Spreadsheet: 5f050ee7-aaa5-453d-9333-6992e7e62282
Sheet: TableS4-Primers,Strains

Primers used
primer name | primer sequence
KV69 | GCACGTCAAGACTGTCAAGG
KV1920 | CCTACCCGGTTGCCTCCAAAGCCCTTCTTT
KV1923 | AACTAGGTTACATAACTGCCTATTGGCAAG
AN_GS1 | TCTAGAAAGCACAGATTAATACCGATTCTAATACAGATTTTAATGACCTCAATAGTTAATatatagatctgtttagcttgcctcg
AN_GS2 | CGCGTCTTTTCTTTTCGCGTTCTGTTATAGACGATTTTTATAATATTTTATCAAATATCAtggcttatcgaaattaatacgactc
AN_GS3 | ATCTTTCAAAGTTCTCTACTTACATTGC
AN_GS4 | ATTAACTATTGAGGTCATTAAAATCTGTATTAGAATCGGTATTAATCTGTGCTTTCTAGAtggcttatcgaaattaatacgactc
AN_GS5 | TCAAAAGCTTATATAGGCAAGGC
AN_GS6 | gagagtatcagtcagtcctcaagcataaaacagcgagaattaaatgcagctgataaatgtatcggtgacggtgctggttt
[NAME] | tttgggagcagtcaaagggattccttatttcttccaaaaaaaaaaaaacaacccttttacgcataggccactagtggatctg
AN_GS8 | atgtgaaaaatcatgtgttatttcgttaaagtacgcgctaaaaaaaagccggcactaattgcataggccactagtggatctg
AN_GS9 | [NAME]
AN_GS10 | CTCCTTTCGCTGCCATAGTAA
AN_GS11 | GGCTTGAGGGACATACAGAGA
AN_GS12 | TTGGTGTTTCTTTCTGATGCTACATAGAAGAACATCAAACAACTAAAAAAATAGTATAATCGTACGCTGCAGGTCGAC
AN_GS13 | TTTATCCTCATTTTTTGAGGCAGCCTTCTTCTTGCTTACCAATGAAATGATATTTTTCATCATCGATGAATTCTCTGTCG
AN_GS14 | TTAAGCAGTTTTTTTGATAATCTCAAATGTACATCAGTCAAGCGTAACTAAATTACATAACGTACGCTGCAGGTCGAC
AN_GS15 | ATAGATTGTGGCCTCTTTCCACCACTTTGGTTCTGTTTCTGGATGATCAGAAATAGTCATCATCGATGAATTCTCTGTCG
AN112 | tacaactgtgatattgtataaactttgttagaaattcacgggatttattcgtgacgataacagctgaagcttcgtacgc
[NAME] | aaaagaaactaaaatcatgtagatttcataaatcgtcatattctttgtctatataaatatcgcataggccactagtggatctg
AN114 | AAACCTCACTAGACGACTACCC
AN115 | CCGTCCTCTACTCATGTGATTCG
AN116 | TAGAGAGGGTTAAAATTGGCGTGC
AN117 | cgtcctctactcatgtgat
AN118 | ctataaaaaagagtaatcctaccc
[NAME] | accttttctttcccagcttc
AN124 | CCACTTAACGACATTAATATTAATTACAAAAGTGTTTGATACACGTACTATTATAGATTTcagctgaagcttcgtacg
AN125 | GCAGTAGGCTTAAAATATATTAAAATTATTAAAGGTATTACTTAATCTTAAAGGTCGTCGcgcataggccactagtggatctg
AN126 | ACCGCATGGTTTTAAAATACATGACTG
[NAME] | TGAAGCATGAATATATGAATATACGTCCTCTTG
AN128 | GGGCAATTTTAGAGCAGTAGGC
AN129 | AATATACGTCCTCTTGTAAAATAGC
AN130 | ATCTTGCAACAAACAATCGG
[NAME] | ATAATTTGAGTTCCAATTCAGG
AN177 | tgacataaactttagtagccaatttatagcgtggggtgcctacttcgtcacatttgatatCAGCTGAAGCTTCGTACGC
AN178 | caagctaaacttgtctcccatcagtacacaatcatctcatccaatctggctcttagcactGCATAGGCCACTAGTGGATCTG
Strains used in Figure 1 (SGRP other than [NAME])
strain name | reference | description
DBVPG6765 | [NAME] et. [NAME]. 2009 | SGRP collection
SK1 | [NAME] et. [NAME]. 2009 | SGRP collection
Y55 | [NAME] et. [NAME]. 2009 | SGRP collection
YPS128 | [NAME] et. [NAME]. 2009 | SGRP collection
[NAME] | [NAME] et. [NAME]. 2009 | SGRP collection
DBVPG1373 | [NAME] et. [NAME]. 2009 | SGRP collection
DBVPG1853 | [NAME] et. [NAME]. 2009 | SGRP collection
[NAME] | [NAME] et. [NAME]. 2009 | SGRP collection
YPS606 | [NAME] et. [NAME]. 2009 | SGRP collection
L-1374 | [NAME] et. [NAME]. 2009 | SGRP collection
[NAME] | [NAME] et. [NAME]. 2009 | SGRP collection
Y12 | [NAME] et. [NAME]. 2009 | SGRP collection
DBVPG1106 | [NAME] et. [NAME]. 2009 | SGRP collection
UWOPS83-787.3 | [NAME] et. [NAME]. 2009 | SGRP collection
YS9 | [NAME] et. [NAME]. 2009 | SGRP collection
YS4 | [NAME] et. [NAME]. 2009 | SGRP collection
[NAME] strains
All MAL gene - yECitrine alleles come from pKT174 (pFA6 type KANMX marker)
All mCherry alleles come from pSR101  (CaURA3 marker)
