Table 1.
Summary information on the 11 alternative reference strains
| Strain | Description | Source (ATCC ID) | NCBI BioSample Accession | Number of ORFs | Phenotype count per strain (%) | References |
|---|---|---|---|---|---|---|
| RM11-1a | A natural isolate collected from a California vineyard | UCD 2788 (UC Davis culture collection ID) | SAMN03020228 | 5323 | 2 (0.002) | (20) |
| Y55 | Laboratory strain originally isolated from wine grapes | ATCC: 52530 | SAMN03020218 | 5359 | 18 (0.015) | (26) |
| FL100 | Laboratory strain | ATCC: 28383 | SAMN03020232 | 5366 | 57 (0.046) | (18) |
| JK9-3d | Laboratory strain | ATCC: MYA-555 | SAMN03020238 | 5385 | 111 (0.09) | (19) |
| CEN.PK | Laboratory strain popular for use in systems biology studies | ATCC: MYA-1108 | SAMN03020234 | 5379 | 213 (0.174) | (16) |
| X2180-1A | S288C derivative laboratory strain | ATCC: 204504 | SAMN03020236 | 5387 | 276 (0.225) | (25) |
| D273-10B | Lab strain used for mitochondrial studies | ATCC: 24657 | SAMN03020237 | 5383 | 278 (0.227) | (17) |
| SEY6210 | Lab strain used in studies of autophagy and protein sorting | ATCC: 96099 | SAMN03020235 | 5400 | 414 (0.337) | (21) |
| SK1 | Lab strain used for studying sporulation and meiosis | ATCC: 204720 | SAMN03020220 | 5350 | 859 (0.7) | (22) |
| Sigma1278b | Used in pseudohyphal growth studies | ATCC: 42800 | SAMN03020229 | 5358 | 2170 (1.768) | (23) |
| W303 | Laboratory strain used for research into aging | ATCC: 20060 | SAMN03020233 | 5397 | 3158 (2.573) | (24) |
We chose 11 non-S288C strains as alternative reference strains based on the number of phenotype annotations curated in SGD. Phenotype studies are most frequently reported using the S288C reference strain, i.e. 84.78% of phenotypic counts in SGD are based on work in S288C. Other than S288C, the 11 alternative reference strains have been most frequently used for yeast phenotype studies. The alternative strains are used for specific areas of biology (e.g. CEN.PK for systems biology, D273-10B for mitochondrial studies, SEY6210 for autophagy and protein sorting, SK1 for sporulation and meiosis, Sigma1278b for pseudohyphal growth, and W303 for aging). The source of the sequenced strain genome is summarized with ATCC ID. The assembly and raw sequence data of each strain has been deposited in NCBI and can be found with NCBI BioSample accession numbers.