Whole-genome sequencing of a laboratory-evolved yeast strain

BMC Genomics

Methodology Article

Celia Payen¹  Carlos L Araya¹  Maitreya J Dunham¹  Stanley Fields² 

[1] Department of Genome Sciences, University of Washington, Box 355065, 98195, Seattle, Washington, USA;Department of Genome Sciences, University of Washington, Box 355065, 98195, Seattle, Washington, USA;Department of Medicine, University of Washington, Box 355065, 98195, Seattle, Washington, USA;Howard Hughes Medical Institute, University of Washington, Box 355065, 98195, Seattle, Washington, USA;

关键词: Read Depth;    Parental Genome;    Ancestor Genome;    Circular Binary Segmentation;    Copy Number Amplification;   

DOI  :  10.1186/1471-2164-11-88

 received in 2009-09-29, accepted in 2010-02-03,  发布年份 2010

来源: Springer

【 摘 要 】

BackgroundExperimental 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.ResultsWe 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.ConclusionsThis 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.

【 授权许可】

Unknown   
© Araya et al; licensee BioMed Central Ltd. 2010. This article is published under license to BioMed Central Ltd. 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.