担当区分：筆頭著者,　責任著者   記述言語：英語   掲載種別：研究論文（学術雑誌）

Most sexually reproducing organisms have the ability to recognize individuals of the same species. In ascomycete fungi including yeasts, mating between cells of opposite mating type depends on the molecular recognition of two peptidyl mating pheromones by their corresponding G-protein coupled receptors (GPCRs). Although such pheromone/receptor systems are likely to function in both mate choice and prezygotic isolation, very few studies have focused on the stringency of pheromone receptors. The fission yeast Schizosaccharomyces pombe has two mating types, Plus (P) and Minus (M). Here, we investigated the stringency of the two GPCRs, Mam2 and Map3, for their respective pheromones, P-factor and M-factor, in fission yeast. First, we switched GPCRs between S. pombe and the closely related species Schizosaccharomyces octosporus, which showed that SoMam2 (Mam2 of S. octosporus) is partially functional in S. pombe, whereas SoMap3 (Map3 of S. octosporus) is not interchangeable. Next, we swapped individual domains of Mam2 and Map3 with the respective domains in SoMam2 and SoMap3, which revealed differences between the receptors both in the intracellular regions that regulate the downstream signaling of pheromones and in the activation by the pheromone. In particular, we demonstrated that two amino acid residues of Map3, F214 and F215, are key residues important for discrimination of closely related M-factors. Thus, the differences in these two GPCRs might reflect the significantly distinct stringency/flexibility of their respective pheromone/receptor systems; nevertheless, species-specific pheromone recognition remains incomplete.

DOI： 10.1093/genetics/iyab150

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担当区分：筆頭著者,　責任著者   記述言語：英語   掲載種別：研究論文（学術雑誌）

The fission yeast Schizosaccharomyces japonicus, comprising S. japonicus var. japonicus and S. japonicus var. versatilis varieties, has unique characteristics such as striking hyphal growth not seen in other Schizosaccharomyces species; however, information on its diversity and evolution, in particular mating and sporulation, remains limited. Here we compared the growth and mating phenotypes of 17 wild strains of S. japonicus, including eight S. japonicus var. japonicus strains newly isolated from an insect (Drosophila). Unlike existing wild strains isolated from fruits/plants, the strains isolated from Drosophila sporulated at high frequency even under nitrogen-abundant conditions. In addition, one of the strains from Drosophila was stained by iodine vapor, although the type strain of S. japonicus var. japonicus is not stained. Sequence analysis further showed that the nucleotide and amino acid sequences of pheromone-related genes have diversified among the eight strains from Drosophila, suggesting crossing between S. japonicus cells of different genetic backgrounds occurs frequently in this insect. Much of yeast ecology remains unclear, but our findings suggest that insects such as Drosophila might be a good niche for mating and sporulation, and will provide a basis for the understanding of sporulation mechanisms via signal transduction, as well as the ecology and evolution of yeast.

DOI： 10.3390/jof7050350

Kyutacar

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担当区分：筆頭著者   記述言語：英語   掲載種別：研究論文（学術雑誌）

Horizontal gene transfer, a process through which an organism acquires genes from other organisms, is a rare evolutionary event in yeasts. Artificial random gene transfer can emerge as a valuable tool in yeast bioengineering to investigate the background of complex phenotypes, such as heat tolerance. In this study, a cDNA library was constructed from the mRNA of a methylotrophic yeast, Ogataea polymorpha, and then introduced into Saccharomyces cerevisiae. Ogataea polymorpha was selected because it is one of the most heat-tolerant species among yeasts. Screening of S. cere-visiae populations expressing O. polymorpha genes at high temperatures identified 59 O. polymorpha genes that contribute to heat tolerance. Gene enrichment analysis indicated that certain S. cerevisiae functions, including protein synthesis, were highly temperature-sensitive. Additionally, the results confirmed that heat tolerance in yeast is a complex phenotype dependent on multiple quantitative loci. Random gene transfer would be a useful tool for future bioengineering studies on yeasts.