pUG6 used for KANMX marker in complementation tests
strain name | progenitor | rationale and description of strain construction | genotype (compared to progenitor) | markers | Ref original
BY4742 | [NAME] | "[NAME] designer deletion series" MAT alpha (only used as progenitor for KV1156) | [NAME];  [NAME] |  | [NAME] (1998) Yeast 14:115-32
KV1156 | BY4742 | maltose fermenting strain (only used as progenitor for AN62) | MAL+ (MAL13::HygR-MAL63_c9) | HygR | Brown, [NAME], [NAME]
AN62 | KV1156 | Low petite frequency maltose fermenting (only used for progenitor of AN63) | MAL+ [NAME] | HygR | this study
AN63 | AN62 | MATa low petite frequency maltose fermenting strain; strain used as progenitor for all [NAME] strains reported in this study. | MAL+ SAL1+ MATa | HygR | this study
AN73 | AN63 | MalS-yECitrine; strain used to track decay of signal after transfer to glucsoe | MAL12-yECitrine MAL+ SAL1+ MATa | [NAME] | this study
AN74 | AN63 | MalS-mCherry; strain used as reference strain in competitions against AN296-descendant clones and as control for comparisons to the behavior of AN355 | MAL12-mCherry MAL+ SAL1+ MATa | HygR URA3+ | this study
AN77 | AN63 | MalT-yECitrine (only used as progenitor for AN148) | MAL11-yECitrine MAL+ SAL1+ MATa | [NAME] | this study
AN104 | AN63 | MalT Overexpression | GPD-MAL11 MAL+ SAL1+ MATa | [NAME] | this study
AN105 | AN63 | MalS overexpression | GPD-MAL12 MAL+ SAL1+ MATa | [NAME] | this study
[NAME] | AN63 | MalS / MalT dual overexpression | GPD MAL12 GPD-MAL11 MAL+ SAL1+ MATa | [NAME] | this study
AN296 | AN63 | Ancestral strain: [NAME] constitutively labeled with yECitrine. | YOR2_TDH3-yECitrine-His MAL+ SAL1+ MATa | HygR His+ | this study
isolate 1 | AN296 | short-lagged descendant 1 AN296 isolated after 6 rounds of selection. This strain and its MalS-mCherry tagged descendant were strains we used to inform more high-throughput experiments performed with the MAL gene labeled strain AN148. Its genome was also sequenced, and it was used in Malthusian fitness competitions reported in figure 3. | Short lagged unknown allele(s); YOR2_TDH3-yECitrine MAL+ SAL1+ MATa | HygR His+ | this study
isolate 2 | AN296 | short-lagged descendant 2 AN296 isolated after 6 rounds of selection. Used for whole-genome sequencing and HXK2 complementations | Short lagged unknown allele(s); YOR2_TDH3-yECitrine MAL+ SAL1+ MATa | HygR His+ | this study
isolate 3 | AN296 | short-lagged descendant 3 AN296 isolated after 6 rounds of selection.  Used for Malthusian fitness competitions and lag measurements in figure 3. | Short lagged unknown allele(s); YOR2_TDH3-yECitrine MAL+ SAL1+ MATa | HygR His+ | this study
Isolate 4 | AN296 | short-lagged descendant 4 AN296 isolated after 6 rounds of selection.  Used for Malthusian fitness competitions and lag measurements in figure 3. | Short lagged unknown allele(s); YOR2_TDH3-yECitrine MAL+ SAL1+ MATa | HygR His+ | this study
AN148 | AN77 | MAL-gene tagged ancestral strain (MAL11-yECitrine and MAL12-mCherry) | MAL12-mCherry MAL11-yECitrine MAL+ SAL1+ MATa | [NAME] | this study
Isolate 5 | AN148 | short-lagged descendant (flocculent) of AN148 isolated after 5 rounds of selection when the flocculent phenotype first arose. | Short lagged and flocculent unknown allele(s); Short lagged; MAL12-mCherry MAL11-yECitrine MAL+ SAL1+ MATa | [NAME] | this study
