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.
Araya
Carlos L
CL
Department of Genome Sciences, University of Washington, Box 355065, Seattle, Washington 98195, USA.
Payen
Celia
C
Dunham
Maitreya J
MJ
Fields
Stanley
S
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