DOI： 10.3390/jof7040302

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担当区分：筆頭著者,　責任著者   記述言語：英語   掲載種別：記事・総説・解説・論説等（学術雑誌）

In fungi, sexual reproduction primarily depends on the interaction between peptide pheromones and their receptors. Most ascomycete fungi produce two classes of peptide mating pheromones, a simple peptide and a modified peptide. These peptides are recognized by their corresponding receptors on the surface of cells of the opposite mating type to induce the mating reaction. Pheromone diversification may be associated with reproductive isolation, which restricts gene flow among populations; thus, it remains unclear how pheromones diversify without loss of successful mating. Here, I provide a brief review of recent findings on the ‘asymmetric’ diversification of peptide pheromones in the fission yeast Schizosaccharomyces pombe, and discuss evolution of the mating pheromones in fission yeast.

DOI： 10.1007/s00294-019-00968-w

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担当区分：筆頭著者   記述言語：英語   掲載種別：研究論文（学術雑誌）

Background: Expression of d-xylose isomerase having high catalytic activity in Saccharomyces cerevisiae (S. cerevisiae) is a prerequisite for efficient and economical production of bioethanol from cellulosic biomass. Although previous studies demonstrated functional expression of several xylose isomerases (XI) in S. cerevisiae, identification of XIs having higher catalytic activity is needed. Here, we report a new strategy to improve xylose fermentation in the S. cerevisiae strain IR-2 that involves an evolutionary engineering to select top-performing XIs from eight previously reported XIs derived from various species. Results: Eight XI genes shown to have good expression in S. cerevisiae were introduced into the strain IR-2 having a deletion of GRE3 and XKS1 overexpression that allows use of d-xylose as a carbon source. Each transformant was evaluated under aerobic and micro-aerobic culture conditions. The strain expressing XI from Lachnoclostridium phytofermentans ISDg (LpXI) had the highest d-xylose consumption rate after 72 h of micro-aerobic fermentation on d-glucose and d-xylose mixed medium. To enhance LpXI catalytic activity, we performed random mutagenesis using error-prone polymerase chain reaction (PCR), which yielded two LpXI candidates, SS82 and SS92, that showed markedly improved fermentation performance. The LpXI genes in these clones carried either T63I or V162A/N303T point mutations. The SS120 strain expressing LpXI with the double mutation of T63I/V162A assimilated nearly 85 g/L d-glucose and 35 g/L d-xylose to produce 53.3 g/L ethanol in 72 h with an ethanol yield of approximately 0.44 (g/g-input sugars). An in vitro enzyme assay showed that, compared to wild-type, the LpXI double mutant in SS120 had a considerably higher V max (0.107 μmol/mg protein/min) and lower K m (37.1 mM). Conclusions: This study demonstrated that LpXI has the highest d-xylose consumption rate among the XIs expressed in IR-2 under micro-aerobic co-fermentation conditions. A combination of novel mutations (T63I and V162A) significantly improved the enzymatic activity of LpXI, indicating that LpXI-T63I/V162A would be a potential construct for highly efficient production of cellulosic ethanol.

DOI： 10.1186/s13068-019-1474-z

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担当区分：筆頭著者,　責任著者   記述言語：英語   掲載種別：研究論文（学術雑誌）

In the fission yeast Schizosaccharomyces pombe, the mating reaction is controlled by two mating pheromones, M-factor and P-factor, secreted by M- and P-type cells, respectively. M-factor is a C-terminally farnesylated lipid peptide, whereas P-factor is a simple peptide. To examine whether this chemical asymmetry in the two pheromones is essential for conjugation, we constructed a mating system in which either pheromone can stimulate both M- and P-cells, and examined whether the resulting autocrine strains can mate. Autocrine M-cells responding to M-factor successfully mated with P-factor-lacking P-cells, indicating that P-factor is not essential for conjugation; by contrast, autocrine P-cells responding to P-factor were unable to mate with M-factor-lacking M-cells. The sterility of the autocrine P-cells was completely restored by expressing the M-factor receptor. These observations indicate that the different chemical characteristics of the two types of pheromone, a lipid and a simple peptide, are not essential; however, a lipid peptide might be required for successful mating. Our findings allow us to propose a model of the differential roles of M-factor and P-factor in conjugation of S. pombe.

