Commonly used strains

This page describes some of the most commonly used yeast lab strains. Much of the information is taken from F. Sherman (2002) Getting started with yeast, Methods Enzymol. 350, 3-41. Other useful papers for strain background information include:

• Mortimer and Johnston (1986) Genetics 113:35-43 - thoroughly describes the genealogy of strain S288C
• van Dijken et al. (2000) Enzyme Microb Technol 26:706-714 - compares various characteristics of commonly used lab strains
• Winzeler et al. (2003) Genetics 163:79-89 - uses SFP (single-feature polymorphisms) analysis to study genetic identity between common lab strains

S288C

Genotype: MATα SUC2 gal2 mal2 mel flo1 flo8-1 hap1 ho bio1 bio6

Notes: Strain used in the systematic sequencing project, the sequence stored in SGD. S288C does not form pseudohyphae. In addition, since it has a mutated copy of HAP1, it is not a good strain for mitochondrial studies. It has an allelic variant of MIP1 which increases petite frequency. S288C strains are gal2- and they do not use galactose anaerobically.

The S288C genome was recently resequenced at the Sanger Institute.

References: Mortimer and Johnston (1986) Genetics 113:35-43.

Sources: ATCC:204508

A364A

Genotype: MATa ade1 ade2 ura1 his7 lys2 tyr1 gal1 SUC mal cup BIO

Notes: Used in the systematic sequencing project, the sequence stored in SGD.

References: Hartwell (1967) J. Bacteriol. 93:1662-1670.

Sources: ATCC:208526

AB972

Genotype: MATα X2180-1B trp1₀ [rho ⁰]

Notes: Isogenic to S288C; used in the systematic sequencing project, the sequence stored in SGD. AB972 is an ethidium bromide-induced rho- derivative of the strain X2180-1B-trp1.

References: Olson MV et al. (1986) Proc. Natl. Acad. Sci. USA 83:7826-7830.

Sources: ATCC:204511

BY4743

Genotype: MATa/α his3Δ1/his3Δ1 leu2Δ0/leu2Δ0 LYS2/lys2Δ0 met15Δ0/MET15 ura3Δ0/ura3Δ0

Notes: Strain used in the systematic deletion project, generated from a cross between BY4741 and BY4742, which are derived from S288C. As in S288c, this strain as well as haploid derivatives BY4741, and BY4742 have allelic variants of MIP1, SAL1 and CAT5 and these polymorphisms, described in the respective locus history notes for these genes (MIP1, SAL1 and CAT5) all contribute to the high observed petite frequency. Details regarding the contributions of these variants to petite formation are referenced in Dimitrov et al. (2009) Genetics 183(1):365-83. See the Brachmann et al., 1998 reference for details of strain construction.

References: Brachmann et al. (1998) Yeast 14:115-32.

Sources: ATCC:201390

Y7092

Y7092 is isogenic with BY4741, except for the markers required for the synthetic genetic array procedure

Reference: Tong AH and Boone C (2006) Synthetic genetic array analysis in Saccharomyces cerevisiae. Methods Mol Biol 313:171-92

CKY8

Genotype: MATα ura3-52 leu2-3,112

Sources: C. Kaiser (Massachusetts Institute of Technology, Boston)

DBY4975

Genotype: MATα his3Δ200 leu2-3,112 lys2-801 ura3-52 ade2

Derived: from S288C

aka IGY6

Reference: Whitacre J, et al. (2001) Generation of an isogenic collection of yeast actin mutants and identification of three interrelated phenotypes. Genetics 157(2):533-43

DBY947

Genotype: MATα SUC2 ade2-101 ura3-52

Derived: from repeated backcrosses of the ura3-52 allele into the S288C background.

Reference: Neff et al. (1983) Cell 33(1):211-9

DFS160

Genotype: MATα ade2-101 leu2 ura3-52 arg8∷URA3 kar1-1 [rho0]

Notes: Derived from DBY947. Used in cytoduction experiments; kar1-1 to prevent nuclear fusion and lacks mitochondria (rho0)

References: Costanzo & Fox (1993) MCB 13(8):4806-13 | Steele et al. (1996) PNAS 93:5253-7

DC5

Genotype: MATa leu2-3,112 his3-11,15 can1-11

Notes: Isogenic to S288C; used in the systematic sequencing project, the sequence stored in SGD.

References: Broach et al. (1979) Gene 8:121-133

EY441

Genotype: kss1 ura3-52 leu2-3,112 his3Δ200 ade2-1 lys2Δ201

Reference: Elion EA, et al. (1990) FUS3 encodes a cdc2+/CDC28-related kinase required for the transition from mitosis into conjugation. Cell 60(4):649-64 PMID:2406028

FY4

Genotype: MATa, srd1Δ0

Notes: Derived from S288C.

