Genomic Adaptations of Saccharomyces Genus to Wine Niche

García‐Ríos, Estéfani; Guillamón, José Manuel

doi:10.3390/microorganisms10091811

Cited by 11 publications

(8 citation statements)

References 168 publications

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“…S. cerevisiae becomes the dominant yeast during wine fermentations, as it can rapidly complete wine fermentations by consuming almost all fermentable sugars from the grape must by its own. This ability is result from the adaptation of S. cerevisiae to the challenging conditions of wine fermentations (Marsit & Dequin, 2015 ; García‐Ríos & Guillamón, 2022 ), due to several genomic features that wine strains acquired over their domestication process (Belda et al , 2019 ). However, we observed that some combinations of yeast strains caused a negative effect on S. cerevisiae function (Fig 4B ; Appendix Figs S10 and S11 ).…”

Section: Discussionmentioning

confidence: 99%

Predictability of the community‐function landscape in wine yeast ecosystems

Ruiz,

de Celis,

Diaz‐Colunga

et al. 2023

Molecular Systems Biology

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Predictively linking taxonomic composition and quantitative ecosystem functions is a major aspiration in microbial ecology, which must be resolved if we wish to engineer microbial consortia. Here, we have addressed this open question for an ecological function of major biotechnological relevance: alcoholic fermentation in wine yeast communities. By exhaustively phenotyping an extensive collection of naturally occurring wine yeast strains, we find that most ecologically and industrially relevant traits exhibit phylogenetic signal, allowing functional traits in wine yeast communities to be predicted from taxonomy. Furthermore, we demonstrate that the quantitative contributions of individual wine yeast strains to the function of complex communities followed simple quantitative rules. These regularities can be integrated to quantitatively predict the function of newly assembled consortia. Besides addressing theoretical questions in functional ecology, our results and methodologies can provide a blueprint for rationally managing microbial processes of biotechnological relevance.

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Section: Discussionmentioning

confidence: 99%

Predictability of the community‐function landscape in wine yeast ecosystems

Ruiz,

de Celis,

Diaz‐Colunga

et al. 2023

Molecular Systems Biology

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“…Previous comparative studies of mitochondrial genomes have indicated that genome arrangements have likely played a strong role in the evolution of crabs ( Wang et al 2021 ; Zhang et al 2021 ; Sun et al 2022 ), and gene arrangement is known to be essential for emergent properties of gene products in development such as HOX genes ( Sun and Patel 2019 ) and in cancer ( Heng and Heng 2021 , 2022 ). Evidence for the extent to which arrangement of nuclear genes is in general involved in adaptative evolution does not yet exist for crabs, but has been observed in other taxa including bacteria ( Kang et al 2022 ), fungal pathogens ( Gourlie et al 2022 ; Ma et al 2022 ), and domesticated yeast ( Garcia-Rios and Guillamon 2022 ), and may represent a generalized aspect of genome evolution during adaptive radiation ( Cao et al 2022 ; Wang et al . 2022 ).…”

Section: Introductionmentioning

confidence: 99%

Genome assemblies of two species of porcelain crab, Petrolisthes cinctipes and Petrolisthes manimaculis (Anomura: Porcellanidae)

Angst,

Dexter,

Stillman

2023

G3: Genes, Genomes, Genetics

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Crabs are a large subtaxon of the Arthropoda, the most diverse and species-rich metazoan group. Several outstanding questions remain regarding crab diversification, including about the genomic capacitors of physiological and morphological adaptation, that cannot be answered with available genomic resources. Physiologically and ecologically diverse Anomuran porcelain crabs offer a valuable model for investigating these questions and hence genomic resources of these crabs would be particularly useful. Here, we present the first two genome assemblies of congeneric and sympatric Anomuran porcelain crabs, Petrolisthes cinctipes and Petrolisthes manimaculis from different microhabitats. Pacific Biosciences high-fidelity sequencing led to genome assemblies of 1.5 and 0.9 Gb, with N50s of 706.7 and 218.9 Kb, respectively. Their assembly length difference can largely be attributed to the different levels of interspersed repeats in their assemblies: The larger genome of P. cinctipes has more repeats (1.12 Gb) than the smaller genome of P. manimaculis (0.54 Gb). For obtaining high-quality annotations of 44,543 and 40,315 protein-coding genes in P. cinctipes and P. manimaculis, respectively, we used RNA-seq as part of a larger annotation pipeline. Contrarily to the large-scale differences in repeat content, divergence levels between the two species as estimated from orthologous protein-coding genes are moderate. These two high-quality genome assemblies allow future studies to examine the role of environmental regulation of gene expression in the two focal species to better understand physiological response to climate change, and provide the foundation for studies in fine-scale genome evolution and diversification of crabs.

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“…Purifying selection is observed in anthropized strains, with fewer genes showing copy number alterations as well as supplemental genes. However, important genes typically associated with anthropization in S. cerevisiae , such as those related to the assimilation of alternative carbon sources (Peris et al, 2023) or nitrogen metabolism (García-Ríos & Guillamón, 2022), exhibit differences in the studied anthropized strains of L. thermotolerans , particularly in homologous genes to DAL5 and MAL31 .…”

Section: Discussionmentioning

confidence: 99%

Whole-genome sequencing and phenotyping reveal specific adaptations ofLachancea thermotoleransto the winemaking environment

Vicente,

Friedrich,

Schacherer

et al. 2024

Preprint

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Adaptation to the environment plays an essential role in yeast evolution as a consequence of selective pressures.Lachancea thermotolerans, a yeast related to the fermentative process and one of the current trends in wine technology research, has undergone an anthropization process that has led to a strong differentiation both from a genomic and phenomic perspective. Using whole-genome sequencing, we have investigated the genomic diversity of 145L. thermotoleransstrains, identifying six well-defined groups primarily delineated by their ecological origin and exhibiting high levels of genetic diversity. Anthropized strains showed lower genetic diversity due to the purifying selection imposed by the winemaking environment. Strong evidence of anthropization and adaptation to the wine environment through modification of gene content was also found. Differences in genes involved in the assimilation of alternative carbon and nitrogen sources, such as theMAL1andDAL5genes, which confer greater fitness in the winemaking environment, were observed. Additionally, we found that phenotypic traits considered domestication hallmarks are present in anthropized strains. Among these, increased fitness in the presence of ethanol and sulphites, assimilation of non-fermentable carbon sources such as glycerol, and lower levels of residual fructose under fermentative conditions highlight. We hypothesize that lactic acid production by wine-related strains is an anthropization signature consequence of the adaption of early Crabtree-positive yeasts to the fermentative environment. Overall, the results of this work provide valuable insight into the anthropization process inL. thermotoleransand demonstrate how fermentation environments give rise to similar adaptations in different yeast species.

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Genomic Adaptations of Saccharomyces Genus to Wine Niche

Cited by 11 publications

References 168 publications

Predictability of the community‐function landscape in wine yeast ecosystems

Predictability of the community‐function landscape in wine yeast ecosystems

Genome assemblies of two species of porcelain crab, Petrolisthes cinctipes and Petrolisthes manimaculis (Anomura: Porcellanidae)

Whole-genome sequencing and phenotyping reveal specific adaptations ofLachancea thermotoleransto the winemaking environment

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