DOI： 10.1242/jcs.230722

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担当区分：筆頭著者,　責任著者   記述言語：英語   掲載種別：記事・総説・解説・論説等（学術雑誌）

Many species, from mammals to microorganisms, release sex pheromones to attract a potential partner of the opposite sex. The combination of a pheromone and its corresponding receptor determines the species-specific ability of males and females to recognize each other, and therefore causes reproductive isolation. This barrier, which has arisen to restrict gene flow between mating pairs, might facilitate reproductive isolation leading to incipient speciation, but how do new combinations of pheromone and receptor evolve? Our recent study demonstrated an “asymmetric” pheromone recognition system in the fission yeast Schizosaccharomyces pombe: among the two phero-mone/receptor pairs in this yeast, recognition between one pair is stringent, while that between the other pair is rather relaxed. We speculate that the asymmetric properties of these pheromone recognition systems are beneficial for gradual evolution resulting in reproductive isolation in yeasts.

DOI： 10.15698/mic2019.04.675

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担当区分：筆頭著者,　責任著者   記述言語：英語   掲載種別：研究論文（学術雑誌）

In fungi, mating between partners depends on the molecular recognition of two peptidyl mating pheromones by their respective receptors. The fission yeast Schizosaccharomyces pombe (Sp) has two mating types, Plus (P) and Minus (M). The mating pheromones P-factor and M-factor, secreted by P and M cells, are recognized by the receptors mating type auxiliary minus 2 (Mam2) and mating type auxiliary plus 3 (Map3), respectively. Our recent study demonstrated that a few mutations in both M-factor and Map3 can trigger reproductive isolation in S. pombe. Here, we explored the mechanism underlying reproductive isolation through genetic changes of pheromones/receptors in nature. We investigated the diversity of genes encoding the pheromones and their receptor in 150 wild S. pombe strains. Whereas the amino acid sequences of M-factor and Map3 were completely conserved, those of P-factor and Mam2 were very diverse. In addition, the P-factor gene contained varying numbers of tandem repeats of P-factor (4-8 repeats). By exploring the recognition specificity of pheromones between S. pombe and its close relative Schizosaccharomyces octosporus (So), we found that So-M-factor did not have an effect on S. pombe P cells, but So-P-factor had a partial effect on S. pombe M cells. Thus, recognition of M-factor seems to be stringent, whereas that of P-factor is relatively relaxed. We speculate that asymmetric diversification of the two pheromones might be facilitated by the distinctly different specificities of the two receptors. Our findings suggest that M-factor communication plays an important role in defining the species, whereas P-factor communication is able to undergo a certain degree of flexible adaptation-perhaps as a first step toward prezygotic isolation in S. pombe.

DOI： 10.1371/journal.pbio.3000101

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担当区分：筆頭著者   記述言語：英語   掲載種別：研究論文（学術雑誌）

DOI： 10.1073/pnas.1501661112

記述言語：英語   掲載種別：研究論文（学術雑誌）

Saccharomyces cerevisiae is often cultivated in complex media for applications in food and other biochemical production. However, 13C-metabolic flux analysis (13C-MFA) has been conducted for S. cerevisiae cultivated in synthetic media, resulting in a limited understanding of the metabolic flux distributions under the complex media. In this study, 13C-MFA was applied to S. cerevisiae cultivated in complex media to quantify the metabolic fluxes in the central metabolic network. S. cerevisiae was cultivated in a synthetic dextrose (SD) medium supplemented with 20 amino acids (SD + AA) and yeast extract peptone dextrose (YPD) medium. The results revealed that glutamic acid, glutamine, aspartic acid, and asparagine are incorporated into the TCA cycle as carbon sources in parallel with glucose consumption. Based on these findings, we successfully conducted 13C-MFA of S. cerevisiae cultivated in SD + AA and YPD media using parallel labeling and measured amino acid uptake rates. Furthermore, we applied the developed approach to 13C-MFA of yeast cultivated in malt extract medium. The analysis revealed that the metabolic flux through the anaplerotic and oxidative pentose phosphate pathways was lower in complex media than in synthetic media. Owing to the reduced carbon loss by the branching pathways, carbon flow toward ethanol production via glycolysis could be elevated. 13C-MFA of S. cerevisiae cultured in complex media provides valuable insights for metabolic engineering and process optimization in industrial yeast fermentation.

