10.5061/DRYAD.K3F17
Williams, Kathryn M.
Washington University in St. Louis
Liu, Ping
Washington University in St. Louis
Fay, Justin C.
Washington University in St. Louis
Data from: Evolution of ecological dominance of yeast species in
high-sugar environments
Dryad
dataset
2015
Innovation
Naumovozyma castellii
Lachancea waltii
Zygosaccharomyces rouxii
Saccharomyces uvarum
Candida glabrata
Torulaspora delbrueckii
Vanderwaltozyma polyspora
Lachancea kluyveri
Hanseniaspora vineae
Saccharomyces mikatae
genome duplication
Lachancea thermotolerans
Kluyveromyces lactis
Fermentation
Kazachstania martiniae
Saccharomyces paradoxus
Nakeseomyces bacillisporus
Kazachstania lodderae
Wine
Tetrapisispora blattae
2015-07-07T15:13:59Z
2015-07-07T15:13:59Z
en
https://doi.org/10.1111/evo.12707
1319812263 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
In budding yeasts, fermentation in the presence of oxygen evolved around
the time of a whole genome duplication (WGD) and is thought to confer
dominance in high-sugar environments because ethanol is toxic to many
species. While there are many fermentative yeast species, only
Saccharomyces cerevisiae consistently dominates wine fermentations. In
this study, we use co-culture experiments and intrinsic growth rate assays
to examine the relative fitness of non-WGD and WGD yeast species across
environments to assess when S. cerevisiae's ability to dominate
high-sugar environments arose. We show that S. cerevisiae dominates nearly
all other non-WGD and WGD species except for its sibling species S.
paradoxus in both grape juice and a high-sugar rich medium. Of the species
we tested, S. cerevisiae and S. paradoxus have evolved the highest ethanol
tolerance and intrinsic growth rate in grape juice. However, the ability
of S. cerevisiae and S. paradoxus to dominate certain species depends on
the temperature and the type of high-sugar environment. Our results
indicate that dominance of high-sugar environments evolved much more
recently than the WGD, most likely just prior to or during the
differentiation of Saccharomyces species, and that evolution of multiple
traits contributes to S. cerevisiae's ability to dominate wine
fermentations.
Pyrosequencing competition dataCalibrated pyrosequencing data from
Competition 1. The frequency of each competitor species in either paired
competition with S. cerevisiae or in pooled monocultures. The adjusted
frequency is based on calibration curves and eliminates negative
values.CalibratedPyrosequencingData.csvSequencing competition
dataCalibrated sequencing data from Competition 2. The frequency of each
competitor species in competition with different reference strains, along
with concatenated barcode and indexes used for sample ID. The fitness
difference and experimental metadata is also
included.biodiversity.data.csvHigh-sugar environmentData from assays
(gren01 and nut01) to determine the intrinsic growth rate of each yeast
species in high-sugar environments including grape juice. The OD600 (cell
density) is given for time-points between zero and 48
hrs.grape_environment.csvEthanol resistanceData from assay to determine
the ethanol tolerance of each yeast species. OD600 (cell density) is given
for time-points between zero and 48 hrs for different concentrations of
ethanol. One sample was omitted from the analysis (Smik, Rep C, 2%
ethanol) due to possible contamination from a pipetting error that
occurred during the experiment.ethanol.csvSupernatant inhibitorsData from
assay to determine whether Saccharomyces cerevisiae produces unknown
compounds that inhibit the growth of other yeast species. OD600 (cell
density) is given for for time-points between zero and 48 hrs in
supernatant cultures. A small number of samples (24/432) registered growth
in un-innoculated controls before 36 hours, and these samples were omitted
from our analysis. Following the removal of those samples, Lachancea
kluyveri lacked sufficient control samples for analysis and was not
included in the analysis.supernatant.csvSequencing metadataBarcodes,
indexes and metadata used to extract species tags from raw sequencing data
for BITS-3 and BITS-4 libraries.Metadata.xlsBITS-3 library readRaw
sequence data with reads containing barcode, linker then species specific
sequences.BITS-3_S1_L001_R1_001.fastq.gzBITS-3 library indexRaw sequence
data with reads containing indexes.BITS-3_S1_L001_I1_001.fastq.gzBITS-4
library readRaw sequence data with reads containing barcode, linker then
species specific sequences.BITS-4_S1_L001_R1_001.fastq.gzBITS-4 library
indexRaw sequence data with reads containing
indexes.BITS-4_S1_L001_I1_001.fastq.gz