Table 3.
Mutations in methanol-adapted P. pastoris clones
| Strain | chr | Position | Type | Ref | Alt | Gene/locus | Effect |
|---|---|---|---|---|---|---|---|
| Y250 1c | chr. 1 | 1,477,448 | SNP | G | A | Upstream of PAS_chr1-4_0035 (SPC110) | |
| chr. 2 | 1,572,979 | SNP | C | G | PAS_chr2-1_0445 (Zn_cluster) | G142 to R142 | |
| chr. 4 | 237,622 | SNP | G | A | PAS_chr4_0821 (AOX1) | W190 to stop | |
| chr. 4 | 1,574,048 | SNP | G | A | PAS_chr4_0108 (YCT1) weak homology | A64 to T64 | |
| Y250 2c | chr. 2 | 1,573,676 | SNP | G | T | PAS_chr2-1_0445 (Zn_cluster) | Upstream of gene |
| chr. 3 | 627,999 | SNP | C | A | PAS_chr3_0836 (ECM22) | W95 to C95 | |
| Y250 3a | chr. 3 | 313,093 | SNP | G | T | PAS_chr3_1001 (TUP1) | C285 to F285 |
| chr. 3 | 628,000 | SNP | C | A | PAS_chr3_0836 (ECM22) | W95 to L95 | |
| Y250 3c | chr. 2 | 2,100,561 | SNP | C | T | PAS_chr2-1_0162 (SLN1) | R336 to K336 |
| chr. 4 | 238,206 | indel | AAGACAAGCC | A | PAS_chr4_0821 (AOX1) | 3 amino acid deletion after E385 | |
| M250 1a | chr. 2 | 1,060,279 | SNP | G | A | PAS_chr2-1_0701 (PKH3) | G354 to D354 |
| chr. 3 | 384,863 | SNP | C | T | PAS_chr3_0956 (RRP45) | G206 to D206 | |
| chr. 3 | 575,412 | SNP | C | T | Downstream of PAS_chr3_1229 (SEC5) and downstream of PAS_chr3_0322 (tRNA-Thr7) | – | |
| M250 2c | chr. 1 | 1,737,822 | SNP | A | C | PAS_chr1-4_0181 (NMA1) | Q118 to H118 |
| chr. 4 | 238,443 | SNP | G | A | PAS_chr4_0821 (AOX1) | R464 to K464 | |
| M250 3b | chr. 3 | 1,260,818 | SNP | G | A | PAS_chr3_0512 (PAH1) | C304 to Y304 |
| chr. 4 | 238,309 | SNP | C | G | PAS_chr4_0821 (AOX1) | F419 to L419 |
Mutations were identified by WGS (Illumina mi-Seq). The type of mutation (Single nucleotide polymorphism—SNP or insertion/deletion—indel) as well as the DNA sequence of the ancestral strain (ref) and the sequence of the evolved clone (alt) is shown. Chromosomal position (chr) and nucleotide position on contigs is shown with respect to the P. pastoris CBS7435 reference sequence