TABLE 3.

Genes present in Brettanomyces bruxellensis AWRI 1499 (ST05.12/62) and CBS 2499 (ST05.12/56) and absent in ST05.12/22^a

AWRI 1499 CDS accession no.	CBS 2499 JGI transcript identifier	AWRI 1499 contig GenBank accession no.	CBS 2499 scaffold (JGI name)	Functionb	GenBank homology (BLASTX)c
					Organism (GenBank accession no.)	% identity	E valued	S scoree
EIF46399	8711	AHIQ01000211	Scaffold 18	Pantothenate transporter Fen2	Meyerozyma guilliermondii ATCC 6260 (XP_001482616)	63.34	0.0	1,538
EIF46400	23063	AHIQ01000211	Scaffold 18	Upf0145 protein	Streptomyces sp. R1-NS-10 (WP_019070227)	55.66	4e−34	316
EIF45404	26687	AHIQ01000280	Scaffold 17	MFS drug transporter	Meyerozyma guilliermondii ATCC 6260 (XP_001482160)	55.11	2e−177	1,342
EIF45405	51428	AHIQ01000280	Scaffold 17	Putative MFS-MDR transporter	Ogataea parapolymorpha DL-1 (EFW97434)	45.75	6e−137	1,073
EIF45407	62814	AHIQ01000280	Scaffold 17	High-affinity glucose transporter	Scheffersomyces stipitis CBS 6054 (XP_01382755)	71.38	0.0	2,037
EIF45408	26690	AHIQ01000280	Scaffold 17	Galactose-1-phosphate uridylyltransferase	Scheffersomyces stipitis CBS 6054 (XP_001383359)	65.94	8e−179	1,322
EIF45409	8686	AHIQ01000280	Scaffold 17	Galactokinase	Meyerozyma guilliermondii ATCC 6260 (EDK41764)	54.07	3e−152	1,164
EIF45410	26691	AHIQ01000280	Scaffold 17	GAL10 bifunctional protein	Candida tenuis ATCC 10573 (EGV61616)	58.08	0.0	2,080
EIF45411	26692	AHIQ01000280	Scaffold 17	dTDP-glucose dehydratase	Debaryomyces hansenii CBS767 (XP_457784)	49.02	8e−99	787
EIF45412	78562	AHIQ01000280	Scaffold 17	Hexose transporter	Candida intermedia (CAO79523)	47.73	6e−144	1,118
EIF45413	8690	AHIQ01000280	Scaffold 17	Maltase	Saccharomyces kudriavzevii IFO 1802 (EJT44539)	63.4	0.0	1,954
EIF45414	36189	AHIQ01000280	Scaffold 17	Multidrug resistance regulator 1	Ogataea parapolymorpha DL-1 (EFW97551)	34.62	4e−61	584
EIF45415	51487	AHIQ01000280	Scaffold 17	β-Glucosidase	Schwanniomyces etchellsii (ACF93471)	59.26	0.0	2,706
EIF45416	51392	AHIQ01000280	Scaffold 17	Hexose transporter	Wickerhamomyces ciferrii (CCH41021)	50.36	0.0	1,439
EIF45248	26813	AHIQ01000303	Scaffold 24	β-Galactosidase	Kluyveromyces lactis NRRL Y-1140 (XP_452194)	58.39	0.0	1,575
EIF45249	51850	AHIQ01000303	Scaffold 24	Nitrate reductase	Ogataea parapolymorpha DL-1 (EFW95688)	59.32	0.0	2,067
EIF45250	26815	AHIQ01000303	Scaffold 24	Nitrite reductase	Ogataea parapolymorpha DL-1 (EFW95689)	62	0.0	1,159
EIF45251	145655	AHIQ01000303	Scaffold 24	Nitrate transporter	Ogataea parapolymorpha DL-1 (EFW95690)	59	0.0	604
EIF45193	8788	AHIQ01000316	Scaffold 20	Cytochrome mitochondrial precursor	Spathaspora passalidarum NRRL Y-27907 (EGW32589)	50.68	2e−113	904
EIF45194	31164	AHIQ01000316	Scaffold 20	Fungus-specific transcription factor domain protein	Kluyveromyces lactis NRRL Y-1140 (XP_453742)	45.55	7e−97	876

^aAs determined by read depth analysis (CNVnator) and/or BLAST analysis of the AWRI 1499 and CBS 2499 genome sequence against the ST05.12/22 genome assembly and confirmed by a PCR screen (see also Data Sets S5 and S6 in the supplemental material).

^bBased on the best B. bruxellensis GenBank BLASTX hit.

^cB. bruxellensis hits excluded.

^dE value, expected value.

^eBit score calculated by the BLAST algorithm.