induced point mutation in Neurospora crassa causes the highest known mutation rate and mutational burden of any cellular life |
title_short | Repeat-induced point mutation in Neurospora crassa causes the highest known mutation rate and mutational burden of any cellular life |
title_sort | repeat-induced point mutation in neurospora crassa causes the highest known mutation rate and mutational burden of any cellular life |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7296669/ https://www.ncbi.nlm.nih.gov/pubmed/32546205 http://dx.doi.org/10.1186/s13059-020-02060-w |
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