Supplementary Table 2. Comparison of O. oeni PSU-1 and BAA-1163 alleles

O. oeni strain
PSU-1 BAA-1163 Annotation / % Identity / # Mismatch / # Transitions / # Transversions
OEOE1855 / OENOO_65078 / protein of unknown function DUF64 / 97.18 / 15 / 11 / 4
OEOE1853 / OENOO_65076 / major facilitator superfamily MFS_1 / 97.25 / 39 / 28 / 11
OEOE1841 / OENOO_65069 / Abortive infection protein / 97.57 / 21 / 18 / 3
OEOE1830 / OENOO_65058 / AraC protein / 97.52 / 21 / 14 / 7
OEOE1717 / OENOO_17002 / NLPA lipoprotein / 97.87 / 21 / 17 / 4
OEOE1699 / OENOO_54029 / methionine aminopeptidase, type I / 97.79 / 18 / 15 / 3
OEOE1693 / OENOO_54023 / glutamyl-tRNA(Gln) amidotransferase / 97.96 / 29 / 24 / 5
OEOE1690 / OENOO_54020 / Alcohol dehydrogenase / 95.78 / 43 / 34 / 9
OEOE1685 / OENOO_54015 / regulatory protein, TetR / 97.22 / 18 / 14 / 4
OEOE1684 / OENOO_54014 / conserved hypothetical protein / 96.32 / 15 / 14 / 1
OEOE1682 / OENOO_54013 / sugar transporter / 97.68 / 32 / 28 / 4
OEOE1681 / OENOO_54012 / sugar transporter / 96.99 / 42 / 38 / 4
OEOE1675 / OENOO_54007 / diacylglycerol kinase, catalytic region / 97.88 / 22 / 17 / 5
OEOE1674 / OENOO_54006 / RNA methyltransferase, TrmA family / 97.36 / 37 / 36 / 1
OEOE1620 / OENOO_30003 / hypothetical protein / 97.39 / 33 / 27 / 6
OEOE1607 / OENOO_43009 / ABC transporter related / 97.17 / 33 / 19 / 14
OEOE1600 / OENOO_43015 / glutamine amidotransferase / 97.55 / 18 / 17 / 1
OEOE1593 / OENOO_43022 / 3-oxoacyl-(acyl-carrier-protein) synthase III / 97.94 / 20 / 16 / 4
OEOE1588 / OENOO_43027 / beta-ketoacyl synthase / 97.56 / 25 / 21 / 4
OEOE1583 / OENOO_20003 / Acetyl-CoA carboxylase / 97.67 / 18 / 15 / 3
OEOE1573 / OENOO_34005 / Alpha/beta hydrolase fold-3 domain protein / 97.04 / 27 / 25 / 2
OEOE1561 / OENOO_63087 / D-alanyl-D-alanine carboxypeptidase 1 / 97.66 / 23 / 18 / 5
OEOE1534 / OENOO_63061 / ABC transporter related / 96.46 / 33 / 26 / 7
OEOE1519 / OENOO_63047 / Amidase / 97.48 / 38 / 27 / 11
OEOE1492 / OENOO_63014 / hypothetical protein / 97.7 / 7 / 6 / 1
OEOE1423 / OENOO_24004 / preprotein translocase, SecE subunit / 97.74 / 4 / 3 / 1
OEOE1414 / OENOO_50039 / methyltransferase small / 97.08 / 18 / 17 / 1
OEOE1412 / OENOO_50037 / ATPase, P-type, HAD superfamily, subfamily IC / 97.49 / 69 / 54 / 15
OEOE1410 / OENOO_50035 / DNA polymerase III, subunits gamma and tau / 97.48 / 44 / 35 / 9
OEOE1409 / OENOO_50034 / recombination protein RecR / 97.69 / 14 / 12 / 2
OEOE1374 / OENOO_28001 / DNA-directed RNA polymerase, beta' subunit / 96.03 / 147 / 129 / 18
