Inter-strain genetic variation at discrete genomic loci.

<p>Data is presented for three distinct genomic loci (A–C). Estimates of copy number and heterozygous allele frequencies were calculated and are presented as in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004161#pgen-1004161-g001" target="_blank">Fig. 1</a>.</p

Loss of nitrate and nitrite assimilation in <i>D. bruxellensis</i> strains.

<p>(A) Sequencing coverage across AWRI1608, AWRI1613 and CBS2499. Bases that are in disagreement to the AWRI1499 reference strain are colored according to their sequence and proportion at that position (AWRI1499, green; AWRI1608, blue; AWRI1613, red). The positions of open reading frames in this region (according to the AWRI1499 genome annotation) are also shown. (B) Phenotypic analysis of <i>D. bruxellensis</i> strains growing on either on ammonium and nitrate. Strains scored as showing either positive (+) or negative (-) growth are indicated.</p

Genes from <i>Oenococcus kitaharae</i> predicted to be involved in cellular defence.

a<p>homolog found in <i>O. oeni</i> AWRIB429.</p

OrthoMCL oxidoreductase clusters expanded in <i>D. bruxellensis</i>.

<p>Alcohol dehydrogenase (A). and aldehyde dehydrogenase (B). Unrooted maximum likelihood trees generated from amino acid alignments of proteins assigned to the same OrthoMCL cluster. Red = <i>D. bruxellensis</i>, blue = <i>S. cerevisiae</i>, green = <i>P. angusta</i>, pink = <i>P. pastoris</i>, orange = <i>Issatchenkia terricola</i>.</p

Resequencing analysis of <i>D. bruxellensis</i> isolates.

<p>(A) Single nucleotide polymorphism analysis. For each strain, heterozygous nucleotides were identified and the proportion of aligned reads containing each of the variant bases recorded. The average major allele frequency was then calculated for sliding windows across the genome (5 kb window, 1 kb step) and plotted central to each window. Any regions that lacked heterozygous bases were classified as regions of loss-of-heterozygosity (LOH) and are indicated by grey bars above each plot. The solid black line represents a major allele frequency of 0.66 that would be expected for heterozygous a triploid genome. (B) Copy number variation analysis. For each strain, the average sequencing read depth was recorded for sliding windows across the genome (5 kb window, 1 kb step) and are presented relative to a predicted triploid state for AWRI1608 and a diploid state for AWRI613 and CBS2499. Solid black lines indicate proposed ploidy levels across the genome based on segmental smoothing (see materials and methods).</p

Data_Sheet_1_A Novel Approach to Isolating Improved Industrial Interspecific Wine Yeasts Using Chromosomal Mutations as Potential Markers for Increased Fitness.pdf

<p>Wine yeast breeding programs utilizing interspecific hybridization deliver cost-effective tools to winemakers looking to differentiate their wines through the development of new wine styles. The addition of a non-Saccharomyces cerevisiae genome to a commercial wine yeast can generate novel phenotypes ranging from wine flavor and aroma diversity to improvements in targeted fermentation traits. In the current study we utilized a novel approach to screen isolates from an evolving population for increased fitness in a S. cerevisiae × S. uvarum interspecific hybrid previously generated to incorporate the targeted phenotype of lower volatile acidity production. Sequential grape-juice fermentations provided a selective environment from which to screen isolates. Chromosomal markers were used in a novel approach to identify isolates with potential increased fitness. A strain with increased fitness relative to its parents was isolated from an early timepoint in the evolving population, thereby minimizing the risk of introducing collateral mutations and potentially undesirable phenotypes. The evolved strain retained the desirable fermentation trait of reduced volatile acidity production, along with other winemaking traits of importance while exhibiting improved fermentation kinetics.</p

Genes involved in citrate utilization in <i>O. oeni</i>.

a<p><i>O. oeni</i> Genbank protein ID from genome accession number NC_008528.1.</p

Schematic representation of two putative conjugative transposons present in the <i>Oenococcus kitaharae</i> genome.

<p>The ORFs present in each genomic element are colour coded by predicted function. The conserved conjugation-associated region present in the centre of each element is also highlighted (red shading).</p

Haplotype analysis of <i>D. bruxellensis</i> isolates.

<p>Distinct haplotypes were assembled for conserved open reading frames and subjected to maximum-likelihood phylogenetic analysis <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004161#pgen.1004161-Gouy1" target="_blank">[15]</a>, <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004161#pgen.1004161-Guindon1" target="_blank">[16]</a>. Nodes are color-coded according to strain AWRI1499 (green), AWRI1608 (blue), AWRI1613 (red), CBS2499 (yellow). Nodes for CBS2499 are only shown where haplotypes were different to those of AWRI1613.</p

Phylogeny of fungal phenolic acid decarboxylase enzymes.

<p>Maximum likelihood tree generated from amino acid alignment of all fungal proteins with homology to <i>S. cerevisiae</i> Pad1p (ScPAD1) or putative <i>D. bruxellensis</i> Padp (DbPAD). Species with homologs of both proteins indicated in blue. Bootstrap values (100 randomisations) for all nodes shown.</p