DOI： 10.1016/j.mec.2025.e00260

Kyutacar

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記述言語：英語   掲載種別：研究論文（学術雑誌）

This study introduces the ΔΔG method, a novel approach to analyzing metabolic regulation using relative quantification metabolome data. The method calculates shifts in the Gibbs free energy change (ΔG) in two different metabolic states. Subsequently, key reactions controlling the metabolic flux can be identified by comparing the ΔΔG values to the reaction rates. Two case studies demonstrated the applicability of this method. First, a metabolome data set was obtained from the wild-type and single-gene-deletion mutant strains of Saccharomyces cerevisiae. The ΔΔG values of the glycolytic reactions were calculated between those of the wild-type and each mutant strain. A positive correlation was observed between the ΔΔG values of phosphofructokinase (PFK) and the approximate glycolytic flux levels. These results suggested that PFK regulates glycolytic flux. Moreover, a comparison between S. cerevisiae (Crabtree-positive yeast) and Kluyveromyces marxianus (Crabtree-negative yeast) revealed that S. cerevisiae primarily regulates glycolysis through PFK, whereas K. marxianus employs a more distributed control. The ΔΔG method provides insights into metabolic regulation that are not apparent from metabolite profiles alone and is applicable to various biological systems, particularly for analyzing glycolysis. Furthermore, the simplicity of this method makes it a valuable tool for metabolic engineering and medical research.

DOI： 10.1021/acs.analchem.4c04480

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記述言語：英語   掲載種別：研究論文（学術雑誌）

Japanese sake is fermented with specific strains of budding yeast Saccharomyces cerevisiae. Sake yeasts can allow the ethanol concentration of sake to exceed 20 % without distillation. While the genetic mutations responsible for these exceptional properties have been investigated, the underlying metabolism has not been fully explored. It is because yeast cells cultured in sake mash are difficult to collect for metabolome analysis. This study aimed to clarify the metabolic differences of K701 sake yeast and the X2180 diploid laboratory strain when cultured under sake fermentation conditions. To find an alternative medium that mimics sake fermentation and is applicable to measurements of intracellular metabolome, we compared three liquid media, including SD2 medium (synthetic dextrose medium containing 2 % glucose), SD20 medium (synthetic dextrose medium containing 20 % glucose and 1.8 % lactic acid) and pseudo-sake medium (a supernatant of saccharified rice supplemented with 1.8 % lactic acid). Culture profile data demonstrated that the pseudo-sake medium successfully reproduced the metabolic traits of K701 observed in sake mash. Targeted metabolome analysis of yeast cells cultured in the pseudo-sake medium revealed that levels of glycolytic metabolites, such as glucose-6-phosphate (G6P), fructose-6-phosphate (F6P), and fructose-1,6-bisphosphate (FBP), were significantly higher with K701. Based on metabolite concentration data, we inferred that K701 cells had a higher ATP regeneration rate. Calculation of differential Gibbs free energy changes revealed that the glucokinase reaction was upregulated in K701. The present study has, for the first time, revealed the metabolism of K701 sake yeast responsible for its exceptional fermentation ability under sake fermentation conditions.

