Table 3. Major reference genomes of the methylotroph and basal lineages.
| Species | Strain | Genome size (Mb)a | No. of chromosomesb | Total no. of CDSc | Reference or source |
|---|---|---|---|---|---|
| Methylotrophs | |||||
| Phaffomycetaceae | |||||
| Komagataella phaffii | CBS 7435 | 9.4 | 4 | 5325 | Küberl et al. (2011) |
| Candida sorboxylosa | JCM1536 | (10.7) | (37) | 4724 | R. Manabe, R. Endoh, S. Uzuhashi, G. Okada, M. Takashima and M. Ohkuma unpublished datad |
| Pichiaceae and related Saccharomycetales incertae sedis | |||||
| Dekkera bruxellensis | CBS 2499 | 13.4 | — | 5208 | Piškur et al., (2012) |
| Dekkera anomala | YV396 | (12.9) | (30) | 5241 | Y. Vervoort, B. Herrera-Malaver, S. Mertens, V. Guadalupe Medina, J. Duitama, L. Michiels, G. Derdelinckx, K. Voordeckers and K. J. Verstrepen unpublished datae |
| Dekkera naardensis | CBS7540 | (11.3) | (76) | — | H. Jiang, unpublished dataf |
| Nakazawaea peltata | JCM9829 | (11.7) | (11) | 5620 | R. Manabe, R. Endoh, S. Uzuhashi, G. Okada, M. Takashima and M. Ohkuma unpublished datad |
| Pichia membranifaciens | NRRL Y-2248T | (11.6) | (11) | 5546 | Riley et al. (2016) |
| Kuraishia capsulata | CBS 1993T | 11.4 | 7 | 6029 | Morales et al. (2013) |
| Ogataea polymorpha | NCYC495 leu1.1 | (9.0) | 7 | 5177 | Riley et al. (2016) |
| Ogataea parapolymorpha | DL-1 | 9.1 | 7 | 5325 | Ravin et al. (2013) |
| Ogataea methanolica | JCM10240 | (15.1) | (32) | 6063 | R. Manabe, R. Endoh, S. Uzuhashi, G. Okada, M. Takashima and M. Ohkuma unpublished datad |
| Candida boidinii | JCM9604 | (19.4) | (32) | 6053 | R. Manabe, R. Endoh, S. Uzuhashi, G. Okada, M. Takashima and M. Ohkuma, unpublished datad |
| Ambrosiozyma kashinagacola | JCM15019 | (12.3) | (23) | 5787 | R. Manabe, R. Endoh, S. Uzuhashi, G. Okada, M. Takashima and M. Ohkuma, unpublished datad |
| Candida succiphila | JCM9445 | (12.1) | (22) | 5455 | R. Manabe, R. Endoh, S. Uzuhashi, G. Okada, M. Takashima and M. Ohkuma, unpublished datad |
| Candida arabinofermentans | NRRL YB-2248T | (13.2) | (62) | 5861 | Riley et al. (2016) |
| Pachysolen tannophilus | CBS 4044 | (12.2) | (34) | 5546 | Liu et al. (2012) |
| Basal lineages | |||||
| Dipodascaceae, Trichomonascaceae, and related Saccharomycetales incertae sedis | |||||
| Geotrichum candidum | CLIB918 | 24.2 | (134)g | 6804 | Morel et al. (2015) |
| Yarrowia lipolytica | CLIB122 (E150) | 20.6 | 6 | 6582 | Dujon et al. (2004) |
| Yarrowia keelungensis | JCM14894 | (21.8) | (41) | 6618 | R. Manabe, R. Endoh, S. Uzuhashi, G. Okada, M. Takashima and M. Ohkuma unpublished datad |
| Yarrowia deformans | JCM1694 | (20.9) | (44) | 6704 | R. Manabe, R. Endoh, S. Uzuhashi, G. Okada, M. Takashima and M. Ohkuma unpublished datad |
| Starmerella bombicola | JCM9596 | (9.6) | (16) | 4887 | R. Manabe, R. Endoh, S. Uzuhashi, G. Okada, M. Takashima and M. Ohkuma unpublished datad |
| Starmerella (Candida) apicola | NRRL Y-50540 | (9.8) | (40) | 3818h | Vega-Alvarado et al. (2015) |
