Ontology highlight
ABSTRACT:
PROVIDER: PRJNA787433 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR17177917_1.fastq.gz | Fastqsanger.gz | |||
| SRR17177917_2.fastq.gz | Fastqsanger.gz | |||
| SRR17177918_1.fastq.gz | Fastqsanger.gz | |||
| SRR17177918_2.fastq.gz | Fastqsanger.gz | |||
| SRR17177919_1.fastq.gz | Fastqsanger.gz |
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Project description:Wine biological aging is a wine making process used to produce specific beverages in several countries in Europe, including Spain, Italy, France, and Hungary. This process involves the formation of a velum at the surface of the wine. Here, we present the first large scale comparison of all European flor strains involved in this process. We inferred the population structure of these European flor strains from their microsatellite genotype diversity and analyzed their ploidy. We show that almost all of these flor strains belong to the same cluster and are diploid, except for a few Spanish strains. Comparison of the array hybridization profile of six flor strains originating from these four countries, with that of three wine strains did not reveal any large segmental amplification. Nonetheless, some genes, including YKL221W/MCH2 and YKL222C, were amplified in the genome of four out of six flor strains. Finally, we correlated ICR1 ncRNA and FLO11 polymorphisms with flor yeast population structure, and associate the presence of wild type ICR1 and a long Flo11p with thin velum formation in a cluster of Jura strains. These results provide new insight into the diversity of flor yeast and show that combinations of different adaptive changes can lead to an increase of hydrophobicity and affect velum formation.
2014-06-01 | GSE55925 | GEO
Project description:The yeast Saccharomyces cerevisiae is a model for biology and is also one of the most important microorganisms for food and drink production. Surprisingly, only a few genes involved in the adaptation to anthropic niches have been described until now. Wine fermentation and flor aging, which are performed by strains from two closely related groups of yeast, are two technologies that have opposite approaches toward oxygen, which results in contrasting lifestyles for yeast: fermentation growth on grape for wine yeast, and biofilm aerobic growth on ethanol and glycerol contained in wine for flor strains. This pair of environments and the associated yeast populations can be a model for studying adaptation to anthropic environments. In this project, we have obtained high-quality genome sequences of 20 yeast strains from 9 flor yeast, 9 wine yeast as well as EC1118 and haploid derivative 59A. Phylogeny and population structure analysis, based on GATK genotyping, enable us to characterize a group of flor yeast that is clearly different from wine yeast. A comparison of the genomes of wine and flor yeasts using various methods (PCA, nucleotidic diversity, McDonald Kreitman test, potentially impacted genes according to SIFT) enabled us to note divergent regions, or genes, with potential non-neutral evolution, and highly variant genes. The results of these genomic comparisons are echoed by the comparison of a wine and a flor yeast transcriptome. These methods, as expected, highlight key genes that are involved in FLO11 regulation as well as in biofilm growth, but they also revealed the presence of many allelic variations in genes that are involved in the sensing and regulation of osmotic pressure (such as SLN1, HKR1, SSK22, AQY2) and specific metabolic traits, such as the fructophily of flor yeast, which carry a fructophile allele of HXT3. More remarkable is the accumulation of mutations in multiple genes, which creates a pattern of convergent mutations in regulatory networks, as seen in FLO11 regulation or the HOG MAP kinase pathway. The rewiring of these regulatory networks is clearly one of the hallmarks of domestication for the flor yeast genome. Data presented here correspond to the comparison of Flor yeast P3-D5 and wine yeast K1-280-2B transcriptomes under conditions potentially enabling the production of a biofilm.
2018-01-31 | GSE76667 | GEO
Project description:Wine biological ageing is led in different countries in Europe: Spain, Italy, France, and Hungary, but until now no comparison of all these flor strains has been led. In this manuscript we investigated the population structure of these European flor strains from their microsatellite genotypes and analysed as well as their ploidy. We showed that almost all of these strains belong to the same cluster, and are mainly diploids. In order to detect a shared amplification pattern, we compared the hybridization profile on array of 6 flor strains from these four countries, and found only 2 genes amplified in the genome of 4 strains. Finally FLO11 polymorphism analysis revealed that most strains carry a 111 deletion in ICR1 non coding RNA, except a group of Jura Flor strains, which in contrast presented longer central core of the protein Flo11p. These results show that amplification is very likely not the main mechanism leading to the adaptation of flor yeast, and suggest that different adaptive itineraries can leading to an increase of hydrophobicity and velum formation. Wine and flor strains hybridization on affymetrix yeast2 arrays are compared to S288C Each strain is compared to S288C and is hybridized in duplicate or triplicate
2014-06-01 | E-GEOD-55925 | biostudies-arrayexpress
Project description:Gene expression analysis of time course experiment of [1] a synthetic must (nitrogen-rich) fermentation by a natural wine yeast; [2] a synthetic must (nitrogen-poor) fermentation by a natural wine yeast; and [3] a synthetic must (nitrogen-poor) fermentation by a natural wine yeast, supplemented at 72 hours with 200 mg/l of nitrogen. This SuperSeries is composed of the SubSeries listed below.
2006-09-15 | GSE5842 | GEO
Project description:Comparison between two commercial wine yeast strains (UCD522 and P29) differing in their production of H2S during wine fermentation.
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Project description:Gene copy number comparison between similar wine yeast strains of Saccharomyces cerevisiae from different geographic origins.
2010-02-14 | GSE16941 | GEO
Project description:The yeast Saccharomyces cerevisiae is an important component of the wine fermentation process and determines various attributes of the final product. However, lactic acid bacteria (LAB) are also an integral part of the microflora of any fermenting must. Various wine microorganism engineering projects have been endeavoured in the past in order to change certain wine characteristics, namely aroma compound composition, ethanol concentration, levels of toxic/ allergenic compounds etc. Most of these projects focus on a specific gene or pathway, whereas our approach aims to understand the genetically complex traits responsible for these phenotypes in a systematic manner by implementing a transcriptomic analysis of yeast in mixed fermentations with the LAB O. oeni. Our aim is to investigate interactions between yeast and LAB on a gene expression level to identify targets for modification of yeast and O. oeni in a directed manner. Our goal was to identify the impact that the common wine microorganism O. oeni (malolactic bacteria) has on fermenting yeast cells on a gene expression level. To this end we co-inoculated the yeast and bacteria at the start of fermentation in a synthetic wine must, using yeast-only fermentations witout O. oeni as a control.
2011-06-02 | GSE27085 | GEO
Project description:The Genowine project: Comparative genomics of wine and flor strains
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Project description:In wine fermentation, the blending of non-Saccharomyces yeast with Saccharomyces cerevisiae to improve the complexity of wine has become common practice, but data regarding the impact on yeast physiology and on genetic and metabolic regulation remain limited. Here we describe a transcriptomic analysis of single species and mixed species fermentations.
2019-02-01 | GSE112581 | GEO