AN355 | isolate 1 | MalS-mCherry tagged; tagged this allele to inform experiments leading into the AN148 evolution experiment, and this strain is used as a representative strain for experiments reported in figure 4; short-lagged descendant 1 AN296 isolated after 6 rounds of selection | MAL12-mCherry; Short lagged; YOR2_TDH3-yECitrine MAL+ SAL1+ MATa | [NAME] | this study
pop1#1; isolate 6 | AN148 | MAL gene-labeled descendant, isolated after final (8th) round of selection for short lags in maltose | AN148 descendant | [NAME] | this study
pop1#2 | AN148 | MAL gene-labeled descendant, isolated after final (8th) round of selection for short lags in maltose | AN148 descendant | [NAME] | this study
pop1#3 | AN148 | MAL gene-labeled descendant, isolated after final (8th) round of selection for short lags in maltose | AN148 descendant | [NAME] | this study
pop2#1 | AN148 | MAL gene-labeled descendant, isolated after final (8th) round of selection for short lags in maltose | AN148 descendant | [NAME] | this study
pop2#2 | AN148 | MAL gene-labeled descendant, isolated after final (8th) round of selection for short lags in maltose | AN148 descendant | [NAME] | this study
pop2#3 | AN148 | MAL gene-labeled descendant, isolated after final (8th) round of selection for short lags in maltose | AN148 descendant | [NAME] | this study
pop3#1 | AN148 | MAL gene-labeled descendant, isolated after final (8th) round of selection for short lags in maltose | AN148 descendant | [NAME] | this study
pop3#2 | AN148 | MAL gene-labeled descendant, isolated after final (8th) round of selection for short lags in maltose | AN148 descendant | [NAME] | this study
pop3#3 | AN148 | MAL gene-labeled descendant, isolated after final (8th) round of selection for short lags in maltose | AN148 descendant | [NAME] | this study
pop4#1 | AN148 | MAL gene-labeled descendant, isolated after final (8th) round of selection for short lags in maltose | AN148 descendant | [NAME] | this study
pop4#2 | AN148 | MAL gene-labeled descendant, isolated after final (8th) round of selection for short lags in maltose | AN148 descendant | [NAME] | this study
pop4#3 | AN148 | MAL gene-labeled descendant, isolated after final (8th) round of selection for short lags in maltose | AN148 descendant | [NAME] | this study
pop5#1 | AN148 | MAL gene-labeled descendant, isolated after final (8th) round of selection for short lags in maltose | AN148 descendant | [NAME] | this study
pop5#2 | AN148 | MAL gene-labeled descendant, isolated after final (8th) round of selection for short lags in maltose | AN148 descendant | [NAME] | this study
pop5#3 | AN148 | MAL gene-labeled descendant, isolated after final (8th) round of selection for short lags in maltose | AN148 descendant | [NAME] | this study
pop6#1 | AN148 | flocculent; MAL gene-labeled descendant, isolated after final (8th) round of selection for short lags in maltose | AN148 descendant | [NAME] | this study
pop6#2 | AN148 | MAL gene-labeled descendant, isolated after final (8th) round of selection for short lags in maltose | AN148 descendant | [NAME] | this study
