Article Figures & Data
Figures
- Figure 1
Resequencing and assembling the genomes of three Saccharomyces species. (A) Schematic showing phylogenetic relationships among nonhybrid members of the Saccharomyces sensu stricto genus plus the outgroup Kluyveromyces lactis based on (Kurtzman and Robnett 2003), (Nieduszynski and Liti 2011), and (Libkind, Hittinger et al., unpublished data). Branch lengths are not proportional to sequence divergence. The branch on which the whole-genome duplication occurred is marked. (B) Schematic depicting co-assembly of genomes from Illumina short-insert paired-end reads and mate-pair Sanger shotgun reads. Illumina reads were used to build contigs, which were stitched into scaffolds using mate-pair reads from the longer-insert Sanger libraries. Scaffolds were then joined into ultra-scaffolds (contiguous with chromosomes) using MEGABLAST and manual scaffold ordering.
- Figure 2
Genes exhibiting lineage-specific rates of evolution in the Saccharomyces sensu stricto genus. (A) The three alternative hypotheses designed to test whether genes are evolving at a different rate in each of five species of the Saccharomyces sensu stricto genus. Under hypothesis H0 all branches of the tree exhibit the same ω ratio of nonsynonymous to synonymous substitutions. Under the set of H1 hypotheses, the ω ratio along a given species’ branch is different from that along all other branches of the tree. Under the H2 hypothesis, each branch exhibits its own ω ratio. (B) Numbers of genes with lineage-specific rates of evolution in the Saccharomyces sensu stricto genus.
- Figure 3
Relaxed molecular clock estimation of relative species divergence within the Saccharomyces sensu stricto genus. The top scale bar and the values above branches denote estimated substitutions per site. The bottom scale bar expresses species divergence in percentage points relative to the origin of the genus.
Tables
- Table 1 Short-read library statistics
Library Insert (bp) Read Length (bp) Assembly Kmer Fold Coverage Raw Processeda Kmer S. bayanus (CBS 7001) 437 51 31 140.7 109.5 45.1 S. kudriavzevii (IFO 1802T) 203 114 61 272.2 202.5 95.9 S. kudriavzevii (ZP 591) 223 114 61 269.4 207.8 98.4 S. mikatae (IFO 1815T) 259 80 61 379.2 267.9 67.0 Coverage calculated assuming a genome size of 12.1Mb.
↵a Read pool after reads failing quality criteria were trimmed, corrected, or discarded. The relevant procedure is described in Materials and Methods.
- Table 2 Genome assembly summary statistics, before and after manual ordering of scaffolds
Unordered Assembly (Scaffolds) Ordered Assembly (Ultra-scaffolds) Percentage of Assemblya Number Bases N50 Gaps Number Bases N50 Gaps S. bayanus (CBS 7001) 629 (147) 11,668,028 444,551 380 16 11,467,582 905,555 394 98.3% S. kudriavzevii (IFO 1802T) 1455 (226) 11,736,856 151,185 17 16 11,294,830 882,337 111 96.2% S. kudriavzevii (ZP 591) 1523 (164) 11,642,553 100,201 10 16 11,185,947 882,203 162 96.2% S. mikatae (IFO 1815T) 1220 (159) 11,922,798 360,232 18 16 11,445,471 800,823 52 96.0% Numbers in parentheses indicate scaffolds longer than 500 bp.
↵a Percentage of base pairs in the unordered assembly that are also present in the ordered assembly. Neither contigs with an average Kmer coverage less than 20 nor gaps in scaffolds (i.e., N bases) were counted toward assembly statistics.
- Table 3 Counts of annotated tRNA and protein-coding genes across representative strains of five Saccharomyces species
tRNAs Protein-Coding Genes (by Homology)a Total YGOB SGD Other S. cerevisiae 275 5490 881 33 6679 S. paradoxus 273 5440 745 46 6504 S. mikatae 291 5454 510 51 6306 S. kudriavzevii 280 5450 409 48 6187 S. bayanus 279 5559 432 48 6318 Orthogroupsb 229 5141 120 0 5490 S. kudriavzevii is represented by IFO 1802T.
