Draft Genome Sequence of Saccharomyces cerevisiae Barra Grande (BG-1), a Brazilian Industrial Bioethanol-Producing Strain

Coutouné, Natalia; Mulato, Aline Tieppo Nogueira; Riaño‐Pachón, Diego Mauricio; Oliveira, Juliana Velasco de Castro

doi:10.1128/genomea.00111-17

Cited by 10 publications

(6 citation statements)

References 12 publications

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“…Little is known about the remarkable genetic features that allow these strains to withstand such pressures while maintaining an excellent fermentation performance. The elucidation of the genomic sequences from the bioethanol strains CAT-1, BG-1, and PE-2 revealed highly heterozygous diploid genomes carrying a rich source of adaptive genetic diversity (Argueso et al, 2009;Babrzadeh et al, 2012;Coutoune et al, 2017). Our H3 and H4 assemblies corroborated that notion, showing that two haploid genomes segregating via meiosis from the same diploid cell can be highly polymorphic.…”

Section: Genetic Signatures Of Bioethanol Yeasts and Adaptation To Industrial Fermentationsupporting

confidence: 73%

“…For more-comprehensive comparative genomic analysis, we focused on 44 bioethanol and cachaça strains (hereinafter referred to as the Brazilian bioethanol group; Supplementary Table 1). They correspond to isolates from ethanol plants, mostly located in the state of São Paulo, Brazil, and include the haploid genomes of H3, H4, JAY291 (Argueso et al, 2009), the diploid genome of BG-1 (Coutoune et al, 2017), five strains sequenced by Gallone et al (2016), plus 35 strains (mostly diploid genomes) from the 1,002 Yeast Genomes Project (Peter et al, 2018). For enrichment analysis of distinct genomic features (including genes and alleles) within those strains, a query specific for each feature was used to search by BLASTN against the genomes of the Brazilian bioethanol group (Supplementary Table 1) plus a dataset of 976 strains derived from the 1,002 Yeast Genomes Project (Peter et al, 2018).…”

Section: S Cerevisiae Strainsmentioning

confidence: 99%

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Comparative Genomics Supports That Brazilian Bioethanol Saccharomyces cerevisiae Comprise a Unified Group of Domesticated Strains Related to Cachaça Spirit Yeasts

et al. 2021

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Ethanol production from sugarcane is a key renewable fuel industry in Brazil. Major drivers of this alcoholic fermentation are Saccharomyces cerevisiae strains that originally were contaminants to the system and yet prevail in the industrial process. Here we present newly sequenced genomes (using Illumina short-read and PacBio long-read data) of two monosporic isolates (H3 and H4) of the S. cerevisiae PE-2, a predominant bioethanol strain in Brazil. The assembled genomes of H3 and H4, together with 42 draft genomes of sugarcane-fermenting (fuel ethanol plus cachaça) strains, were compared against those of the reference S288C and diverse S. cerevisiae. All genomes of bioethanol yeasts have amplified SNO2(3)/SNZ2(3) gene clusters for vitamin B1/B6 biosynthesis, and display ubiquitous presence of a particular family of SAM-dependent methyl transferases, rare in S. cerevisiae. Widespread amplifications of quinone oxidoreductases YCR102C/YLR460C/YNL134C, and the structural or punctual variations among aquaporins and components of the iron homeostasis system, likely represent adaptations to industrial fermentation. Interesting is the pervasive presence among the bioethanol/cachaça strains of a five-gene cluster (Region B) that is a known phylogenetic signature of European wine yeasts. Combining genomes of H3, H4, and 195 yeast strains, we comprehensively assessed whole-genome phylogeny of these taxa using an alignment-free approach. The 197-genome phylogeny substantiates that bioethanol yeasts are monophyletic and closely related to the cachaça and wine strains. Our results support the hypothesis that biofuel-producing yeasts in Brazil may have been co-opted from a pool of yeasts that were pre-adapted to alcoholic fermentation of sugarcane for the distillation of cachaça spirit, which historically is a much older industry than the large-scale fuel ethanol production.

