Génolevures

Supplementary Table 11: Conservation series of dispersed paralogs

Species-specific formation of dispersed paralogs

Fam. Size	Protein family	CDS	Short description

*Z. rouxii*
2	GL3C0630	ZYRO0D09702g	weakly similar to SACE YPR154W PIN3 Protein that induces appearance of prion when overproduced
		ZYRO0G20372g	weakly similar to SACE YPR154W PIN3 Protein that induces appearance of prion when overproduced
2	GL3C0706	ZYRO0A03256g	weakly similar to SACE YDR028C REG1 Regulatory subunit of type 1 protein phosphatase Glc7p
		ZYRO0G05060g	similar to SACE YNL166C BNI5 Protein involved in organization of septins at the mother-bud neck
2	GL3C0903	ZYRO0D14102g	Zygosaccharomyces rouxii sod2 Na /H antiporter
		ZYRO0F13816g	similar to SACE YLR138W NHA1 Na+/H+ antiporter
2	GL3C0982	ZYRO0C13662g	weakly similar to SACE YJL020C BBC1 Protein possibly involved in assembly of actin patches
		ZYRO0F02640g	weakly similar to SACE YJL020C BBC1 Protein possibly involved in assembly of actin patches
2	GL3R0496	ZYRO0F13552g	similar to SACE YJR019C TES1 Thioesterase peroxisomal acyl-CoA thioesterase
		ZYRO0G11528g	similar to SACE YJR019C TES1 Thioesterase peroxisomal acyl-CoA thioesterase
2	GL3R0659	ZYRO0F04246g	highly similar to SACE YML106W URA5 Orotate phosphoribosyltransferase 1
		ZYRO0G13816g	highly similar to SACE YML106W URA5 Orotate phosphoribosyltransferase 1
2	GL3R0660	ZYRO0C10406g	weakly similar to SACE YPL123C RNY1 RNAse member of the T(2) family of endoribonucleases
		ZYRO0F06072g	similar to SACE YPL123C RNY1 RNAse member of the T(2) family of endoribonucleases
2	GL3R0775	ZYRO0B15356g	highly similar to SACE YJR016C ILV3 Dihydroxyacid dehydratase
		ZYRO0G11638g	highly similar to SACE YJR016C ILV3 Dihydroxyacid dehydratase
2	GL3R0872	ZYRO0B00528g	highly similar to SACE YPR086W SUA7 Transcription factor TFIIB required for initiation and start site selection by RNA polymerase II
		ZYRO0C17116g	highly similar to SACE YPR086W SUA7 Transcription factor TFIIB required for initiation and start site selection by RNA polymerase II
2	GL3R3015	ZYRO0A06050g	weakly similar to SACE YOR279C RFM1 DNA-binding protein that directs the Hst1p histone deacetylase to some of the promoters regulated by Sum1p
		ZYRO0F13574g	weakly similar to SACE YOR279C RFM1 DNA-binding protein that directs the Hst1p histone deacetylase to some of the promoters regulated by Sum1p

*K. thermotolerans*
2	GL3C0549	KLTH0D17930g	similar to SACE YJR130C STR2 Cystathionine gamma-synthase converts cysteine into cystathionine
		KLTH0G00418g	similar to SACE YLL058W
2	GL3C0569	KLTH0A05214g	similar to SACE YIL079C AIR1 and YDL175C AIR2
		KLTH0G17424g	similar to SACE YIL079C
2	GL3C0590	KLTH0B00440g	similar to SACE YFL054C
		KLTH0E05676g	similar to SACE YLL043W FPS1 Plasma membrane glycerol channel member of the major intrinsic protein family
2	GL3C0711	KLTH0C10516g	similar to SACE YOR380W RDR1 Transcriptional repressor involved in the control of multidrug resistance
		KLTH0H02684g	weakly similar to SACE YPL248C GAL4 DNA-binding transcription factor
2	GL3C0754	KLTH0C00814g	similar to SACE YKL015W PUT3 Positive regulator of proline utilization genes
		KLTH0E03256g	weakly similar to SACE YJL206C
2	GL3C0942	KLTH0C09570g	similar to SACE YOL098C
		KLTH0G04092g	similar to SACE YDR430C CYM1 Cytosolic metalloprotease
2	GL3C0956	KLTH0B00176g	similar to SACE YER152C
		KLTH0G19624g	similar to SACE YER152C
2	GL3R0474	KLTH0B00418g	highly similar to SACE YFL053W DAK2 Dihydroxyacetone kinase
		KLTH0D16412g	highly similar toSACE YML070W DAK1 Dihydroxyacetone kinase
2	GL3R0904	KLTH0D12958g	similar to SACE YOR289W
		KLTH0F06204g	similar to SACE YOR289W
3	GL3R0661	KLTH0B08470g	some similarities with SACE YNL234W Similar to globins and has a functional heme-binding domain involved in glucose signaling or metabolism regulated by Rgt1p
		KLTH0F19866g	some similarities with SACE YNL234W Similar to globins and has a functional heme-binding domain involved in glucose signaling or metabolism regulated by Rgt1p
		KLTH0H00286g	some similarities with SACE YNL234W similar to globins and has a functional heme-binding domain involved in glucose signaling or metabolism regulated by Rgt1p