DOI： 10.1016/j.jbiosc.2025.04.001

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記述言語：英語   掲載種別：研究論文（学術雑誌）

Budding yeast, Saccharomyces cerevisiae, adapts to low-temperature stress by altering the amounts and proportions of phospholipids, as well as the structures of acyl chains. To better understand this process, a data-independent acquisition-based lipidomics using liquid chromatography–quadrupole time-of-flight mass spectrometry method was developed to quantify acyl chain isomers in glycerolipids and phospholipids. This method distinguished lipid molecular species, such as phosphatidylcholine (PC) 16:1_18:0 and PC16:0_18:1, at the level of acyl chain isomers. These species were previously identified only at the total acyl chain level as PC 34:1 using the conventional data-dependent acquisition (DDA) method. Using this approach, 145 diacyl lipid molecular species were identified in S. cerevisiae at 30 °C, compared to only 101 identified using the conventional DDA method. Analysis of S. cerevisiae at 10 °C revealed 121 phospholipid and diacylglycerol (DG) molecular species and 260 triacylglycerol (TG) features as well as other 51 sphingolipids and sterol lipids. The results demonstrated unique increases in phosphatidylinositol (PI), phosphatidylethanolamine (PE), monomethyl (MM) PE, and TG containing both 16:1 and medium-chain fatty acids (MCFAs). The knockout strains ole1Δ and slc1Δ, lacking the desaturase that produces 16:1 and the acyltransferase favoring MCFAs, respectively, exhibited growth defects exclusively while growing at 10 °C. These findings suggest that S. cerevisiae regulates its lipid profiles to address low-temperature stress.

DOI： 10.1016/j.jbiosc.2025.03.004

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記述言語：英語   掲載種別：研究論文（学術雑誌）

Overexpression of proteins by introducing a DNA vector is among the most important tools for the metabolic engineering of microorganisms such as Escherichia coli. Protein overexpression imposes a burden on metabolism because metabolic pathways must supply building blocks for protein and DNA synthesis. Different E. coli strains have distinct metabolic capacities. In this study, two proteins were overexpressed in four E. coli strains (MG1655(DE3), W3110(DE3), BL21star(DE3), and Rosetta(DE3)), and their effects on metabolic burden were investigated. Metabolomic analysis showed that E. coli strains overexpressing green fluorescent protein had decreased levels of several metabolites, with a positive correlation between the number of reduced metabolites and green fluorescent protein expression levels. Moreover, nucleic acid-related metabolites decreased, indicating a metabolic burden in the E. coli strains, and the growth rate and protein expression levels were improved by supplementation with the five nucleosides. In contrast, two strains overexpressing delta rhodopsin, a microbial membrane rhodopsin from Haloterrigena turkmenica, led to a metabolic burden and decrease in the amino acids Ala, Val, Leu, Ile, Thr, Phe, Asp, and Trp, which are the most frequent amino acids in the delta rhodopsin protein sequence. The metabolic burden caused by protein overexpression was influenced by the metabolic capacity of the host strains and the sequences of the overexpressed proteins. Detailed characterization of the effects of protein expression on the metabolic state of engineered cells using metabolomics will provide insights into improving the production of target compounds.

DOI： 10.1016/j.jbiosc.2023.12.003

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記述言語：英語   掲載種別：研究論文（学術雑誌）

Saccharomyces cerevisiae is a promising host for the bioproduction of higher alcohols, such as 2,3-butanediol (2,3-BDO). Metabolically engineered S. cerevisiae strains that produce 2,3-BDO via glycolysis have been constructed. However, the specific 2,3-BDO production rates of engineered strains must be improved. To identify approaches to improving the 2,3-BDO production rate, we investigated the factors contributing to higher ethanol production rates in certain industrial strains of S. cerevisiae compared to laboratory strains. Sequence analysis of 11 industrial strains revealed the accumulation of many nonsynonymous substitutions in RIM15, a negative regulator of high fermentation capability. Comparative metabolome analysis suggested a positive correlation between the rate of ethanol production and the activity of the pyruvate-consuming pathway. Based on these findings, RIM15 was deleted, and the pyruvate-consuming pathway was activated in YHI030, a metabolically engineered S. cerevisiae strain that produces 2,3-BDO. The titer, specific production rate, and yield of 2,3-BDO in the test tube-scale culture using the YMS106 strain reached 66.4 ± 4.4 mM, 1.17 ± 0.017 mmol (g dry cell weight h)−1, and 0.70 ± 0.03 mol (mol glucose consumed)−1. These values were 2.14-, 2.92-, and 1.81-fold higher than those of the vector control, respectively. These results suggest that bioalcohol production via glycolysis can be enhanced in a metabolically engineered S. cerevisiae strain by deleting RIM15 and activating the pyruvate-consuming pathway.