pop6#3 | AN148 | flocculent; MAL gene-labeled descendant, isolated after final (8th) round of selection for short lags in maltose | AN148 descendant | [NAME] | this study
pop7#1 | AN148 | MAL gene-labeled descendant, isolated after final (8th) round of selection for short lags in maltose | AN148 descendant | [NAME] | this study
pop7#2 | AN148 | MAL gene-labeled descendant, isolated after final (8th) round of selection for short lags in maltose | AN148 descendant | [NAME] | this study
pop7#3 | AN148 | MAL gene-labeled descendant, isolated after final (8th) round of selection for short lags in maltose | AN148 descendant | [NAME] | this study
pop8#1 | AN148 | MAL gene-labeled descendant, isolated after final (8th) round of selection for short lags in maltose | AN148 descendant | [NAME] | this study
pop8#2 | AN148 | MAL gene-labeled descendant, isolated after final (8th) round of selection for short lags in maltose | AN148 descendant | [NAME] | this study
pop8#3 | AN148 | MAL gene-labeled descendant, isolated after final (8th) round of selection for short lags in maltose | AN148 descendant | [NAME] | this study
pop9#1 | AN148 | MAL gene-labeled descendant, isolated after final (8th) round of selection for short lags in maltose | AN148 descendant | [NAME] | this study
pop9#2 | AN148 | MAL gene-labeled descendant, isolated after final (8th) round of selection for short lags in maltose | AN148 descendant | [NAME] | this study
pop9#3 | AN148 | MAL gene-labeled descendant, isolated after final (8th) round of selection for short lags in maltose | AN148 descendant | [NAME] | this study
pop10#1 | AN148 | MAL gene-labeled descendant, isolated after final (8th) round of selection for short lags in maltose | AN148 descendant | [NAME] | this study
pop10#2 | AN148 | MAL gene-labeled descendant, isolated after final (8th) round of selection for short lags in maltose | AN148 descendant | [NAME] | this study
pop10#3 | AN148 | MAL gene-labeled descendant, isolated after final (8th) round of selection for short lags in maltose | AN148 descendant | [NAME] | this study
pop11#1 | AN148 | MAL gene-labeled descendant, isolated after final (8th) round of selection for short lags in maltose | AN148 descendant | [NAME] | this study
pop11#2 | AN148 | MAL gene-labeled descendant, isolated after final (8th) round of selection for short lags in maltose | AN148 descendant | [NAME] | this study
pop11#3 | AN148 | MAL gene-labeled descendant, isolated after final (8th) round of selection for short lags in maltose | AN148 descendant | [NAME] | this study
pop12#1 | AN148 | MAL gene-labeled descendant, isolated after final (8th) round of selection for short lags in maltose | AN148 descendant | [NAME] | this study
pop12#2 | AN148 | MAL gene-labeled descendant, isolated after final (8th) round of selection for short lags in maltose | AN148 descendant | [NAME] | this study
pop12#3 | AN148 | MAL gene-labeled descendant, isolated after final (8th) round of selection for short lags in maltose | AN148 descendant | [NAME] | this study
Complementation experiment strains
strain name | progenitor | rationale and description of strain construction | genotype | markers | Ref original
