| Comments |
P.1244 right column bottom paragraph: "In terms of evolution, gene duplications and especially the whole-genome duplication (WGD) that occurred in the hemiascomycete lineage ∼100 million years ago (primary sources) are known to have played a significant role in shaping the yeast genome and especially metabolism (Papp et al. 2004, Conant and Wolfe 2007, Conant 2014). Intriguingly, a significant fraction of total kinase–substrate relationships may have been rewired during this period by the evolutionary forces of nonfunctionalization, neofunctionalization, and subfunctionalization, suggesting rapid adaption at this level (Amoutzias et al. 2010, Freschi et al. 2011). On average, 19% (1096/5884) of S. cerevisiae protein-coding genes are present in duplicate as a result of the WGD, whereas 23% (207/909) of the genes encoding metabolic proteins are WGD paralogs. For the metabolic enzymes that are phosphoproteins, this proportion increases to 28% (ALL:115/412) and 32% (HC: 64/197). All the above differences are statistically significant (p-value < 0.05), according to the hypergeometric test. This agrees with a previous observation, based on a smaller dataset, that phosphorylation is a factor that affects the survival of genes after WGD (Amoutzias et al. 2010)." |