DOI： 10.3390/ijms242216378

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記述言語：英語   掲載種別：研究論文（学術雑誌）

A light-driven ATP regeneration system using rhodopsin has been utilized as a method to improve the production of useful substances by microorganisms. To enable the industrial use of this system, the proton pumping rate of rhodopsin needs to be enhanced. Nonetheless, a method for this enhancement has not been established. In this study, we attempted to develop an evolutionary engineering method to improve the proton-pumping activity of rhodopsins. We first introduced random mutations into delta-rhodopsin (dR) from Haloterrigena turkmenica using error-prone PCR to generate approximately 7000 Escherichia coli strains carrying the mutant dR genes. Rhodopsin-expressing E. coli with enhanced proton pumping activity have significantly increased survival rates in prolonged saline water. Considering this, we enriched the mutant E. coli cells with higher proton pumping rates by selecting populations able to survive starvation under 50 μmol m−2 s−1 at 37 °C. As a result, we successfully identified two strains, in which proton pumping activity was enhanced two-fold by heterologous expression in E. coli in comparison to wild-type strains. The combined approach of survival testing using saline water and evolutionary engineering methods used in this study will contribute greatly to the discovery of a novel rhodopsin with improved proton pumping activity. This will facilitate the utilization of rhodopsin in industrial applications.

DOI： 10.1016/j.jbiosc.2022.08.006

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記述言語：英語   掲載種別：研究論文（学術雑誌）

Saccharomyces cerevisiae has been widely used in bioproduction. To produce a target product other than ethanol, ethanol production must be decreased to enhance target production. An ethanol non-producing yeast strain was previously constructed by knocking out pyruvate decarboxylase (PDC) genes in the ethanol synthetic pathway. However, glucose uptake by the ethanol-non-producing yeast strain was significantly decreased. In this study, dead Cas9 (dCas9) was used to reduce ethanol synthesis during 2,3-butanediol production without reduction of glucose. The binding site of guide RNA used to effectively suppress PDC1 promoter-driven red fluorescent protein expression by dCas9 was identified and applied to control PDC1 expression. The production of 2,3-butanediol rather than ethanol was improved in repetitive test tube culture. Additionally, ethanol production was decreased and 2,3-butanediol production was increased in the strain expressing dCas9 targeting the PDC1 promoter in the third round of cultivation, compared with the control strain.

DOI： 10.1016/j.jbiosc.2021.12.007

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記述言語：英語   掲載種別：研究論文（学術雑誌）

Background: Various industrial Saccharomyces cerevisiae strains are used for specific processes, such as sake, wine brewing and bread making. Understanding mechanisms underlying the fermentation performance of these strains would be useful for further engineering of the S. cerevisiae metabolism. However, the relationship between the fermentation performance, intra-cellular metabolic states, and other phenotypic characteristics of industrial yeasts is still unclear. In this study, 13C-metabolic flux analysis of four diploid yeast strains—laboratory, sake, bread, and wine yeasts—was conducted. Results: While the Crabtree effect was observed for all strains, the metabolic flux level of glycolysis was elevated in bread and sake yeast. Furthermore, increased flux levels of the TCA cycle were commonly observed in the three industrial strains. The specific rates of CO2 production, net ATP regeneration, and metabolic heat generation estimated from the metabolic flux distribution were two to three times greater than those of the laboratory strain. The elevation in metabolic heat generation was correlated with the tolerance to low-temperature stress. Conclusion: These results indicate that the metabolic flux distribution of sake and bread yeast strains contributes to faster production of ethanol and CO2. It is also suggested that the generation of metabolic heat is preferable under the actual industrial fermentation conditions.

DOI： 10.1002/biot.202000438

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記述言語：英語   掲載種別：研究論文（学術雑誌）

We present the draft genome sequence of an isogenic haploid strain, IR-2idA30(MATa), established from Saccharomyces cerevisiae IR-2. Assembly of long reads and previously obtained contigs from the genome of diploid IR-2 resulted in 50 contigs, and the variations and sequencing errors were corrected by short reads.

DOI： 10.1128/MRA.00018-19

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