*S. kluyveri*
2	GL3C0553	SAKL0B08008g	similar to SACE YBR114W RAD16 Protein subunit of Nucleotide Excision Repair Factor 4 (NEF4) member of the SWI/SNF family
		SAKL0E09658g	weakly similar to SACE YBR114W RAD16 Protein subunit of Nucleotide Excision Repair Factor 4 (NEF4) member of the SWI/SNF family
2	GL3C0557	SAKL0B12496g	highly similar to SACE YHR208W BAT1 Mitochondrial branched-chain amino acid aminotransferase
		SAKL0G09064g	some similarities SACE YHR208W BAT1 Mitochondrial branched-chain amino acid aminotransferase
2	GL3C0694	SAKL0B02178g	weakly similar SACE YFL010C WWM1 WW domain containing protein interacting with Metacaspase (MCA1)
		SAKL0E13596g	no similarity
2	GL3C0710	SAKL0F13354g	similar to SACE YBL097W BRN1 Essential protein required for chromosome condensation
		SAKL0H21890g	weakly similar to SACE YBL097W BRN1 Essential protein required for chromosome condensation
2	GL3C0713	SAKL0D05302g	highly similar to SACE YKR026C GCN3 Alpha subunit of the translation initiation factor eIF2B
		SAKL0F06622g	highly similar SACE YPR118W Methylthioribose-1-phosphate isomerase
2	GL3C0794	SAKL0B00594g	similar to SACE YLR078C BOS1 v-SNARE (vesicle specific SNAP receptor) localized to the endoplasmic reticulum membrane and necessary for vesicular transport from the ER to the Golgi
		SAKL0H25894g	similar to SACE YHL031C GOS1 v-SNARE protein involved in Golgi transport homolog of the mammalian protein GOS-28/GS28
2	GL3C0976	SAKL0F07370g	similar to SACE YFR033C QCR6 ubiquinol-cytochrome c oxidoreductase subunit 6 (17 kDa)
		SAKL0H25982g	weakly similar to SACE YFR033C QCR6 ubiquinol-cytochrome c oxidoreductase subunit 6 (17 kDa)
2	GL3C1461	SAKL0D13816g	conserved hypothetical protein
		SAKL0E08096g	similar to SACE YNL044W YIP3 Interacts with YPT proteins
2	GL3C3180	SAKL0H15686g	some similarities with SACE YDR143C SAN1 Ubiquitin-protein ligase
		SAKL0H17116g	weakly similar to SACE YDR143C SAN1 Ubiquitin-protein ligase
2	GL3R0843	SAKL0E05742g	similar to SACE YDL052C SLC1 fatty acyltransferase
		SAKL0H03762g	similar to SACE YDL052C SLC1 fatty acyltransferase
2	GL3R2315	SAKL0C05632g	similar to SACE YBR163W
		SAKL0H10648g	similar to SACE YBR163W
2	GL3R2424	SAKL0F01738g	conserved hypothetical protein
		SAKL0H20526g	conserved hypothetical protein
3	GL3R0604	SAKL0C01760g	weakly similar to SACE YLR247C
		SAKL0C03586g	weakly similar to SACE YLR247C
		SAKL0D08272g	similar to SACE YLR247C
3	GL3R0923	SAKL0B00220g	similar to SACE YIL162W SUC2
		SAKL0D11946g	similar to SACE YIL162W SUC2
		SAKL0F01122g	similar to SACE YIL162W SUC2
5	GL3R0543	SAKL0B12826g	weakly similar to SACE YBR158W AMN1 Involved in daughter cell separation and Chromosome STability
		SAKL0G00110g	weakly similar to SACE YBR158W AMN1 Involved in daughter cell separation and Chromosome Stability
		SAKL0G00132g	weakly similar to SACE YBR158W AMN1 Involved in daughter cell separation and Chromosome Stability
		SAKL0G19866g	weakly similar to SACE YBR158W AMN1 Involved in daughter cell separation and Chromosome Stability
		SAKL0H10824g	similar to SACE YBR158W AMN1 Involved in daughter cell separation and Chromosome Stability

