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Adaptation to nutrient-limitation results in massive remodeling of global gene expression.

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posted on 2008-12-12, 01:01 authored by David Gresham, Michael M. Desai, Cheryl M. Tucker, Harry T. Jenq, Dave A. Pai, Alexandra Ward, Christopher G. DeSevo, David Botstein, Maitreya J. Dunham

(A) Gene expression data, presented as the log2-transformed ratio of each gene's expression value in the evolved versus ancestral strain, were hierarchically clustered on both axes (y-axis, 5443 genes; x-axis, 48 clone and 15 population samples). The dendrogram for the clustered experiments (x-axis) is color-coded by nutrient limitation (sulfate-limitation in red, glucose-limitation in green, and phosphate-limitation in blue). Orange horizontal bars represent groupings where the two clones and their corresponding population sample are more correlated with each other than with any other experiments. Glucose expression states fall into three phenoclusters (Gluc1, Gluc2, Gluc3) while phosphate expression states fall into four (Phos1, Phos2, Phos3, Phos4). (B) Density estimates of the distribution of pairwise pearson correlations (N = 112) of the expression states of clones selected under three different nutrient limitations. Clonal isolates from independent sulfate-limitation evolutions (red) were more similar to each other (median pearson distance = 0.425) than those obtained from independent glucose (green, median pearson distance = 0.152) or phosphate (blue, median pearson distance = 0.088) evolutions. The three distributions were compared using the Wilcoxon-Mann-Whitney rank-sum test. The distributions of pairwise correlations between sulfate and glucose clones are significantly different (U = 3097, p-value = 5.9×10−11) as are the distributions between sulfate and phosphate clones (U = 2545, p-value = 1.54×10−14). The distributions of pairwise distances between phosphate and glucose clones are not significantly different (U = 7103, p-value = 0.08681).