Figure 6.—

The BY strain contains alleles of SAL1, CAT5, and MIP1 that likely encode partial or complete loss-of-function proteins. (A) DNA sequence alignment of the region of the SAL1 gene that contains the sal1-1 allele in BY (the inserted nucleotide in the BY lineage is boxed with a dashed line). The brackets above the alignment indicate the register of the open reading frame. The sal1-1 allele was also found in an old S288C isolate (not shown). The most common nucleotide at each position is boxed in black. (B) Sequence alignment of the Sal1 protein. The amino acid position of the frameshift is indicated above the alignment. Protein sequence alignments are shown of Cat5 (C), Mip1 (D), and YOR114W (E) from BY, RM, several closely related Saccharomyces species with available orthologs, and several distantly related Ascomycetes species with available orthologs. Only the regions of the sequence alignments that contain the relevant nonsynonymous polymorphisms are shown. RM contains the evolutionarily conserved ancestral allele while BY contains a derived allele. The position of the allele is numbered above the alignment. The most common amino acid within the Saccharomyces species at each position is boxed in black for all species.