. Author manuscript; available in PMC: 2013 Apr 6.

Published in final edited form as: Nat Genet. 2005 May 1;37(6):630–635. doi: 10.1038/ng1553

Table 2.

Duplication in the Saccharomyces cerevisiae genome where 0.80 < f₂ < 0.86

SGD name	gi number	Trivial name	Annotation and comments
Inosine-5′-monophosphate dehydrogenase family (3 paralogs, 3 pairs, 2 duplications)^a
f₂ = 0.803^b	Pair associated with Wolfe duplication blocks 1 and 44
YAR073W	gi\|456156	IMD1	Nonfunctional homolog, near telomere, not expressed
YLR432W	gi\|665971	IMD3	Inosine-5′-monophosphate dehydrogenase
f₂ = 0.825^b
YLR432W	gi\|665971	IMD3	Inosine-5′-monophosphate dehydrogenase
YHR216W	gi\|458916	IMD2	Inosine-5′-monophosphate dehydrogenase
Subfamily pair: YHR216W and YAR073W	f₂ = 0.93 (proposed recent duplication creating a pseudogene)
Sugar transporter family A (4 paralogs, 4 pairs, 3 duplications)^c
f₂ = 0.805^b	Pair not associated with any duplication block
YJR158W	gi\|1015917	HXT16	Sugar transporter repressed by high glucose levels
YNR072W	gi\|1302608	HXT17	Sugar transporter repressed by high glucose levels
f₂ = 0.806^b	Pair not associated with any duplication block
YDL245C	gi\|1431418	HXT15	Sugar transporter induced by low glucose, repressed by high glucose
YNR072W	gi\|1302608	HXT17	Sugar transporter repressed by high glucose levels
f₂ = 0.809^b	Pair not associated with any duplication block
YJR158W	gi\|1015917	HXT16	Sugar transporter repressed by high glucose levels
YEL069C	gi\|603249	HXT13	Sugar transporter induced by low glucose, repressed by high glucose
f₂ = 0.810^b	Pair not associated with any duplication block
YEL069C	gi\|603249	HXT13	Sugar transporter induced by low glucose, repressed by high glucose
YDL245C	gi\|1431418	HXT15	Sugar transporter
Subfamily pair: YEL069C and YNR072W	f₂ = 0.932 (proposed recent duplication)
Subfamily pair: YJR158W and YDL245C	f₂ = 1.000 (proposed very recent duplication)
Chaperone family A (2 paralogs, 1 pair, 1 duplication)^a
f₂ = 0.81	Pair associated with Wolfe duplication block 48
YMR186W	gi\|854456	HSC82	Cytoplasmic chaperone induced 2–3 fold by heat shock
YPL240C	gi\|1370495	HSP82	Cytoplasmic chaperone, pheromone signaling, Hsf1p regulation
Phosphatase/thiamine transport family A (2 paralogs, 1 pair, 1 duplication)^c
f₂ = 0.818	Pair not associated with any duplication block
YBR092C	gi\|536363	PHO3	Acid phosphatase implicated in thiamine transport
YBR093C	gi\|536365	PHO5	Acid phosphatase, one of three repressible phosphatases
Pyruvate decarboxylase family A (2 paralogs, 1 pair, 1 duplication)^c
f₂ = 0.835	Pair not associated with any duplication block
YlR044C	gi\|1360375	PDC1	Pyruvate decarboxylase, major isoform
YlR134W	gi\|1360549	PDC5	Pyruvate decarboxylase, minor isoform
By ortholog analysis, Saccharomyces bayanus (gi\|515236) diverged from S. cerevisiae after the f₂ = 0.835 duplication; Kluyveromyces diverged before.
Glyceraldehyde-3-phosphate dehydrogenase family (3 paralogs, 3 pairs, 2 duplications)^c
f₂ = 0.845^b	Pair not associated with any duplication block
YJL052W	gi\|1008189	TDH1	Glyceraldehyde-3-phosphate dehydrogenase
YGR192C	gi\|1323341	TDH3	Glyceraldehyde-3-phosphate dehydrogenase
f₂ = 0.845^b	Pair not associated with any duplication block
YJL052W	gi\|1008189	TDH1	Glyceraldehyde-3-phosphate dehydrogenase
YJR009C	gi\|1015636	TDH2	Glyceraldehyde-3-phosphate dehydrogenase
Subfamily pair: YJR009C and YGR192C	f₂ = 0.991 (proposed very recent duplication)
Alcohol dehydrogenase family (2 paralogs, 1 pair, 1 duplication)^c
f₂ = 0.848	Pair not associated with any duplication block
YMR303C	gi\|798945	Adh2	Alcohol dehydrogenase, glucose-repressible
YOL086C	gi\|1419926	Adh1	Alcohol dehydrogenase, constitutive
Spermine transporter family (2 paralogs, 1 pair, 1 duplication)^a
f₂ = 0.86	Pair associated with Wolfe duplication block 34
YGR138C	gi\|1323230	TPO2	Spermine transporter activity
YPR156C	gi\|849164	TPO3	Spermine transporter activity
Sugar transporter family B (3 paralogs, 3 pairs, 2 duplications)^c
f₂ = 0.847^b	Pair not associated with any duplication block
YDR343C	gi\|1230670	HXT6	Sugar transporter, high-affinity high basal levels
YDR345C	gi\|1230672	HXT3	Sugar transporter, low-affinity glucose transporter
f₂ = 0.854^b	Pair not associated with any duplication block
YDR342C	gi\|1230669	HXT7	Sugar transporter, high-affinity, high basal levels
YDR345C	gi\|1230672	HXT3	Sugar transporter, low affinity
Subfamily pair: YDR342C and YDR343C	f₂ = 0.994 (proposed very recent duplication)

Not associated with fermentation. These are associated with duplication blocks in the yeast genome¹⁶, where the high value of f₂ (typically equilibrated in block paralog pairs) may reflect either variance or selective pressure to conserve silent sites in individual codons.

These pairs represent a family generated with a single duplication with f₂ value between 0.80 and 0.86 and subsequent duplication(s) in the derived lineages. Trees are shown in Supplementary Figure 2 online. Paralog pairs were considered only if they have with at least 100 aligned silent sites and are not separated by more than 120 point-accepted mutations per 100 aligned amino acid sites.

Associated with the pathway to make, accumulate and then consume ethanol. Genes involved in the fermentation pathway that are not rate-limiting^1,25 generally do not have duplicates in the yeast genome (e.g., hexokinase, glucose-6-phosphate isomerase, phosphofructokinase, aldolase, triose phosphate isomerase and phosphoglycerate kinase are all present in one isoform). Enolase has two paralogs (ENO1 and ENO2), where f₂ = 0.946. These are distantly related to a homolog known as ERR1, with the silent sites equilibrated. Phosphoglycerate mutase has three paralogs, GM1, GM2 and GM3, with silent sites that are essentially equilibrated (Supplementary Note online).