Whole-genome sequencing of a laboratory-evolved yeast strain
<p>Abstract</p> <p>Background</p> <p>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 genet...
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| Format: | Article |
| Language: | English |
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BMC
2010-02-01
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| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/11/88 |
| _version_ | 1818833540391895040 |
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| author | Dunham Maitreya J Payen Celia Araya Carlos L Fields Stanley |
| author_facet | Dunham Maitreya J Payen Celia Araya Carlos L Fields Stanley |
| author_sort | Dunham Maitreya J |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>We sequenced >93.5% of the genome of a laboratory-evolved strain of the yeast <it>Saccharomyces cerevisiae </it>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.</p> <p>Conclusions</p> <p>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.</p> |
| first_indexed | 2024-12-19T02:20:33Z |
| format | Article |
| id | doaj.art-4b16da9228fc4c8b8248e460d7cd7d42 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-19T02:20:33Z |
| publishDate | 2010-02-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-4b16da9228fc4c8b8248e460d7cd7d422022-12-21T20:40:14ZengBMCBMC Genomics1471-21642010-02-011118810.1186/1471-2164-11-88Whole-genome sequencing of a laboratory-evolved yeast strainDunham Maitreya JPayen CeliaAraya Carlos LFields Stanley<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>We sequenced >93.5% of the genome of a laboratory-evolved strain of the yeast <it>Saccharomyces cerevisiae </it>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.</p> <p>Conclusions</p> <p>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.</p>http://www.biomedcentral.com/1471-2164/11/88 |
| spellingShingle | Dunham Maitreya J Payen Celia Araya Carlos L Fields Stanley Whole-genome sequencing of a laboratory-evolved yeast strain BMC Genomics |
| 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 |
| url | http://www.biomedcentral.com/1471-2164/11/88 |
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