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Whole-genome sequencing of a laboratory-evolved yeast strain
BACKGROUND: Experimental evolution of microbial populations provides a unique opportunity to study evolutionary adaptation in response to controlled selective pressures. However, until recently it has been difficult to identify the precise genetic changes underlying adaptation at a genome-wide scale...
Autores principales: | , , , |
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Formato: | Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2010
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2829512/ https://www.ncbi.nlm.nih.gov/pubmed/20128923 http://dx.doi.org/10.1186/1471-2164-11-88 |
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author | Araya, Carlos L Payen, Celia Dunham, Maitreya J Fields, Stanley |
author_facet | Araya, Carlos L Payen, Celia Dunham, Maitreya J Fields, Stanley |
author_sort | Araya, Carlos L |
collection | PubMed |
description | BACKGROUND: Experimental evolution of microbial populations provides a unique opportunity to study evolutionary adaptation in response to controlled selective pressures. However, until recently it has been difficult to identify the precise genetic changes underlying adaptation at a genome-wide scale. New DNA sequencing technologies now allow the genome of parental and evolved strains of microorganisms to be rapidly determined. RESULTS: We sequenced >93.5% of the genome of a laboratory-evolved strain of the yeast Saccharomyces cerevisiae and its ancestor at >28× depth. Both single nucleotide polymorphisms and copy number amplifications were found, with specific gains over array-based methodologies previously used to analyze these genomes. Applying a segmentation algorithm to quantify structural changes, we determined the approximate genomic boundaries of a 5× gene amplification. These boundaries guided the recovery of breakpoint sequences, which provide insights into the nature of a complex genomic rearrangement. CONCLUSIONS: This study suggests that whole-genome sequencing can provide a rapid approach to uncover the genetic basis of evolutionary adaptations, with further applications in the study of laboratory selections and mutagenesis screens. In addition, we show how single-end, short read sequencing data can provide detailed information about structural rearrangements, and generate predictions about the genomic features and processes that underlie genome plasticity. |
format | Text |
id | pubmed-2829512 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2010 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-28295122010-02-28 Whole-genome sequencing of a laboratory-evolved yeast strain Araya, Carlos L Payen, Celia Dunham, Maitreya J Fields, Stanley BMC Genomics Methodology Article BACKGROUND: Experimental evolution of microbial populations provides a unique opportunity to study evolutionary adaptation in response to controlled selective pressures. However, until recently it has been difficult to identify the precise genetic changes underlying adaptation at a genome-wide scale. New DNA sequencing technologies now allow the genome of parental and evolved strains of microorganisms to be rapidly determined. RESULTS: We sequenced >93.5% of the genome of a laboratory-evolved strain of the yeast Saccharomyces cerevisiae and its ancestor at >28× depth. Both single nucleotide polymorphisms and copy number amplifications were found, with specific gains over array-based methodologies previously used to analyze these genomes. Applying a segmentation algorithm to quantify structural changes, we determined the approximate genomic boundaries of a 5× gene amplification. These boundaries guided the recovery of breakpoint sequences, which provide insights into the nature of a complex genomic rearrangement. CONCLUSIONS: This study suggests that whole-genome sequencing can provide a rapid approach to uncover the genetic basis of evolutionary adaptations, with further applications in the study of laboratory selections and mutagenesis screens. In addition, we show how single-end, short read sequencing data can provide detailed information about structural rearrangements, and generate predictions about the genomic features and processes that underlie genome plasticity. BioMed Central 2010-02-03 /pmc/articles/PMC2829512/ /pubmed/20128923 http://dx.doi.org/10.1186/1471-2164-11-88 Text en Copyright ©2010 Araya et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Methodology Article Araya, Carlos L Payen, Celia Dunham, Maitreya J Fields, Stanley Whole-genome sequencing of a laboratory-evolved yeast strain |
title | Whole-genome sequencing of a laboratory-evolved yeast strain |
title_full | Whole-genome sequencing of a laboratory-evolved yeast strain |
title_fullStr | Whole-genome sequencing of a laboratory-evolved yeast strain |
title_full_unstemmed | Whole-genome sequencing of a laboratory-evolved yeast strain |
title_short | Whole-genome sequencing of a laboratory-evolved yeast strain |
title_sort | whole-genome sequencing of a laboratory-evolved yeast strain |
topic | Methodology Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2829512/ https://www.ncbi.nlm.nih.gov/pubmed/20128923 http://dx.doi.org/10.1186/1471-2164-11-88 |
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