References: Winston et al. (1995) Yeast 11:53-55.

Brachmann et al. (1998) Yeast 14:115-32.

DBY12020

Genotype: MATa(P_GAL10+gal1)Δ::loxP, leu2Δ0::P_ACT1-GEV-NatMX, gal4Δ::LEU2, HAP1⁺

Notes: Derived from FY4.

Reference: McIsaac et al. (2011) Mol Biol Cell 22(22):4447-59.

DBY12021

Genotype: MATα(P_GAL10+gal1)Δ::loxP, leu2Δ0::P_ACT1-GEV-NatMX, gal4Δ::LEU2, HAP1⁺

Notes: Derived from FY4.

Reference: McIsaac et al. (2011) Mol Biol Cell 22(22):4447-59.

FY1679

Genotype: MATa/α ura3-52/ura3-52 trp1Δ63/TRP1 leu2Δ1/LEU2 his3Δ200/HIS3 GAL2/GAL

Notes: Isogenic to S288C; used in the systematic sequencing project, the sequence stored in SGD.

References: Winston et al. (1995) Yeast 11:53-55.

Sources: EUROSCARF:10000D

NY13

isogenic with S288C PMID:24476960

TB50

isogenic with S288C PMID:24476960

X2180-1A

Genotype: MATa SUC2 mal mel gal2 CUP1

Notes:S288c spontaneously diploidized to give rise to X2180. The haploid segregants X2180-1a and X2180-1b were obtained from sporulated X2180

References: Mortimer and Johnston

Sources: ATCC:204504

CEN.PK (aka CEN.PK2)

Genotype: MATa/α ura3-52/ura3-52 trp1-289/trp1-289 leu2-3,112/leu2-3,112 his3 Δ1/his3 Δ1 MAL2-8C/MAL2-8C SUC2/SUC2

Notes: CEN.PK possesses a mutation in CYR1 (A5627T corresponding to a K1876M substitution near the end of the catalytic domain in adenylate cyclase which eliminates glucose- and acidification-induced cAMP signalling and delays glucose-induced loss of stress resistance (Vanhalewyn et al., 1999; Dumortier et al., 2000).

References: van Dijken et al. (2000) Enzyme Microb Technol 26:706-714

Sources: EUROSCARF:30000D

D273-10B

Genotype: MATα mal GAL

Notes: Normal cytochrome content and respiration; low frequency of rho-. This strain and its auxotrophic derivatives were used in numerious laboratories for mitochondrial and related studies and for mutant screens. Good respirer that's relatively resistant to glucose repression.

References: Sherman, F. (1963) Genetics 48:375-385.

Sources: ATCC:24657

FL100

Genotype: MATa

References: Lacroute, F. (1968) J. Bacteriol. 95:824-832.

Sources: ATCC:28383

JK9-3d

There are a, alpha and a/alpha diploids of JK9-3d with the following genotypes:

Genotypes: JK9-3da MATa leu2-3,112 ura3-52 rme1 trp1 his4

JK9-3dα has the same genotype as JK9-3da with the exception of the MAT locus

JK9-3da/α is homozygous for all markers except mating type

Notes: JK9-3d was constructed by Jeanette Kunz while in Mike Hall's lab. She made the original strain while Joe Heitman isolated isogenic strains of opposite mating type and derived the a/alpha isogenic diploid by mating type switching. It has in its background S288c, a strain from the Oshima lab, and a strain from the Herskowitz lab. It was chosen because of its robust growth and sporulation, as well as good growth on galactose (GAL+) (so that genes under control of the galactose promoter could be induced). It may also have a SUP mutation that allows translation through premature STOP codons and therefore produces functional alleles with many point mutations.

Recent work shows that JK9-3d carries an rme1 mutation that may be responsible for the rapid G1 arrest of this strain upon exposure to rapamycin (Moreno-Torres M, et al. (2015) Nat Commun 6:8256)

References: Heitman et al. (1991a) Science 253(5022):905-9 and Heitman et al. (1991b) Proc Natl Acad Sci U S A 88(5):1948-52

RM11-1a

Genotype: MATa leu2Δ0 ura3-Δ0 HO::kanMX

Notes: RM11-1a is a haploid derivative of RM11, which is a diploid derivative of Bb32(3), which is an ascus derived from Bb32, which is a natural isolate collected by Robert Mortimer from a California vineyard (Ravenswood Zinfandel) in 1993, as in Mortimer et al. (1994). It has high spore viability (80–90%) and has been extensively characterized phenotypically under a wide range of conditions. It has a significantly longer life span than typical lab yeast strains and accumulates age-associated abnormalities at a lower rate. It displays approximately 0.5–1% sequence divergence relative to S288c. More information is available at the Broad Institute website.