↵a Protein-coding gene counts are subdivided by homology to families in the Yeast Gene Order Browser (YGOB) (Byrne and Wolfe 2005), genes annotated in the Saccharomyces Genome Database (SGD) (Engel et al. 2010), or other protein databases (Other) (see Materials and Methods).
↵b Each column shows the number of genes for which syntenic orthologs were detected in all five species.
- Table 4 Genes not previously reported in the Saccharomyces sensu stricto
Representative Gene(s) Homolog Presence Patterna Functional Annotation Smik_18.9 KLTH0F00110 0:0:1:0:0 S-adenosylmethionine-dependent methyltransferase; weak homolgy to Anc_8.241 Sbay_15.364 Anc_5.74 0:0:0:0:1 Uncharacterized (YJR107C-A) Anc_7.495 1:1:1:1:1 Not annotated in SGD. dN/dS = 0.29; between YJR107W/YJR108W Sbay_10.240 Anc_8.350 0:0:0:0:1 Uncharacterized Spar_6.12 Anc_8.663 0:1:1:1:1 Nonsyntenic; uncharacterized Sbay_13.12 Anc_8.869 0:0:0:0:1 Uncharacterized Sbay_13.48 Anc_8.880 0:0:0:0:1 Endoribonuclease in the RNase III family (budding yeast Dicer)b Sbay_15.267 CAGL0J10714g 0:0:0:0:1 Syntenic homolog. dN/dS = 0.33; also annotated in N. castellii Smik_10.15 RCFBP_mp20323 0:0:1:0:0 NTF2_like superfamily; similar to RCFBP_mp20323 from Ralstonia solanacearum Smik_29.1/Spar_12.256 CGSSp3BS71_00010 0:1:1:0:0 Similar to CGSSp3BS71_00010 from Streptococcus pneumoniae Sbay_15.427 Kwal_8.576 0:0:0:0:1 Nitrilase superfamily Sbay_17.1 SAKL0C00330g 0:0:0:0:1 Hyphal_reg_CWP superfamily - Table 5 Loss of duplicate genes from the ancient whole-genome duplication in the Saccharomyces sensu stricto clade
S. cerevisiae Gene(s) YGOB Locus Retention Patterna Functional Annotation YCL048W-A / YDR524C-B Anc_1.22 2:1:1:1:2 Uncharacterized YFR017C / YOL024W Anc_1.363 2:2:1:2:2 Predicted to have thiol-disulfide oxidoreductase active site ECM10/SSC1 Anc_1.474 2:2:1:2:2 Hsp70 family; localized in mitochondrial nucleoids; plays a role in protein translocation GAL80 Anc_1.500 1:1:1:1:2 Inhibits transcriptional activation by Gal4p HEK2 Anc_3.318 1:1:1/ψ:2:2 RNA binding protein with similarity to hnRNP-K; localizes to the cytoplasm and subtelomeric DNA PMT4 Anc_4.379 1:1:1:1:2 Protein amino acid O-linked glycosylation SLT2 / YKL161C Anc_5.274 2:2:1:2:2 Serine/threonine MAP kinase involved in regulating the maintenance of cell wall integrity CAD1/YAP1 Anc_5.528 2:2:2:2:1 AP-1-like basic leucine zipper (bZIP) transcriptional activator involved in stress responses, iron metabolism, and pleiotropic drug resistance YML020W Anc_5.554 1:2:1/ψ:1/ψ:1/ψ Uncharacterized YDR066C / YER139C Anc_8.181 2:2:2:1:2 Uncharacterized SSU1 Anc_8.569 1:2:1:1:1 Plasma membrane sulfite pump ARL1 Anc_8.597 1/ψ:1/ψ:1:1/ψ:2 Soluble GTPase with a role in regulation of membrane traffic URA5/URA10 Anc_8.827 2:2:1:2:2 Phosphoribosyltransferase; fifth step in pyrimidine biosynthesis pathway ↵a Number of detected copies or pseudogenes (ψ) in S. cerevisiae, S. paradoxus, S. mikatae, S. kudriavzevii, and S. bayanus, respectively.
