Table 1. Major reference genomes of the Saccharomycetaceae and related families.

Species	Strain	Genome size (Mb)a	No. of chromosomesb	Total no. of CDSc	Reference or source
Saccharomycetaceae (post-WGD)
Saccharomyces cerevisiae	S288C	12.2	16	5771	Goffeau et al. (1996)
Saccharomyces paradoxus	CBS432T	12.0	16	5527	unpublished datad
Saccharomyces mikatae	IFO1815T	(11.4)	16	6384	Scannell et al. (2011)
Saccharomyces kudriavzevii	IFO1812T	(11.3)	16	5968	Scannell et al. (2011)
Saccharomyces arboricola	CBS10644T	(11.6)	16	5413	Liti et al. (2013)
Saccharomyces uvarum	CBS7001	(11.5)	16	5915	Scannell et al. (2011)
Saccharomyces eubayanus	CBS12357T	(11.7)	16	5515	Baker et al. (2015)
Candida glabrata	CBS138T	12.3	13	5203	Dujon et al. (2004)
Candida bracarensis	CBS10154T	(12.2)	12	5315	Gabaldón et al. (2013)
Nakaseomyces delphensis	CBS2170T	(10.7)	10	5168	Gabaldón et al. (2013)
Candida nivariensis	CBS9983T	(11.5)	13	5238	Gabaldón et al. (2013)
Candida castelii	CBS4332T	(10.1)	8	4875	Gabaldón et al. (2013)
Nakaseomyces bacillisporus	CBS7720T	(10.9)	15	5086	Gabaldón et al. (2013)
Kazachstania africanae	CBS 2517T	11.1	12	5378	Gordon et al. (2011)
Kazachstania naganishiie	CBS8797T	10.8	13	5321	Gordon et al. (2011)
Naumovozyma castelliie	CBS 4309T	11.2	10	5592	Gordon et al. (2011)
Naumovozyma dairenensise	CBS 421T	13.5	11	5548	Gordon et al. (2011)
Tetrapisispora phaffiie	CBS 4417T	12.1	16	5250	Gordon et al. (2011)
Tetrapisispora blattaee	CBS 6284T	14.0	10	5389	Gordon et al. (2011)
Vanderwaltozyma polysporae	DSMZ70294T	(14.7)	(41)	5652	Scannell et al. (2007a,b)
Saccharomycetaceae (ZT clade)
Zygosaccharomyces rouxii	CBS732T	9.8	7	4997	Souciet et al. (2009)
Zygosaccharomyces bailii	CLIB213T	(10.3)	(27)	5084	Galeote et al. (2013)
Torulaspora delbrueckiie	CBS1146T	9.2	8	4972	Gordon et al. (2011)
Saccharomycetaceae (KLE clade)
Lachancea fantastica nom. nud.	CBS6924	11.3	7	5060	Vakirlis et al. (2016)
Lachancea meyersii	CBS8951T	11.3	8	4997	Vakirlis et al. (2016)
Lachancea dasiensis	CBS10888	10.7	8	5099	Vakirlis et al. (2016)
Lachancea nothofagi	CBS11611T	11.3	8	5153	Vakirlis et al. (2016)
Lachancea thermotolerans	CBS6340T	10.4	8	5177	Souciet et al. (2009)
Lachancea quebecensis	CBS14088	(10.2)	(51)	5075	Freel et al. (2016)
Lachancea waltii	NCYC2644	(10.2)	(8)	(4768)	Kellis et al. (2004)
Lachancea lanzarotensis	CBS12615T	(11.5)	(24)	5058	Sarilar et al. (2015)
Lachancea mirantina	CBS11717	10.1	8	5057	Vakirlis et al. (2016)
Lachancea fermentati	CBS6772	10.3	8	5233	Vakirlis et al. (2016)
Lachancea cidri	CBS2950	10.1	8	5188	Vakirlis et al. (2016)
Lachancea kluyveri	CBS3082T	11.3	8	5378	Souciet et al. (2009)
Kluyveromyces lactis	CLIB210	10.6	6	5108	Dujon et al. (2004)
Kluyveromyces dobzhanskii	CBS 2104	(10.7)	(86)	4957	B. Nystedt and S. Astrom; unpublished dataf
Kluyveromyces marxianus	NBRC1777	10.9	8	4912	Inokuma et al. (2015)
—	DMKU3-1042	11.0	8	4952	Lertwattanasakul et al. (2015)
Eremothecium gossypii	ATCC10895	8.7	7	4718	Dietrich et al. (2004), (2013)
Eremothecium cymbalariae	DBVPG 7215	9.7	8	4712	Wendland and Walther. (2011)
Eremothecium coryli	CBS5749	(9.1)	6	4682	Wendland and Walther, (2014)
Eremothecium aceri	FM-2008	8.9	7	4479	Dietrich (2013)
Eremothecium sinecaudum	ATCC58844	8.9	7	4528	F. S. Dietrich; unpublished datag
Saccharomycodaceae
Hanseniaspora opuntiae	AWRI3578	(8.8)	(18)	4176	Sternes et al. (2016)
Hanseniaspora osmophila	AWRI3579	(11.4)	(17)	4660	Sternes et al. (2016)
Hanseniaspora uvarum	AWRI3580	(8.8)	(18)	4061	Sternes et al. (2016)
Wickerhamomycetaceae
Wickerhamomyces anomalus	NRRL Y-366-8	(14.1)	(46)	6423	Riley et al. (2016)
Cyberlindnera jadinii	NRRL Y-1542	(13.0)	(76)	6038	Riley et al. (2016)
Cyberlindnera fabianii	JCM3601	(12.3)	(12)	5874	R. Manabe - unpublished datah
Saccharomycopsidaceae
Saccharomycopsis malanga	JCM7620	(16.7)	(44)	6280	R. Manabe, R. Endoh, S. Uzuhashi, G. Okada, M. Takashima and M. Ohkuma; unpublished datah
Saccharomycopsis fibuligera	KPH12		7	6155	Choo et al. (2016)