*K. lactis*
2	GL3C0665	KLLA0E00243g	similar to SACE YPR200C ARR2 Arsenate reductase required for arsenate resistance
		KLLA0E16589g	similar to SACE YGR203W Probable protein tyrosine phosphatase of the CDC25-like phosphatase family
2	GL3C0688	KLLA0A02233g	highly similar to SACE YOR157C PUP1 Endopeptidase with trypsin- like activity that cleaves after basic residues
		KLLA0D11506g	highly similar to SACE YFR050C PRE4 20S proteasome beta-type subunit
2	GL3C0736	KLLA0B07227g	similar to SACE YJL163C
		KLLA0E24883g	weakly similar to SACE YJL163C
2	GL3C0876	KLLA0A12089g	similar to Bacillus clausii ABC3243 paiA Septation and degradation transcriptional repressor of sporulation
		KLLA0C09845g	similar to SACE YOR253W NAT5 Subunit of the N-terminal acetyltransferase NatA
2	GL3C0944	KLLA0D15356g	some similarities with SACE YIR023W DAL81 Positive regulator of genes in multiple nitrogen degradation pathways
		KLLA0E18195g	similar to SACE YIR023W DAL81 Positive regulator of genes in multiple nitrogen degradation pathways
2	GL3C1005	KLLA0A04587g	highly similar to SACE YOR187W TUF1 Mitochondrial translation elongation factor Tu
		KLLA0C05214g	highly similar to SACE YOR187W TUF1 Mitochondrial translation elongation factor Tu
2	GL3R0562	KLLA0C14949g	weakly similar to SACE YOL137W
		KLLA0E07063g	similar to SACE YOL137W BSC6 Protein of unknown function containing 8 putative transmembrane seqments
2	GL3R0834	KLLA0A04543g	similar to SACE YLR295C ATP14 Subunit h of the F0 sector of mitochondrial F1F0 ATP synthase
		KLLA0C05170g	similar to SACE YLR295C ATP14 Subunit h of the F0 sector of mitochondrial F1F0 ATP synthase
2	GL3R2918	KLLA0A04565g	weakly similar to SACE YLR298C YHC1 U1 snRNP protein required for pre- mRNA splicing
		KLLA0C05192g	weakly similar to SACE YLR298C YHC1 U1 snRNP protein required for pre- mRNA splicing

*A. gossypii*
2	GL3C0709	ERGO0D10186g	Syntenic homolog of SACE YPR112C (MRD1)
		ERGO0G11110g	Syntenic homolog of SACE YER165W (PAB1)
2	GL3M4606	ERGO0B09350g	Syntenic homolog of SACE YPR161C (SGV1)
		ERGO0F10538g	Syntenic homolog of SACE YKL139W (CTK1)
2	GL3M4611	ERGO0C11308g	Syntenic homolog of SACE YOL051W (GAL11)
		ERGO0F01034g	Syntenic homolog of SACE YMR164C (MSS11)
2	GL3R0346	ERGO0F11088g	Non-syntenic homolog of SACE YKR093W (PTR2)
		ERGO0G00220g	No homolog in SACE
2	GL3R0841	ERGO0B02178g	Syntenic homolog of SACE YMR284W (YKU70)
		ERGO0F16126g	Syntenic homolog of SACE YMR284W (YKU70)
3	GL3R0662	ERGO0D00264g	Syntenic homolog of SACE YNL244C (SUI1)
		ERGO0E18766g	Syntenic homolog of SACE YNL244C (SUI1)
		ERGO0F20856g	Syntenic homolog of SACE YNL244C (SUI1)
3	GL3R0858	ERGO0D00242g	Syntenic homolog of SACE YNL246W
		ERGO0E18788g	Syntenic homolog of SACE YNL246W (VPS75)
		ERGO0F20834g	Syntenic homolog of SACE YNL246W (VPS75)

The table indicates the series of dispersed paralogs specific to one of the protoploid yeasts corresponding to a unique gene in all other species.