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BMC Genomics. 2010 Feb 3;11:88. doi: 10.1186/1471-2164-11-88.

Whole-genome sequencing of a laboratory-evolved yeast strain.

Author information

1
Department of Genome Sciences, University of Washington, Box 355065, Seattle, Washington 98195, USA.

Abstract

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 >28x 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 5x 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.

PMID:
20128923
PMCID:
PMC2829512
DOI:
10.1186/1471-2164-11-88
[Indexed for MEDLINE]
Free PMC Article
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