Data from: Adaptation of Saccharomyces cerevisiae to saline stress through laboratory evolution.

Most laboratory evolution studies that characterize evolutionary
adaptation genomically focus on genetically simple traits that can be
altered by one or few mutations. Such traits are important, but they are
few compared with complex, polygenic traits influenced by many genes. We
know much less about complex traits, and about the changes that occur in
the genome and in gene expression during their evolutionary adaptation.
Salt stress tolerance is such a trait. It is especially attractive for
evolutionary studies, because the physiological response to salt stress is
well-characterized on the molecular and transcriptome level. This provides
a unique opportunity to compare evolutionary adaptation and physiological
adaptation to salt stress. The yeast Saccharomyces cerevisiae is a good
model system to study salt stress tolerance, because it contains several
highly conserved pathways that mediate the salt stress response. We
evolved three replicate lines of yeast under continuous salt (NaCl) stress
for 300 generations. All three lines evolved faster growth rate in high
salt conditions than their ancestor. In these lines, we studied gene
expression changes through microarray analysis and genetic changes through
next generation population sequencing. We found two principal kinds of
gene expression changes, changes in basal expression (82 genes) and
changes in regulation (62 genes). The genes that change their expression
involve several well-known physiological stress-response genes, including
CTT1, MSN4 and HLR1. Next generation sequencing revealed only one
high-frequency single-nucleotide change, in the gene MOT2, that caused
increased fitness when introduced into the ancestral strain. Analysis of
DNA content per cell revealed ploidy increases in all the three lines. Our
observations suggest that evolutionary adaptation of yeast to salt stress
is associated with genome size increase and modest expression changes in
several genes.