OEOE1361 / OENOO_42011 / protein of unknown function DUF335, SprT / 97.93 / 10 / 8 / 2
OEOE1358 / OENOO_32012 / Alcohol dehydrogenase, / 97.05 / 28 / 22 / 6
OEOE1346 / OENOO_32003 / regulatory protein, MarR / 97.88 / 13 / 9 / 4
OEOE1345 / OENOO_32002 / ABC transporter related / 95.51 / 82 / 69 / 13
OEOE1322 / OENOO_49021 / competence protein ComFC / 96.92 / 20 / 19 / 1
OEOE1291 / OENOO_53008 / hypothetical protein / 97.58 / 8 / 7 / 1
OEOE1290 / OENOO_53009 / Alcohol dehydrogenase GroES domain protein / 97.92 / 19 / 16 / 3
OEOE1259 / OENOO_53035 / pantetheine-phosphate adenylyltransferase / 97.3 / 3 / 3 / 0
OEOE1208 / OENOO_52044 / PTS system, lactose -specific IIB subunit / 96.45 / 8 / 6 / 2
OEOE1140 / OENOO_64015 / RNA-binding S4 domain protein / 97.15 / 22 / 19 / 3
OEOE1117 / OENOO_57008 / protein of unknown function DUF59 / 97.76 / 8 / 7 / 1
OEOE1107 / OENOO_57016 / conserved hypothetical protein / 97.08 / 10 / 8 / 2
OEOE1106 / OENOO_57017 / Exodeoxyribonuclease V / 97.83 / 49 / 43 / 6
OEOE1104 / OENOO_57019 / Fmu (Sun) domain protein / 96.8 / 44 / 39 / 5
OEOE0947 / OENOO_45023 / glutamate 5-kinase / 97.9 / 9 / 6 / 3
OEOE0943 / OENOO_45019 / Methenyltetrahydrofolate cyclohydrolase / 97.67 / 20 / 15 / 5
OEOE0936 / OENOO_45010 / thiamine pyrophosphate enzyme / 97.39 / 47 / 38 / 9
OEOE0908 / OENOO_47005 / nicotinate nucleotide adenylyltransferase / 96.68 / 13 / 9 / 4
OEOE0905 / OENOO_47007 / HAD superfamily (subfamily IIIA) phosphatase / 97.67 / 14 / 12 / 2
OEOE0868 / OENOO_35008 / GCN5-related N-acetyltransferase / 96.24 / 17 / 16 / 1
OEOE0866 / OENOO_35010 / GCN5-related N-acetyltransferase / 97.82 / 11 / 10 / 1
OEOE0861 / OENOO_35013 / hypothetical protein / 96.42 / 10 / 7 / 3
OEOE0846 / OENOO_31007 / polysaccharide biosynthesis protein / 97.72 / 38 / 32 / 6
OEOE0845 / OENOO_31006 / ABC transporter related / 97.39 / 24 / 19 / 5
OEOE0828 / OENOO_44011 / cobalt transport protein / 97.76 / 17 / 15 / 2
OEOE0804 / OENOO_22002 / 4-oxalocrotonate tautomerase / 97.85 / 4 / 3 / 1
OEOE0694 / OENOO_48024 / protein of unknown function UPF0074 / 97.96 / 9 / 7 / 2
OEOE0693 / OENOO_48023 / acetoin reductases / 97.56 / 19 / 15 / 4
OEOE0692 / OENOO_48022 / hypothetical protein / 98 / 12 / 10 / 2
OEOE0641 / OENOO_38012 / hypothetical protein / 95.39 / 32 / 24 / 8
OEOE0586 / OENOO_58049 / hypothetical protein / 97.84 / 9 / 6 / 3
OEOE0585 / OENOO_58048 / protein of unknown function / 97.98 / 15 / 12 / 3
OEOE0580 / OENOO_58044 / Choloylglycine hydrolase / 97.84 / 20 / 18 / 2
OEOE0557 / OENOO_58021 / phosphate ABC transporter, PstC / 97.97 / 19 / 18 / 1