[NAME] | AN296 | Ancestral strain engineered to be a template for complementation of HXK2 mutations in mutants isolated in short-lag experimental evolution. KANMX gene transformed downstream of HXK2 ORF; KANMX downstream of WT HXK2 gene; primers AN112 x [NAME] on pUG6 template | AN296 HXK2_WT-KANMX | [NAME] His+ | this study
AN401 | AN296 | Anc > HKX2(isolate 1) ancestral strain bearing HXK2 mutations in mutants isolated in short-lag experimental evolution. KANMX gene transformed downstream of HXK2 ORF; [NAME] from isolate 1 transformed into native HXK2 gene; primers AN115 x AN116 on AN403 gDNA | AN296 HXK2:c.488_489delAA-KANMX | [NAME] His+ | this study
[NAME] | AN296 | Anc > HKX2(anc) control transformat that did not integrate the evolved HXK2 allele. KANMX gene transformed downstream of HXK2 ORF; Control for HXK2 allele from WT transformed into native HXK2 gene; primers AN115 x AN116 on AN403 gDNA | AN296 HXK2_WT-KANMX | [NAME] His+ | this study
AN403 | isolate 1 descended from AN296 | Isolate 1 strain engineered to be a template for complementation of HXK2 mutations in mutants isolated in short-lag experimental evolution. KANMX gene transformed downstream of HXK2 ORF; KANMX downstream of mutant HXK2 gene; primers AN112 x [NAME] on pUG6 template | Isolate 1 HXK2:c.488_489delAA-KANMX | [NAME] His+ | this study
AN404 | isolate 1 descended from AN296 | isolate 1 > HXK2(anc) evolved strain bearing WT HXK2 allele from ancestor. KANMX gene transformed downstream of HXK2 ORF; HXK2 allele from WT transformed into native (mutant) HXK2 gene; primers AN115 x AN116 on [NAME] gDNA | Isolate 1 HXK2_WT-KANMX | [NAME] His+ | this study
[NAME] | isolate 1 descended from AN296 | isolate 1 > HXK2(isolate 1) control transformant that did not integrate the ancestral allele. KANMX gene transformed downstream of HXK2 ORF; Control for HXK2 allele from WT transformed into native (mutant) HXK2 gene; primers AN115 x AN116 on [NAME] gDNA | Isolate 1 HXK2:c.488_489delAA-KANMX | [NAME] His+ | this study
AN406 | AN296 | Ancestral strian engineered to be a template for complementation of STD1 mutations in mutants isolated in short-lag experimental evolution. KANMX gene transformed downstream of STD1 ORF; KANMX downstream of WT STD1 gene; primers AN124 x AN125 on pUG6 template | AN296 STD1_WT-KANMX | [NAME] His+ | this study
AN407 | AN296 | Anc > STD1(isolate 3) ancestral strain bearing the STD1 mutations of isolate 3. KANMX gene transformed downstream of STD1 ORF; STD1 allele from isolate 3 transformed into native STD1 gene; primers AN127 x AN128 on AN409 gDNA template | AN296 STD1-KANMX | [NAME] His+ | this study
AN408 | AN296 | Anc > STD1(anc) control transformant that did not integrate the isolate 3 STD1 allele. KANMX gene transformed downstream of STD1 ORF; primers AN127 x AN128 on AN409 gDNA template | AN296 STD1:c.245C>A-KANMX | [NAME] His+ | this study
AN409 | isolate 3 descended from AN296 | Isolate 3 engineered to be a template for complementation of STD1 mutations. KANMX gene transformed downstream of STD1 ORF; KANMX downstream of mutant STD1 gene; primers AN124 x AN125 on pUG6 template | Isolate 3 STD1:c.245C>A-KANMX | [NAME] His+ | this study
[NAME] | isolate 3 descended from AN296 | isolate 3 > STD1(anc) isolate 3 bearing the WT STD1 allele from AN296. KANMX gene transformed downstream of STD1 ORF; STD1 allele from WT transformed into native (mutant) STD1 gene; primers AN127 x AN128 on AN406 gDNA template | Isolate 3 STD1_WT-KANMX | [NAME] His+ | this study