- Table 6 Construction of heterothallic haploid strains with auxotrophic markers for S. mikatae, S. kudriavzevii and S. bayanus
Species Strain Original Genotype Reference S. mikatae JRY9171 IFO 1815T MATa hoΔ::KanMX ura3Δ::HygMX This study S. mikatae JRY9172 IFO 1815T MATα hoΔ::KanMX ura3Δ::HygMX This study S. mikatae JRY9173 IFO 1815T MATa hoΔ::NatMX ura3Δ::HygMX This study S. mikatae JRY9174 IFO 1815T MATα hoΔ::NatMX ura3Δ::HygMX This study S. mikatae JRY9175 IFO 1815T MATa hoΔ::KanMX his3Δ::HygMX This study S. mikatae JRY9176 IFO 1815T MATα hoΔ::NatMX trp1Δ::HygMX This study S. mikatae JRY9177 IFO 1815T MATa hoΔ::KanMX his3Δ::HygMX ura3Δ::HygMX This study S. mikatae JRY9178 IFO 1815T MATα hoΔ::KanMX his3Δ::HygMX ura3Δ::HygMX This study S. mikatae JRY9179 IFO 1815T MATa hoΔ::NatMX his3Δ::HygMX ura3Δ::HygMX This study S. mikatae JRY9180 IFO 1815T MATα hoΔ::NatMX his3Δ::HygMX ura3Δ::HygMX This study S. mikatae JRY9181 IFO 1815T MATa hoΔ::KanMX trp1Δ::HygMX ura3Δ::HygMX This study S. mikatae JRY9182 IFO 1815T MATα hoΔ::KanMX trp1Δ::HygMX ura3Δ::HygMX This study S. mikatae JRY9183 IFO 1815T MATa hoΔ::NatMX trp1Δ::HygMX ura3Δ::HygMX This study S. mikatae JRY9184 IFO 1815T MATα hoΔ::NatMX trp1Δ::HygMX ura3Δ::HygMX This study S. kudriavzevii FM1097 IFO 1802T MATα hoΔ::natMX Hittinger et al. 2010 S. kudriavzevii FM1098 IFO 1802T MATa hoΔ::natMX Hittinger et al. 2010 S. kudriavzevii FM1363 IFO 1802T MATα hoΔ::kanMX This study S. kudriavzevii FM1403 IFO 1802T MATa/MATα hoΔ::kanMX/hoΔ::kanMX This study S. kudriavzevii FM1122 IFO 1802T MATα hoΔ::natMX ura3Δ0 This study S. kudriavzevii FM1141 IFO 1802T MATα hoΔ::natMX ura3Δ0 trp1Δ::ScerURA3+ This study S. kudriavzevii FM1388 IFO 1802T MATα hoΔ::natMX ura3Δ0 his3Δ0 This study S. kudriavzevii JRY9185 IFO 1802T MATa hoΔ::natMX ura3Δ0 This study S. kudriavzevii JRY9186 IFO 1802T MATα hoΔ::natMX trp1Δ0 This study S. kudriavzevii JRY9187 IFO 1802T MATa hoΔ::natMX trp1Δ0 ura3Δ0 This study S. kudriavzevii JRY9188 IFO 1802T MATα hoΔ::natMX trp1Δ0 ura3Δ0 This study S. kudriavzevii FM1109 ZP 591 MATa hoΔ::kanMX Hittinger et al. 2010 S. kudriavzevii FM1110 ZP 591 MATα hoΔ::kanMX Hittinger et al. 2010 S. kudriavzevii FM1071 ZP 591 MATa/MATα Hittinger et al. 2010 S. kudriavzevii FM1158 ZP 591 MATa/MATα This study S. kudriavzevii FM1400 ZP 591 MATa/MATα hoΔ::kanMX/hoΔ::kanMX This study S. kudriavzevii FM1340 ZP 591 MATa hoΔ::natMX ura3Δ0 Hittinger et al. 2010 S. kudriavzevii FM1123 ZP 591 MATa hoΔ::kanMX ura3Δ0 Hittinger et al. 2010 S. kudriavzevii FM1192 ZP 591 MATα