OEOE0553 / OENOO_58017 / Lactate/malate dehydrogenase / 97.7 / 12 / 11 / 1
OEOE0510 / OENOO_55017 / aldo/keto reductase / 97.5 / 22 / 19 / 3
OEOE0332 / OENOO_66082 / protein-tyrosine phosphatase (putative) / 97.1 / 23 / 21 / 2
OEOE0330 / OENOO_66084 / dehydrogenase complex catalytic domain / 97.1 / 39 / 33 / 6
OEOE0327 / OENOO_66087 / lipoyltransferase and lipoate-protein ligase / 97.31 / 27 / 25 / 2
OEOE0324 / OENOO_66090 / aldehyde dehydrogenase / 97.73 / 33 / 30 / 3
OEOE0312 / OENOO_66101 / DNA-3-methyladenine glycosylase I / 97.69 / 14 / 13 / 1
OEOE0306 / OENOO_66106 / conserved hypothetical protein / 96.75 / 8 / 8 / 0
OEOE0280 / OENOO_66129 / O-succinylbenzoate-CoA ligase / 97.46 / 37 / 30 / 7
OEOE0262 / OENOO_52003 / orotidine 5'-phosphate decarboxylase / 97.39 / 19 / 14 / 5
OEOE0233 / OENOO_52032 / PEP-dependent sugar PTS, EIIA 2 / 95.89 / 17 / 13 / 4
OEOE0231 / OENOO_52034 / Aldose 1-epimerase / 96.01 / 41 / 26 / 15
OEOE0227 / OENOO_52037 / carbohydrate kinase, FGGY / 96.26 / 60 / 45 / 15
OEOE0225 / OENOO_52042 / sugar isomerase (SIS) / 97.26 / 20 / 19 / 1
OEOE0130 / OENOO_46018 / PfkB domain protein / 96.68 / 32 / 26 / 6
OEOE0119 / OENOO_46008 / response regulator receiver / 97.98 / 14 / 13 / 1
OEOE0098 / OENOO_62067 / conserved hypothetical protein / 97.81 / 14 / 10 / 4
OEOE0060 / OENOO_62048 / hypothetical protein / 96.79 / 17 / 16 / 1
OEOE0059 / OENOO_62047 / conserved hypothetical protein / 96.79 / 18 / 15 / 3
OEOE0051 / OENOO_62042 / peptidase S58, DmpA / 97.93 / 23 / 19 / 4
OEOE0048 / OENOO_62039 / oxidoreductase domain protein / 97.71 / 22 / 17 / 5
OEOE0045 / OENOO_62037 / regulatory protein, TetR / 95.22 / 25 / 21 / 4
OEOE0038 / OENOO_62024 / glucokinase regulatory-like protein / 96.53 / 31 / 24 / 7
OEOE0031 / OENOO_62020 / membrane protein / 97.77 / 12 / 11 / 1
OEOE0008 / OENOO_65094 / NAD+ synthetase / 97.83 / 18 / 17 / 1
Totals / 2225 / 1838 / 387
% Transitions / 83
% Transversions / 17

Identification of polymorphisms between highly conserved oenococcal genes was also performed by querying the 1691 O. oeni PSU-1 ORFs (Genbank accession CP000411) against a target database comprised of cognate O. oeni BAA-1163 ORFs (GenBank accession AAUV00000000) using the BLASTP algorithm (1). Top hits were sorted by identity along the alignable region and allele pairs that possessed between 95-98% nucleotide identity (a total of 91 genes) were selected for analysis. Pair-wise alignments of these 91 genes were constructed with the ClustalW algorithm (3), and analyzed using the MEGA3 suite of computational tools (26) to score nucleotide polymorphisms.