The table lists the yeast species of indicated families whose genomes were published in the form of complete sequences or permanent drafts with reasonable numbers of scaffolds (<100). Exploratory sequences (low coverage), sequence read archives, and preliminary assemblies with excessive numbers of contigs or scaffolds were ignored. Readers can find some of these additional sequences with their references in Hittinger et al. (2015). Strain numbers correspond to the reference indicated. Species in which several isolates have been sequenced in complete form or permanent drafts are indicated by bold type, and only one isolate is listed (the first one or the best one). Note that an exception was made for K. marxianus because two independent sequences of equivalent quality were published simultaneously. Species designation follows Kurtzman et al. (2011) and may, therefore, differ from original publications. Hybrid genomes and unspecified isolates are ignored.

^aGenome sizes are indicated in bold type when determined from complete sequences and in brackets when deduced from scaffolds in assemblies (figures are haploid equivalent in case of known diploid strains). Sizes ignore rDNA, mtDNA, and plasmids.

^bNumbers of chromosomes are indicated in bold type when known. Figures in brackets correspond to numbers of scaffolds in assemblies.

^cTotal numbers of predicted protein-coding genes (CDS) are taken from original publications or subsequent annotations, as most appropriate. Figures in brackets represent estimate from incomplete sequence.

^dUnpublished data taken from https://yjx1217.github.io/Yeast_PacBio_2016/data/.

^eSequence data taken from http://ygob.ucd.ie.

^fUnpublished data taken from GenBank: CCBQ000000000.1.

^gUnpublished data taken from GenBank: CP014248.1.

^hUnpublished data taken from the National BioRecource Project (www.jcm.riken.jp/cgi-bin/nbrp/nbrp_list.cgi).