Whole-genome sequencing of a laboratory-evolved yeast strain

Abstract

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.

Discovery of Mutations inSaccharomyces cerevisiaeby Pooled Linkage Analysis and Whole-Genome Sequencing

“…The main decision point for most researchers will thus be whether to perform sequencing using (i) an isogenic backcross strain, ideal for simple point mutations in known genes; (ii) a backcross strain deliberately chosen to yield a large number of SNPs, ideal for linkage mapping of problematic loci (Wenger et al 2010); or (iii) no backcrossing at all, ideal when the goal is to catalog all changes in a strain (Araya et al 2010). Importantly, with the latter options it may not be possible to positively identify even a simple causative mutation within a linked locus, and especially not within an entire genome, due to the high density of nonsynonymous sequence alterations typically present (Figures 3 and 4) (Liti et al 2009).…”

Multiple Pathways of Duplication Formation with and Without Recombination (RecA) in Salmonella enterica

“…The palindrome stimulates deletions that generate the asymmetric (aTID) and tandem duplications with short junction sequences (see Figure 4B). Duplications of the initial symmetrical sTID type have been observed in yeast following extensive growth under selection for copy-number increase (Araya et al 2010). A TID amplification with one symmetrical and one modified junction has been reported in bacteria (Kugelberg et al 2010).…”

“…Figure 4 Tandem inversion duplications and their modification. Amplifications of this type were recovered in bacteria and yeast after prolonged growth under selection for additional gene copies (Araya et al 2010;Kugelberg et al 2010) the asymmetric TID structures found after growth under selection have been attributed to secondary modifications of sTIDs that form during growth under selection (Kugelberg et al 2010).…”

Experimental Microbial Evolution of Extremophiles

“…Understandably, high-throughput technologies have become indispensable to the study of EME. Advances in DNA sequencing throughput has expanded the research potential of experimental microbial evolution in extremophiles (Araya et al 2010;Barrick et al 2009;Hong and Gresham 2014;Kvitek and Sherlock 2013;Lang et al 2013;Herring et al 2006). Since the first archaeal genome was sequenced for Methanocaldococcus jannaschii (Bult et al 1996), many more genomes have become available for extremophiles (Allers and Mevarech 2005).…”