References: Brem et al. (2002) Science 296(5568):752-5

SEY6210/SEY6211

Genotype: MATa/MATα leu2-3,112/leu2-3,112 ura3-52/ura3-52 his3-Δ200/his3-Δ200 trp1-Δ901/trp1-Δ901 ade2/ADE2 suc2-Δ9/suc2-Δ9 GAL/GAL LYS2/lys2-801

Notes: SEY6210/SEY6211, also known as SEY6210.5, was constructed by Scott Emr and has been used in studies of autophagy, protein sorting etc. It is the product of crossing with strains from 5 different labs (Gerry Fink, Ron Davis, David Botstein, Fred Sherman, Randy Schekman). It has several selectable markers, good growth properties and good sporulation.

References: Robinson et al. (1988) Mol Cell Biol 8(11):4936-48

Sources: ATCC:201392

SEY6210

Genotype: MATα leu2-3,112 ura3-52 his3-Δ200 trp1-Δ901 suc2-Δ9 lys2-801; GAL

Notes: SEY6210 is a MATalpha haploid constructed by Scott Emr and has been used in studies of autophagy, protein sorting etc. It is the product of crossing with strains from 5 different labs (Gerry Fink, Ron Davis, David Botstein, Fred Sherman, Randy Schekman). It has several selectable markers and good growth properties.

References: Robinson et al. (1988) Mol Cell Biol 8(11):4936-48

Sources: ATCC:96099

SEY6211

Genotype: MATa leu2-3,112 ura3-52 his3-Δ200 trp1-Δ901 ade2-101 suc2-Δ9; GAL

Notes: SEY6211 is a MATa haploid constructed by Scott Emr and has been used in studies of autophagy, protein sorting etc. It is the product of crossing with strains from 5 different labs (Gerry Fink, Ron Davis, David Botstein, Fred Sherman, Randy Schekman). It has several selectable markers and good growth properties.

References: Robinson et al. (1988) Mol Cell Biol 8(11):4936-48

Sources: ATCC:96100

Sigma1278b

Genotype: MATα

Sigma1278b was first isolated in the lab of Marcelle Grenson in the early 1960s, as described in André B (2018) Tribute to Marcelle Grenson (1925-1996), A Pioneer in the Study of Amino Acid Transport in Yeast. Int J Mol Sci 19(4), PMID:29659503, which contains the complete, exact pedigree of Σ1278b from the Grenson lab archives. A short excerpt:

"A new, prototrophic reference strain was thus isolated: strain Σ1278b. It was obtained by first crossing the YFa-derived yeast D77 (auxotrophic for uracil and glutamate) with the yeast 1422-11D that was received from the American geneticist Donald C. Hawthorne. The derived haploid strain Σ15d (Σ stands for “segregant”) was then crossed with strain DP1-1B received from Piotr Slonimski, and one of the spores issued from this cross gave rise to Σ1278b."

In September 1970, Grenson sent to Gerry Fink a aap/apf1/shr3 mutant isolated from Σ1278b. This strain, which likely diploidized during successive subculturing, was classified as “Fink lab Foreigner strains, F35”. As detailed in the note provided by the Fink lab, collected Nov. 1998 by Cora Styles, analysis twenty years later of this mutant by C. Gimeno and P. Ljungdahl allowed them to discover pseudohyphal growth : Gimeno, C. J., Ljungdahl, P. O., Styles, C. A., & Fink, G. R. (1992). Unipolar cell divisions in the yeast S. cerevisiae lead to filamentous growth: regulation by starvation and RAS. Cell, 68(6), 1077–1090, PMID:1547504.

Thanks to Bruno André for contacting SGD directly to share and disseminate this information.

Notes: Used in pseudohyphal growth studies. Detailed notes about the sigma strains have been kindly provided by Cora Styles.

Granek and Magwene, PLoS Genet. 2010 Jan 22;6(1):e1000823, established that certain lineages of the Sigma1278B background contain a nonsense mutation in RIM15, a G-to-T transversion at position 1216 that converts a Gly codon to an opal stop codon. This rim15 mutation interacts epistatically with mutations in certain other genes to affect colony morphology. The Sigma1278b genome is closely related to S288c, and shares some other genomic regions with W303 [1].

Annotation of the Sigma1278b genome and information about the systematic deletion collection can be found in Dowell et al. (2010).