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Section: Genetic Signatures Of Bioethanol Yeasts and Adaptation To Industrial Fermentationsupporting

confidence: 73%

Section: S Cerevisiae Strainsmentioning

confidence: 99%

Comparative Genomics Supports That Brazilian Bioethanol Saccharomyces cerevisiae Comprise a Unified Group of Domesticated Strains Related to Cachaça Spirit Yeasts

et al. 2021

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“…JAY270 is heterothallic (i.e., its meiotic spores are unable to switch mating type to self-mate and generate fully homozygous diploids), and it has a complex diploid genomic architecture, marked by abundant structural and single nucleotide polymorphisms between most pairs of homologous chromosomes (Argueso et al, 2009). This heterozygous genomic architecture is also a feature of other bioethanol strains (e.g., CAT-1, BG-1) that, like JAY270, were isolated as robust contaminants at sugarcane distilleries (Babrzadeh et al, 2012; Carvalho-Netto et al, 2013; Della-Bianca et al, 2013; Coutoune et al, 2017).…”

Section: Introductionmentioning

confidence: 83%

Controlled Reduction of Genomic Heterozygosity in an Industrial Yeast Strain Reveals Wide Cryptic Phenotypic Variation

2019

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Abundant genomic heterozygosity can be found in wild strains of the budding yeast Saccharomyces cerevisiae isolated from industrial and clinical environments. The extent to which heterozygosity influences the phenotypes of these isolates is not fully understood. One such case is the PE-2/JAY270 strain, a natural hybrid widely adopted by sugarcane bioethanol distilleries for its ability to thrive under harsh biotic and abiotic stresses during industrial scale fermentation, however, it is not known whether or how the heterozygous configuration of the JAY270 genome contributes to its many desirable traits. In this study, we took a step toward exploring this question by conducting an initial functional characterization of JAY270’s heteroalleles. We manipulated the abundance and distribution of heterozygous alleles through inbreeding and targeted uniparental disomy (UPD). Unique combinations of homozygous alleles in each inbred strain revealed wide phenotypic variation for at least two important industrial traits: Heat stress tolerance and competitive growth. Quantitative trait loci analyses allowed the identification of broad genomic regions where genetic polymorphisms potentially impacted these traits, and there was no overlap between the loci associated with each. In addition, we adapted an approach to induce bidirectional UPD of three targeted pairs of chromosomes (IV, XIV, and XV), while heterozygosity was maintained elsewhere in the genome. In most cases UPD led to detectable phenotypic alterations, often in opposite directions between the two homozygous haplotypes in each UPD pair. Our results showed that both widespread and regional homozygosity could uncover cryptic phenotypic variation supported by the heteroalleles residing in the JAY270 genome. Interestingly, we characterized multiple examples of inbred and UPD strains that displayed heat tolerance or competitive growth phenotypes that were superior to their heterozygous parent. However, we propose that homozygosity for those regions may be associated with a decrease in overall fitness in the complex and dynamic distillery environment, and that may have contributed to slowing down the erosion of heterozygosity from the JAY270 genome. This study also laid a foundation for approaches that can be expanded to the identification of specific alleles of interest for industrial applications in this and other hybrid yeast strains.

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“…Little is known about the remarkable genetic features that allow these strains to withstand such pressures while maintaining an excellent fermentation performance. The elucidation of the genomic sequences from the bioethanol strains CAT-1, BG-1, and PE-2 (including JAY291, and our H3 and H4 assemblies) revealed highly heterozygous diploid genomes carrying a rich source of adaptive genetic diversity (Argueso et al, 2009;Babrzadeh et al, 2012;Coutoune et al, 2017).…”

