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. 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.
Department of Genome Sciences, University of Washington, Box 355065, Seattle, Washington 98195, USA.
Carlos L
CL
Araya
Celia
C
Payen
Maitreya J
MJ
Dunham
Stanley
S
Fields
D000465:Algorithms; D056905:Chromosome Breakpoints; D004271:DNA, Fungal / Q000235:genetics; D019143:Evolution, Molecular; D018628:Gene Dosage; D016681:Genome, Fungal; D015698:Genomic Library; D017354:Point Mutation; D020641:Polymorphism, Single Nucleotide; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*
D004271:DNA, Fungal