hoΔ::kanMX ura3Δ0 This study S. kudriavzevii FM1194 ZP 591 MATa hoΔ::kanMX trp1Δ0 This study S. kudriavzevii FM1131 ZP 591 MATα hoΔ::kanMX trp1Δ0 Hittinger et al. 2010 S. kudriavzevii FM1183 ZP 591 MATa hoΔ::kanMX ura3Δ0 trp1Δ0 Hittinger et al. 2010 S. kudriavzevii FM1193 ZP 591 MATα hoΔ::kanMX ura3Δ0 trp1Δ0 This study S. kudriavzevii FM1389 ZP 591 MATa hoΔ::kanMX ura3Δ0 his3Δ0 This study S. bayanus JRY9189 CBS 7001 MATa hoΔ::NatMX This study S. bayanus JRY9190 CBS 7001 MATα hoΔ::NatMX This study S. bayanus JRY8149 CBS 7001 MATa hoΔ::NatMX his3 lys2 ura3 Gallagher et al. 2009 S. bayanus JRY8150 CBS 7001 MATα hoΔ::NatMX his3 lys2 ura3 Gallagher et al. 2009 S. bayanus JRY8153 CBS 7001 MATa hoΔ::NatMX his3 lys2 trp ura3 Gallagher et al. 2009 S. bayanus JRY8154 CBS 7001 MATα hoΔ::NatMX his3 lys2 trp ura3 Gallagher et al. 2009 S. bayanus JRY8147 CBS 7001 MATa hoΔ::NatMX ade2 his3 lys2 ura3 Gallagher et al. 2009 S. bayanus JRY8148 CBS 7001 MATα hoΔ::NatMX ade2 his3 lys2 ura3 Gallagher et al. 2009 S. bayanus JRY9191 CBS 7001 MATa hoΔ::NatMX his3 ura3 This study S. bayanus JRY9040 CBS 7001 MATa hoΔ::NatMX lys2 ura3 Zill et al. 2010 S. bayanus JRY9192 CBS 7001 MATa hoΔ::NatMX ade2 ura3 This study S. bayanus JRY9193 CBS 7001 MATα hoΔ::NatMX ade2 ura3 This study S. bayanus JRY9194 CBS 7001 MATa hoΔ::loxP his3 lys2 ura3 This study S. bayanus JRY9195 CBS 7001 MATα hoΔ::loxP his3 lys2 ura3 This study All strains are available upon request from C. T. Hittinger.
Supporting Information for Scannell et al., 2011
Files in this Data Supplement:
- Supporting Information - Figure S1, Files S1 and S2, and Tables S1-S3 (PDF, 756 KB)
- Figure S1 - Multiple sequence alignment of centromeres from (A) S. bayanus, (B) S. mikatae, and S. kudriavzevii (C) IFO 1802T and (D) ZP 591 (PDF, 588 KB)
- Table S2 - YGOB-HMM families detected in representative strains of five Saccharomyces species (PDF, 52 KB)
- File S1 - Likelihood-ratio tests for variation in selection pressure along the branches of the Saccharomyces sensu stricto phylogeny in 5,152 orthologs (Microsoft Excel, .xls, 2.7 MB)
- File S2 - Complete lists of candidate gene gains and losses detected by computational screens in five Saccharomyces species (Microsoft Excel, .xls, 48 KB)
- Table S1 - Genes orthologous among representative strains of five Saccharomyces sensu stricto yeast species (Microsoft Excel, .xls, 2.9 MB)
- Table S3 - tRNA gene content in representative strains of five Saccharomyces species as detected by tRNAScan-SE (Microsoft Excel, .xls, 24 KB)