| Sporopachydermia quercuum | JCM9486 | (16.4) | (15) | 5992 | R. Manabe, R. Endoh, S. Uzuhashi, G. Okada, M. Takashima and M. Ohkuma unpublished datad |
| Blastobotrys adeninivorans | LS3 | 11.8 | 4 | 6150 | Kunze et al. (2014) |
| Blastobotrys attinorum | NRRL Y27639 | (14.0) | (14) | 6184 | J. K. Magnuson unpublished datai |
| Trichomonascus petasosporus | NRRL YB2093 | (14.5) | (79) | 6567 | J. K. Magnuson unpublished datai |
| Sugiyamaella lignohabitans | CBS10342 | 16.0 | 4 | 6820 | Bellasio et al. (2016) |
| Sugiyamaella americana | NRRL YB2067 | (16.5) | (48) | 6288 | J. K. Magnuson unpublished datai |
| Wickerhamiella domercqiae | JCM9478 | 8.5 | 4 | 4928 | R. Manabe, R. Endoh, S. Uzuhashi, G. Okada, M. Takashima and M. Ohkuma unpublished datad |
| Zygoascus hellenicus | Y7136 | (12.2) | (11) | 5430 | R. Manabe, R. Endoh, S. Uzuhashi, G. Okada, M. Takashima and M. Ohkuma unpublished datad |
| Candida infanticola | DS02 | (8.1) | (22) | — | H. Lee, C. Han, G. Park, W. Jeon, H. Lee and J. Ahn. unpublished dataj |
| Nadsonia fulvescens var. elongata | DSM6958 | (13.7) | (20) | 5657 | Riley et al. (2016) |
| Tortispora caseinolytica | NRRL Y-17796T | 9.2 | 6 | 4657 | Riley et al. (2016) |
| Early branchingk | |||||
| Ascoideaceae | |||||
| Ascoidea rubescens | NRRL Y-17699T | (17.5) | (63) | 6802 | Riley et al. (2016) |
| Ascoidea asiatica | JCM7603 | (20.3) | (71) | 7694 | R. Manabe, R. Endoh, S. Uzuhashi, G. Okada, M. Takashima and M. Ohkuma unpublished datad |
| Lipomycetaceae | |||||
| Lipomyces starkeyi | NRRL Y-11557 | (21.3) | (117)g | 8192 | Riley et al. (2016) |
The table lists the yeast species of indicated families under the same conditions as specified in Table 1. 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).
Genome 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.
Numbers of chromosomes are indicated in bold type when known. Figures in brackets correspond to numbers of scaffolds in assemblies.
Total numbers of predicted protein-coding genes (CDS) are taken from original publications or subsequent annotations, as most appropriate. Data not found indicated by —.
Unpublished data taken from the National BioRecource Project (www.jcm.riken.jp/cgi-bin/nbrp/nbrp_list.cgi).
Unpublished data taken from GenBank: LCTY00000000.1.
Unpublished data taken from GenBank: MDSA000000000.1.
G. candidum and L. starkeyi are listed here despite their large number of scaffolds because each genome represents the only reference available, so far, in its respective lineage.
Automated prediction based on comparisons to the CTG clade.
Unpublished data taken from http://genome.jgi.doe.gov (nonpublic).
Unpublished data taken from GenBank: LWLF00000000.1.
These are listed here for convenience and are the few sequenced yeast species not included in the four major subgroups of Saccharomycotina defined in this review. See Shen et al. (2016) for a recent genome-based phylogenetic reconstruction. The Lipomycetaceae family is basal to all Saccharomycotina.