Genome variation and genetic distance revealed by whole-genome sequencing. (A) The distribution and density of SNPs in the YJSH1 genome within a sliding window of 1,000 bp. (B) A neighbor-joining tree representing the genetic distances between strains calculated from the total number of SNPs present in whole-genome alignments. The wine strains group is shown in plum, the laboratory strains in orange, and the sake strains in gray. (C) Chromosomal rearrangement events on chromosome 1 of the YJS329 genome. The full-length chromosome 1 sequences were aligned using the Artemis Comparative Tool (13). Sequences with >85% similarity are connected by red lines and sequences with <85% similarity or with no similarity are indicated by the white gaps. The green box indicates the largest indel on chromosome 1 of YJS329 and the red boxes indicate the novel ORFs EPH1 (left) and BIO6 (right). (D) From left to right, the sequence at the 5’ end of chromosome 2 in YJS329 was similar to regions of the sequences from chromosome 10 of S288c, gene MEL1, and chromosome 3 of S288c.