Section: Genetic Signatures Of Bioethanol Yeasts and Adaptation To Inmentioning

confidence: 93%

“…For more-comprehensive comparative genomic analysis, we focused on 44 bioethanol and cachaça strains (hereinafter referred to as the Brazilian bioethanol group; Supplementary Table 1 ). They correspond to isolates from ethanol plants, mostly located in the state of São Paulo, Brazil, and include the haploid genomes of H3, H4, JAY291 (Argueso et al, 2009), the diploid genome of BG-1 (Coutoune et al, 2017), five strains sequenced by Gallone et al (Gallone et al, 2016), plus 35 strains (mostly diploid genomes) from the 1,002 Yeast Genomes Project (Peter et al, 2018). For enrichment analysis of distinct genomic features (including genes and alleles) within those strains, a query specific for each feature was used to search by BLASTN against the genomes of the Brazilian bioethanol group ( Supplementary Table 1 ) plus a dataset of 976 strains derived from the 1,002 Yeast Genomes Project (Peter et al, 2018).…”

Section: Methodsmentioning

confidence: 99%

Comparative genomics supports that Brazilian bioethanolSaccharomyces cerevisiaecomprise a unified group of domesticated strains related to cachaça spirit yeasts

Jacobus

Stephens

Youssef

et al. 2020

Preprint

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Ethanol production from sugarcane is a key renewable fuel industry in Brazil. Major drivers of this alcoholic fermentation are Saccharomyces cerevisiae strains that originally were contaminants to the system and yet prevail in the industrial process. Here we present newly sequenced genomes (using Illumina short-read and PacBio long-read data) of two monosporic isolates (H3 and H4) of the S. cerevisiae PE-2, a predominant bioethanol strain in Brazil. The assembled genomes of H3 and H4, together with 42 draft genomes of sugarcane-fermenting (fuel ethanol plus cachaça) strains, were compared against those of the reference S288c and diverse S. cerevisiae. All genomes of bioethanol yeasts have amplified SNO2(3)/SNZ2(3) gene clusters for vitamin B1/B6 biosynthesis, and display ubiquitous presence of SAM-dependent methyl transferases, a gene family rare in S. cerevisiae. Widespread amplifications of quinone oxidoreductases YCR102C/YLR460C/YNL134C, and the structural or punctual variations among aquaporins and components of the iron homeostasis system, likely represent adaptations to industrial fermentation. Interesting is the pervasive presence among the bioethanol/cachaça strains of a five-gene cluster (Region B) that is a known phylogenetic signature of European wine yeasts. Combining genomes of H3, H4, and 195 yeast strains, we comprehensively assessed whole-genome phylogeny of these taxa using an alignment-free approach. The 197-genome phylogeny substantiates that bioethanol yeasts are monophyletic and closely related to the cachaça and wine strains. Our results support the hypothesis that biofuel-producing yeasts in Brazil may have been co-opted from a pool of yeasts that were pre-adapted to alcoholic fermentation of sugarcane for the distillation of cachaça spirit, which historically is a much older industry than the large-scale fuel ethanol production.

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Draft Genome Sequence of Saccharomyces cerevisiae Barra Grande (BG-1), a Brazilian Industrial Bioethanol-Producing Strain

Abstract: Here, we present the draft genome sequence of Saccharomyces cerevisiae BG-1, a Brazilian industrial strain widely used for bioethanol production from sugarcane. The 11.7-Mb genome sequence consists of 216 scaffolds and harbors 5,607 predicted protein-coding genes.

Cited by 10 publications

References 12 publications

Comparative Genomics Supports That Brazilian Bioethanol Saccharomyces cerevisiae Comprise a Unified Group of Domesticated Strains Related to Cachaça Spirit Yeasts

Comparative Genomics Supports That Brazilian Bioethanol Saccharomyces cerevisiae Comprise a Unified Group of Domesticated Strains Related to Cachaça Spirit Yeasts

Controlled Reduction of Genomic Heterozygosity in an Industrial Yeast Strain Reveals Wide Cryptic Phenotypic Variation

Comparative genomics supports that Brazilian bioethanolSaccharomyces cerevisiaecomprise a unified group of domesticated strains related to cachaça spirit yeasts

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