Structural variations in S. cerevisiae strains
Below are reported the main translocations identified in the Vineyard Yeast Project through the genomic comparison of six S. cerevisiae strains: four vineyard strains (P283, R008, R103, P301), an industrial wine strain (EC1118) and the reference laboratory strain S288c.
More informations can be found in the paper
Treu L, Toniolo C, Nadai C, Sardu A, Giacomini A, Corich V, Campanaro S. The impact of genomic variability on gene expression in environmental Saccharomyces cerevisiae strains. Environ Microbiol. 2013.
Genome alignment of the four vineyard yeast strains, of the wine industrial strain EC1118 and of the laboratory strain S288C revealed nine major translocations (detailed description was reported in the Table S3 of the paper) .
As previously identified using PFGE (Supplementary methods S1), most of these are localized on chrs VIII-XVI, while the chrs I-VII were more conserved; the more interesting regions were verified using PCR (Table S3).
Translocated region "XVI-t-VIII" (363 Kbp), verified by PCR TR16-8
Translocated region "XV-t-XVI" (150 Kbp), verified by PCR TR15-16a
Inverted and translocated region "III-t-XI" (10 Kbp), verified by PCR, duplicated in P301 TR3-11a
Inverted and translocated region "III-t-XI" (12 Kbp), left subtelomeric region TR3-11b
Translocated region "VIII-t-XVI" (10 Kbp), verified by PCR TR8-16
Translocated region "XI-t-VIII" (10 Kbp) TR11-8
Translocated region "XVI-t-IX" (10 Kbp) TR16-9
Translocated region "IX-t-XIV" (70 kbp) TR9-14
Translocated region "IX-t-XIII" (25 Kbp), flanking a 15 Kbp invertion TR9-13
Inverted and translocated region "XV-t-XVI" (<10 Kbp) TR15-16b
Inverted and translocated region "V-t-XIV" (13 Kbp) TR5-14
The more interesting translocations identified are evidenced in bold.
“XV-t-XVI” (TR15-16a) involving genes SSU1 and ADH1 was a new translocation identified in the strain P283 (a vineyard isolate) and commented in our paper in light of the high SO2 resistance of this strain. Resistance of the strains examined (four vineyard strains, EC1118 and S288c) was determined at various SO2 concentrations ranging from 25 to 100 mg/l and reported in supplementary methods S1 file associated to the paper. Correlation between the translocation “XV-t-XVI” and the increased expression of the SSU1 gene was identified by means of RNA-seq analysis performed on the six strains analyzed. Moreover the high SO2 resistance determined by the translocation “XV-t-XVI” in P283 strain, was compared with the similat phenotype determined by the translocation “VIII-t-XVI” previously identified by Perez-Ortin and colleagues in 2002.
A second interesting translocation (XV-t-XVI) was identified in R008 and EC1118 strains, and involves the gene YPL277C encoding a protein whose expression is inversely correlated with copper level. A direct correlation with copper resistance is still under verification.