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Extraordinary Genetic Diversity in a Wood Decay Mushroom
Populations of different species vary in the amounts of genetic diversity they possess. Nucleotide diversity π, the fraction of nucleotides that are different between two randomly chosen genotypes, has been known to range in eukaryotes between 0.0001 in Lynx lynx and 0.16 in Caenorhabditis brenneri....
Autores principales: | , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4576712/ https://www.ncbi.nlm.nih.gov/pubmed/26163667 http://dx.doi.org/10.1093/molbev/msv153 |
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author | Baranova, Maria A. Logacheva, Maria D. Penin, Aleksey A. Seplyarskiy, Vladimir B. Safonova, Yana Y. Naumenko, Sergey A. Klepikova, Anna V. Gerasimov, Evgeny S. Bazykin, Georgii A. James, Timothy Y. Kondrashov, Alexey S. |
author_facet | Baranova, Maria A. Logacheva, Maria D. Penin, Aleksey A. Seplyarskiy, Vladimir B. Safonova, Yana Y. Naumenko, Sergey A. Klepikova, Anna V. Gerasimov, Evgeny S. Bazykin, Georgii A. James, Timothy Y. Kondrashov, Alexey S. |
author_sort | Baranova, Maria A. |
collection | PubMed |
description | Populations of different species vary in the amounts of genetic diversity they possess. Nucleotide diversity π, the fraction of nucleotides that are different between two randomly chosen genotypes, has been known to range in eukaryotes between 0.0001 in Lynx lynx and 0.16 in Caenorhabditis brenneri. Here, we report the results of a comparative analysis of 24 haploid genotypes (12 from the United States and 12 from European Russia) of a split-gill fungus Schizophyllum commune. The diversity at synonymous sites is 0.20 in the American population of S. commune and 0.13 in the Russian population. This exceptionally high level of nucleotide diversity also leads to extreme amino acid diversity of protein-coding genes. Using whole-genome resequencing of 2 parental and 17 offspring haploid genotypes, we estimate that the mutation rate in S. commune is high, at 2.0 × 10(−8) (95% CI: 1.1 × 10(−8) to 4.1 × 10(−8)) per nucleotide per generation. Therefore, the high diversity of S. commune is primarily determined by its elevated mutation rate, although high effective population size likely also plays a role. Small genome size, ease of cultivation and completion of the life cycle in the laboratory, free-living haploid life stages and exceptionally high variability of S. commune make it a promising model organism for population, quantitative, and evolutionary genetics. |
format | Online Article Text |
id | pubmed-4576712 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-45767122015-09-25 Extraordinary Genetic Diversity in a Wood Decay Mushroom Baranova, Maria A. Logacheva, Maria D. Penin, Aleksey A. Seplyarskiy, Vladimir B. Safonova, Yana Y. Naumenko, Sergey A. Klepikova, Anna V. Gerasimov, Evgeny S. Bazykin, Georgii A. James, Timothy Y. Kondrashov, Alexey S. Mol Biol Evol Discoveries Populations of different species vary in the amounts of genetic diversity they possess. Nucleotide diversity π, the fraction of nucleotides that are different between two randomly chosen genotypes, has been known to range in eukaryotes between 0.0001 in Lynx lynx and 0.16 in Caenorhabditis brenneri. Here, we report the results of a comparative analysis of 24 haploid genotypes (12 from the United States and 12 from European Russia) of a split-gill fungus Schizophyllum commune. The diversity at synonymous sites is 0.20 in the American population of S. commune and 0.13 in the Russian population. This exceptionally high level of nucleotide diversity also leads to extreme amino acid diversity of protein-coding genes. Using whole-genome resequencing of 2 parental and 17 offspring haploid genotypes, we estimate that the mutation rate in S. commune is high, at 2.0 × 10(−8) (95% CI: 1.1 × 10(−8) to 4.1 × 10(−8)) per nucleotide per generation. Therefore, the high diversity of S. commune is primarily determined by its elevated mutation rate, although high effective population size likely also plays a role. Small genome size, ease of cultivation and completion of the life cycle in the laboratory, free-living haploid life stages and exceptionally high variability of S. commune make it a promising model organism for population, quantitative, and evolutionary genetics. Oxford University Press 2015-10 2015-07-10 /pmc/articles/PMC4576712/ /pubmed/26163667 http://dx.doi.org/10.1093/molbev/msv153 Text en © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Discoveries Baranova, Maria A. Logacheva, Maria D. Penin, Aleksey A. Seplyarskiy, Vladimir B. Safonova, Yana Y. Naumenko, Sergey A. Klepikova, Anna V. Gerasimov, Evgeny S. Bazykin, Georgii A. James, Timothy Y. Kondrashov, Alexey S. Extraordinary Genetic Diversity in a Wood Decay Mushroom |
title | Extraordinary Genetic Diversity in a Wood Decay Mushroom |
title_full | Extraordinary Genetic Diversity in a Wood Decay Mushroom |
title_fullStr | Extraordinary Genetic Diversity in a Wood Decay Mushroom |
title_full_unstemmed | Extraordinary Genetic Diversity in a Wood Decay Mushroom |
title_short | Extraordinary Genetic Diversity in a Wood Decay Mushroom |
title_sort | extraordinary genetic diversity in a wood decay mushroom |
topic | Discoveries |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4576712/ https://www.ncbi.nlm.nih.gov/pubmed/26163667 http://dx.doi.org/10.1093/molbev/msv153 |
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