yea3676-sup-0001-REVISED_Madden_etal_Supplemental_Information_211007.docxWord 2007 document , 1 MB

Table S1. GenBank accession IDs, species and strain names, and Type status of reference sequences used in our alignment. All sequences downloaded from the NCBI GenBank database.

Table S2. The list of strains tested for their ability to leaven dough and produce a baked loaf of bread. Average bread slice area and standard deviation are reported (n=3).

Table S3. Complete growth data for strains (attached as an excel file).

Optical density (OD) over time was measured from replicates of each strain used in baking analyses under 4 conditions (2% glucose, 2% sucrose, 25% sucrose, and 0.5M NaCl+2% sucrose). Here, we report the parameters estimated by fitting the OD data to the logistic equation used in the program “growthcurver” (Sprouffske and Wagner, 2016). The growthrate (r) and population size (k) are analyzed in Figs 3, S1.

Table S4. Full list of North Carolina State University students in The Student Yeast Cooperative who contributed data as part of the CURE.

Figure S1. Growth rate and population size of candidate baking strains. Candidate baking strains were grown in 2% sucrose, and 2% dextrose. A.) Box plots of maximum population size (the x-axis is the parameter “k” estimated from optical density data fit to a logistic growth equation). B.) Box plots of maximum growth rate during the exponential growth phase (the x-axis is the parameter “r” estimated from optical density data fit to a logistic growth equation). See Table S3 for full dataset.

Figure S2. Environmental S. cerevisiae strain VS189A utilizes a wider range of carbon sources than lab strain BY4743. A.-B. Biolog YT plates were used to compare the growth of VS189A, BY4743, and a commercial baking strain F01 yeasts on a variety of carbon sources. For VS189A and BY4743, five replicate plates were incubated at 30°C, and OD600 readings were taken at 16 h, 40 h, 64 h, and 88 h timepoints. For F01, a single YT plate was incubated in a BioTek Epoch2 at 30°C, with OD600 readings taken every 30 minutes. For each plate at each time point, the OD600 reading of well D1 (water) was subtracted from the OD600 readings of each well. A. Growth of the VS189A and BY4743 strains on each carbon source was compared by performing a 2-way ANOVA with Šídák’s multiple comparisons test at each time point. Differences greater than 0 indicate a carbon source in which the lab strain grew faster than the environmental strain, and differences less than 0 indicate a carbon source in which the environmental strain grew faster than the lab strain. Error bars indicate 95% confidence interval. Red indicates carbon sources in which the strains differed in growth for at least one time point (from bottom to top: D12, inulin; E6, D-melibiose; E7, palatinose; E8, D-raffinose; E9, Stachyose; E10, sucrose; E12, turanose; F4, galactose; F8, α-methyl-D-glucoside; H8, D-melibiose + D-xylose). B. Bar graphs show the OD600 reading in the listed carbon source after subtraction of the OD600 reading for well D1 (water) in the same plate. F01 is the commercial baking strain of yeast. Error bars represent SD. The carbon sources shown are those for which a difference was observed between strains VS189A and BY4743. C. Representative spot plates comparing the growth of strains BY4743 (lab, top) and VS189A (environmental, bottom) on YPD (left) and YP-galactose (right). Images are representative of more than 200 replicates performed by The Student Yeast Cooperative as experimental controls.

Figure S3. Growth of lab and environmental S. cerevisiae strains at various temperatures. Members of The Student Yeast Cooperative performed spot plate assays to compare the growth of the three environmental S. cerevisiae strains to that of the lab strain BY4743 at temperatures outside of the optimal range of 28-30°C. Each spot plate image shown is a representative image selected from at least 10-20 student experiments. All three environmental strains produce larger colonies than BY4743 at every temperature tested, with these differences most apparent at the lower end of the temperature range.

Figure S4. Environmental S. cerevisiae strains are more resistant to KCl than lab strain BY4743, but less resistant to NaCl. Members of The Student Yeast Cooperative performed spot plate assays to compare the growth of the three environmental S. cerevisiae strains to that of the lab strain BY4743 in the presence and absence of various concentrations of KCl and NaCl. Each spot plate image shown is a representative image selected from at least 10-20 student experiments. All three environmental strains produce larger colonies at low to moderate concentrations of KCl than does BY4743, and strains M_1_D and VS189A produce barely-visible colonies at 2.0 M KCl, while BY4743 and VS195D fail to grow. Conversely, BY4743 is able to grow in NaCl concentrations up to 1.0 M, while VS189A and VS195D fail to grow in any NaCl concentrations tested. M_1_D produces clearly visible colonies in the presence of 0.4 M NaCl, and barely visible colonies in the presence of 0.6 M NaCl.

Figure S5. Conservation of HOG1 pathway genes among environmental and lab S. cerevisiae strains. In an effort to identify genetic differences that may underlie the observed differences in osmotolerance among the S. cerevisiae strains, members of The Student Yeast Cooperative performed alignments of the nucleotide and amino acid sequences of genes encoding the HOG1 osmotic stress response signaling pathway. Shown are all protein-level polymorphisms identified in Pbs2p, Ste20p, Ssk1p, Hog1p, and Ste50p. Numbers indicate the amino acid residue number, and letters indicate the amino acid present at that position in each strain. Pink indicates the amino acid present in BY4743, and blue indicates an amino acid that differs from that present in BY4743. For all genes examined, VS189A and VS195D exhibited 100% amino acid identity.