AN411 | isolate 3 descended from AN296 | isolate 3 > STD1(isolate 3) control transformant that did not integrate the ancestral allele. KANMX gene transformed downstream of STD1 ORF; Control for STD1 allele from WT transformed into native (mutant) STD1 gene; primers AN127 x AN128 on AN406 gDNA template | Isolate 3 STD1:c.245C>A-KANMX | [NAME] His+ | this study
AN413 | isolate 2 descended from AN296 | Isolate 2 engineered to be a template for complementation of HXK2 mutations in mutants isolated in short-lag experimental evolution. KAN gene transformed downstream of HXK2 ORF; KAN downstream of isolate 2 mutant HXK2 gene; primers AN112 x [NAME] on pUG6 template | Isolate 2 HXK2:c.812G>T-KANMX | [NAME] His+ | this study
AN414 | AN296 | Anc > HKX2(isolate 2) complementation of HXK2 mutations in mutants isolated in short-lag experimental evolution. KAN gene transformed downstream of HXK2 ORF; [NAME] from isolate 1 transformed into native HXK2 gene; primers AN115 x AN116 on AN413 gDNA | AN296 HXK2:c.812G>T-KANMX | [NAME] His+ | this study
AN416 | isolate 2 descended from AN296 | isolate 2 > HXK2(anc) evolved strain bearing WT HXK2 allele from ancestor. KANMX gene transformed downstream of HXK2 ORF; HXK2 allele from WT transformed into native (mutant) HXK2 gene; primers AN115 x AN116 on [NAME] gDNA | Isolate 2 HXK2_WT-KANMX | [NAME] His+ | this study
AN417 | isolate 2 descended from AN296 | isolate 2 > HXK2(isolate 2) control transformant that did not integrate the ancestral allele.  KANMX gene transformed downstream of HXK2 ORF; Control for HXK2 allele from WT transformed into native (mutant) HXK2 gene; primers AN115 x AN116 on [NAME] gDNA | Isolate 2 HXK2:c.812G>T-KANMX | [NAME] His+ | this study
MAL activator deletion strains
strain name | progenitor | rationale and description of strain construction | genotype | markers | Ref original
AN443 | AN355 | This strain was generated to demonstrate the role that the MAL activator plays in inducing the MAL genes in maltose/glucose media. See figure S5 and S8. Primers AN177 and AN178 were used to generate a KANMX cassette from pUG6. These primers made a product that deleted the Hygromycin cassette originally integrated upstream of MAL63 in this strain in addition to the MAL63 coding region itself. This PCR product was transformed into strain AN355 and transformants selected on G418. Samples were patched to hygromycin-containing YPD plates to confirm that the transformation had resulted in deletion of the hygromycin cassette. Strains were then screened in maltose media to confirm that they could no longer activate their MAL genes. | AN355 ∆HYG-MAL63::KANMX | KANR URA+ HIS+ MAL- | this study
AN444 | AN355 | This strain was a vector control for AN443. The strain integrated the KANMX cassette used to make AN443 however remained MAL+. See figure S5 and S8. After selection on G418 media, samples were patched to hygromycin-containing YPD plates to confirm that the transformation had resulted in deletion of the hygromycin cassette. Strains were then screened in maltose media to confirm that they could still activate their MAL genes. | AN355 ∆HYG::KANMX | KANR URA+ HIS+ MAL+ | this study