Fig. 5: Sequence variations of SH-D regions in 972SD4 and PomBase-972.

a Schematic illustration of homologous block (I–XI) and box (Ψ and Ω) sequences in the SH-D regions in 972SD4 and PomBase-972 (see Supplementary Table 1 for their positions in PomBase). All SH sequences are aligned with telomeres to the left and centromeres to the right. b Comparison of SH-D regions between subtelomeres. Sequences of SH1L, SH1R, and SH2L in PomBase (indicated by green boxes) were combined with sequences newly determined in this study (yellow boxes, showing #1 clones of each SH sequence), whereas newly sequenced SH2R fragments are shown separately with PomBase-SH2R. Green and yellow numbers indicate positions in each chromosome in PomBase at the ends of overlaps between PomBase and newly determined regions. All SH sequences are aligned with telomeres to the left and centromeres to the right. Insertions (orange arrowheads) or deletions (blue arrowheads) of 10–40 bp are shown in comparison with PomBase-SH2R (thin dotted lines). Insertions and deletions of <10 bp are omitted in this panel. The thick lines connect the corresponding positions in chromosomes that are boundaries of the long regions with sequence alterations. Purple and pink boxes (Ψ) and brown, red, and orange boxes (Ω) indicate homologous sequences at the ends of the long sequence changes, 3.7 and ~7.1 kb, respectively (see Supplementary Fig. 7 for the sequences and identities between them). Numbers in black indicate chromosomal position in PomBase-SH2R. Chromosomal positions of insertions and deletions are indicated by the positions in PomBase-SH2R that are immediately before the changes (closer to the telomeres). Blue arrows in PomBase-SH2R indicate the positions of ORFs for tlh2⁺ and SPBCPT2R1.03. Pale pink arrows in PomBase-SH2R indicate homologous regions (H1–5 and their inverted sequences, H1′–5′) that are utilized for chromosome fusion when telomeres are lost⁵³. Gray arrows at the top indicate ranges of PCR products i–ix analyzed in c. Note that the PCR fragments i–ix in b roughly correspond to blocks I–IX in a. c Lengths of the SH-D regions in 972SD4 strains. DNA fragments i–ix were amplified by PCR using genomic DNAs of the 972 (JK107), SD5 (ST3479), and two independent 972SD4 strains (#1 and #2) as templates. Approximate DNA lengths estimated by the sequences in PomBase and 972SD4 are indicated on the right. The rap1 locus was amplified as a control. PCRs were performed at least twice.