SK1

Genotype: MATa/α HO gal2 cup^S can1^R BIO

Notes: Commonly used for studying sporulation or meiosis. Canavanine-resistant derivative.

The SK1 genome was sequenced at the Sanger Institute.

References: Kane SM and Roth J. (1974) Bacteriol. 118: 8-14

Sources: ATCC:204722

g833-1B

Genotype: MATa leu2 can1 HOM3 his1-1 trp2 ADE2 ho gal2

Notes: Haploid derivative of SK1, constructed by JC Game in the 1980s.

Sources: ATCC:204720

W303

Genotype: MATa/MATα {leu2-3,112 trp1-1 can1-100 ura3-1 ade2-1 his3-11,15} [phi⁺]

allele	locus	mutation (1)
ade2-1	YOR128C	nonsense, glu64STOP
trp1-1	YDR007W	nonsense, glu83STOP
can1-100	YEL063C	frameshift, lys47
leu2-3,112	YCL018W	frameshift, gly83
his3-11,15	YOR202W	2x frameshifts, ala70 and glu106

Notes: The W303 genome is to 85.4% derived from S288c, part of the other regions are similar to non-S288c regions of Sigma1278b. In total, some 800 CDS differ between W303 and S288c, but in most cases only one or two residues differ [2]. These include a bud4 mutation that causes haploids to bud with a mixture of axial and bipolar budding patterns. In addition, the original W303 strain contains the rad5-535 allele. As S288c, W303 has an allelic variant of MIP1 which increases petite frequency. Unlike S288C, W303 lacks a functional copy of the RNA-binding protein and translational repressor, Ssd1 [3], [4],[5].

The W303 genome was sequenced at the Sanger Institute and by Ralser M. et al. (2012) Open Biol 2: 120093. 1 (DDBJ/EMBL/GenBank ALAV00000000).

References: W303 constructed by Rodney Rothstein (see detailed notes from RR and Stephan Bartsch).
bud4 info: Original mutant description Voth et al. (2005) Eukaryotic Cell, 4:1018-28. Mutation: deletion of one of four Gs at positions 2456-2459 of BUD4 ORF. Seq data from: Ralser et al above
rad5-535 info: see detailed notes

Sources: ATCC:200060

W303-1A

Genotype: MATa {leu2-3,112 trp1-1 can1-100 ura3-1 ade2-1 his3-11,15}

Notes: W303-1A possesses a ybp1-1 mutation (I7L, F328V, K343E, N571D) which abolishes Ybp1p function, increasing sensitivity to oxidative stress.

References: W303 constructed by Rodney Rothstein (see detailed notes from RR and Stephan Bartsch).
ybp1-1 info: Veal et al. (2003) J. Biol. Chem. 278:30896-904.

Sources: ATCC:208352

W303-1B

Genotype: MATα {leu2-3,112 trp1-1 can1-100 ura3-1 ade2-1 his3-11,15}

References: W303 constructed by Rodney Rothstein (see detailed notes from RR and Stephan Bartsch).

Sources: ATCC:201238

W303-K6001

Genotype: MATa; {ade2-1, trp1-1, can1-100, leu2-3,112, his3-11,15, GAL, psi+, ho::HO::CDC6 (at HO), cdc6::hisG, ura3::URA3 GAL-ubiR-CDC6 (at URA3)}

References: K6001 was created in Kim Nasmyth's lab Piatti at al (PMID: 7641697) and Bobola et al (PMID: 8625408). K6001 has become a popular model in yeast aging research, as it allows a replicative aging assay based on microcolonies (PMID: 15489200). Its genome has been sequenced by Timmermann et al (PMID: 20729566), Ralser et al [6].

W1536 8B

Genotype: MATα, ade2Δ, ade3Δ, can1-100, his3-11,15, leu2-3,112, trp1-1, ura3-1

References: Shvetsova A, et al. (2021) PMID:34713605

W1588-4C

RAD5 derivative of W303

Genotype: MATa ade2-1 can1-100 ura3-1 his3-11,15 leu2-3,112 trp1-1 RAD5

Reference: Dhingra N, et al. (2019) Replication protein A (RPA) sumoylation positively influences the DNA damage checkpoint response in yeast. J Biol Chem 294(8):2690-2699 PMID:30591583

DY1457

Genotype: MATa; {ade6 can1-100(oc) his3-11,15 leu2-3,112 trp1-1 ura3-52}

References: Askwith C, et al. (1994) Cell 76(2):403-10 PMID: 8293473

EY699

Genotype: MATa ura3-1 his3-11,15 leu2-3,112 trp1-1 ade2 can1-100 Gal+

References:

1. Rodney Rothstein
2. Elion EA, et al. (1991) Functional redundancy in the yeast cell cycle: FUS3 and KSS1 have both overlapping and unique functions. Cold Spring Harb Symp Quant Biol 56:41-9

XJ24-24a

Genotype: MATa ho HMa HMα ade6 arg4-17 trp1-1 tyr7-1 MAL2

Notes: Likely quite different from S288C. A strain derived from XJ24-24a called XG1#24 had a recombination between HML and MAT that generated a large ring chromosome (Strathern et al. 1979 Cell), and Carol Newlon generated an ordered map of plasmid sub clones from this ring chromosome (Newlon et al. 1991 Genetics) that was then used for the initial sequencing of Chromosome III (Oliver et al. 1992), which has since been updated numerous times. The provenance of XJ24-24a is unclear. Newlon was able to trace it back about 5 generations: some of the progenitor strains were from the Cold Spring Harbor Yeast course, and some of those strains had some markers similar to S288C (none of which are still in XJ24-24a).
Thanks to Joachim Li for sharing this history of XJ24-24a with SGD.

References:

• Strathern et al. (1979) Cell 18:309-319
• Newlon et al. (1979) Genetics 129:343-57
• Oliver et al. (1992) Nature 357:38-46

Y55

Genotype: MATa /MATalpha HO/HO

Notes: Y55 is a prototrophic, homothallic diploid strain that was originally isolated by Dennis Winge. Many auxotrophic mutant derivatives have been created by John McCusker by using ethidium bromide treatment to eliminate non-auxotrophs. Y55 background strains have been used to study the timing of meiotic recombination (Borts et al. 1984); to isolate almost all the subunits of the proteasome (McCusker and Haber 1988a, 1988b); to get mutations in PMA1 and related genes (McCusker 1986); and to do meiotic mapping and interference experiments (Malkova et al. 2004).

YNN216

Genotype: MATa/α ura3-52/ura3-52 lys2-801^amber/lys2-801^amber ade2-101^ochre/ade2-101^ochre

Notes: Congenic to S288C (see Sikorski and Hieter). Used to derive YSS and CY strains (see Sobel and Wolin).

References: Sikorski RS and Hieter P (1989) Genetics 122:19-27.
Sobel and Wolin (1999) Mol. Biol. Cell 10:3849-3862.

YPH499

Genotype: MATa ura3-52 lys2-801_amber ade2-101_ochre trp1-Δ63 his3-Δ200 leu2-Δ1

Notes: Contains nonrevertible (deletion) auxotrophic mutations that can be used for selection of vectors. Note that trp1-Δ63, unlike trp1-Δ1, does not delete adjacent GAL3 UAS sequence and retains homology to TRP1 selectable marker. gal2-, does not use galactose anaerobically. Derived from the diploid strain YNN216 (Johnston and Davis 1984; original source: M. Carlson, Columbia University), which is congenic with S288C.

References: Sikorski RS and Hieter P (1989) Genetics 122:19-27.
Sobel and Wolin (1999) Mol. Biol. Cell 10:3849-3862.
Johnston M and Davis RW (1984) Mol Cell Biol 4(8):1440-8.

Sources: ATCC:204679

YPH500

Genotype: MATα ura3-52 lys2-801_amber ade2-101_ochre trp1-Δ63 his3-Δ200 leu2-Δ1

Notes:MATα strain isogenic to YPH499 except at mating type locus. Derived from the diploid strain YNN216 (Johnston and Davis 1984; original source: M. Carlson, Columbia University), which is congenic with S288C.

References: Sikorski RS and Hieter P (1989) Genetics 122:19-27.
Sobel and Wolin (1999) Mol. Biol. Cell 10:3849-3862.
Johnston M and Davis RW (1984) Mol Cell Biol 4(8):1440-8.

Sources: ATCC:76626

YPH501

Genotype: MATa/MATα ura3-52/ura3-52 lys2-801_amber/lys2-801_amber ade2-101_ochre/ade2-101_ochre trp1-Δ63/trp1-Δ63 his3-Δ200/his3-Δ200 leu2-Δ1/leu2-Δ1

Notes: a/α diploid isogenic to YPH499 and YPH500. Derived from the diploid strain YNN216 (Johnston and Davis 1984; original source: M. Carlson, Columbia University), which is congenic with S288C.

References: Sikorski RS and Hieter P (1989) Genetics 122:19-27.
Sobel and Wolin (1999) Mol. Biol. Cell 10:3849-3862.
Johnston M and Davis RW (1984) Mol Cell Biol 4(8):1440-8.

Sources: ATCC:204681