Whole-genome sequencing of a laboratory-evolved yeast strain

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

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Chromosome Breakpoints
  • DNA, Fungal / genetics
  • Evolution, Molecular
  • Gene Dosage
  • Genome, Fungal*
  • Genomic Library
  • Point Mutation
  • Polymorphism, Single Nucleotide
  • Saccharomyces cerevisiae / genetics*
  • Sequence Analysis, DNA / methods*

Substances

  • DNA, Fungal