Supplementary material for Comparative genomics between Saccharomyces kudriavzevii and S. cerevisiae applied to identify mechanisms involved in adaptation

TABLE S1 | Assembly statistics for Sk CA111 and CR85 genome assemblies. TABLE S2 | Positive selection, evolutionary rate test and functional divergence results for all genes analyzed in both Sk and Sc species. PS, positive selection; FD, number of positions contributing to functional divergence in every protein; SCOP, annotations with SCOP domains as explained in Methods; NA (not available), protein domain annotation was not possible; Tajima’s test, Sk: acceleration of evolutionary rates leading to Sk branch; Sc, acceleration of evolutionary rates leading to Sc branch. TABLE S3 | GO term enrichment for genes showing evidence of functional divergence in Sk and Sc branch. TABLE S4 | Amino acids sites under positive selection according to branch-site model and BEB method. Specific amino acids sites and the probability of being under positive selection were retrieved for those candidates obtained with the branch-site model. TABLE S5 | Enriched/Impoverished chromosome regions in proteins with functional divergence evidence. FIGURE S1 | Functional divergence among metabolic pathways. Normalized contribution of genes showing evidence of functional divergence to every path. The height of the bars represents Φ, the normalized contribution of each pathway (i) of size (t) to the total number of genes under functional divergence when considering the whole dataset (T), calculated as Φ = (ni / t) (t / T). Bars above the dashed line represent enriched pathways in genes under functional divergence while bars below the line show impoverished pathways. B, biosynthesis; M, metabolism; D, degradation; aa, amino acid. FIGURE S2 |Sk vs. Sc differences in functional divergence among metabolic pathways. Normalized functional divergence values among metabolic pathways. The significance of the differences in every pathway between analysis performed with Sk or Sc as clade-of-interest was assessed by a Wilcoxon paired signed-rank test, those significant were indicated with an “∗.” B, biosynthesis; M, metabolism; D, degradation; aa, amino acid.

Bibliographic Details

Main Authors:	Macías, Laura G., Morard, Miguel, Toft, Christina, Barrio, Eladio
Format:	dataset biblioteca
Language:	English
Published:	Frontiers Media 2019
Online Access:	http://hdl.handle.net/10261/364212
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