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Apiculate yeasts belonging to the genus Hanseniaspora are predominant on grapes and other fruits. While some species, such as Hanseniaspora uvarum, are well known for their abundant presence in fruits, they are generally characterized by their detrimental effect on fermentation quality because the excessive production of acetic acid. However, the species Hanseniaspora vineae is adapted to fermentation and currently is considered as an enhancer of positive flavour and sensory complexity in foods. Since 2002, we have been isolating strains from this species and conducting winemaking processes with them. In parallel, we also characterized this species from genes to metabolites. In 2013, we sequenced the genomes of two H. vineae strains, being these the first apiculate yeast genomes determined. In the last 10 years, it has become possible to understand its biology, discovering very peculiar features compared to the conventional Saccharomyces yeasts, such as a natural and unique G2 cell cycle arrest or the elucidation of the mandelate pathway for benzenoids synthesis. All these characteristics contribute to phenotypes with proved interest from the biotechnological point of view for winemaking and the production of other foods.
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Hanseniaspora , Vino , Hanseniaspora/genética , Fermentación , Vino/análisis , Levaduras/genética , BiologíaRESUMEN
Motivation: The use of high precision for representing quality scores in nanopore sequencing data makes these scores hard to compress and, thus, responsible for most of the information stored in losslessly compressed FASTQ files. This motivates the investigation of the effect of quality score information loss on downstream analysis from nanopore sequencing FASTQ files. Results: We polished de novo assemblies for a mock microbial community and a human genome, and we called variants on a human genome. We repeated these experiments using various pipelines, under various coverage level scenarios and various quality score quantizers. In all cases, we found that the quantization of quality scores causes little difference (or even sometimes improves) on the results obtained with the original (non-quantized) data. This suggests that the precision that is currently used for nanopore quality scores may be unnecessarily high, and motivates the use of lossy compression algorithms for this kind of data. Moreover, we show that even a non-specialized compressor, such as gzip, yields large storage space savings after the quantization of quality scores. Availability and supplementary information: Quantizers are freely available for download at: https://github.com/mrivarauy/QS-Quantizer.
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An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Salmonella enterica serovar Enteritidis is a major cause of foodborne disease in Uruguay since 1995. We used a genomic approach to study a set of isolates from different sources and years. Whole genome phylogeny showed that most of the strains are distributed in two major lineages (E1 and E2), both belonging to MLST sequence type 11 the major ST among serovar Enteritidis. Strikingly, E2 isolates are over-represented in periods of outbreak abundance in Uruguay, while E1 span all epidemic periods. Both lineages circulate in neighbor countries at the same timescale as in Uruguay, and are present in minor numbers in distant countries. We identified allelic variants associated with each lineage. Three genes, ycdX, pduD and hsdM, have distinctive variants in E1 that may result in defective products. Another four genes (ybiO, yiaN, aas, aceA) present variants specific for the E2 lineage. Overall this work shows that S. enterica serovar Enteritidis strains circulating in Uruguay have the same phylogenetic profile than strains circulating in the region, as well as in more distant countries. Based on these results we hypothesize that the E2 lineage, which is more prevalent during epidemics, exhibits a combination of allelic variants that could be associated with its epidemic ability.
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Proteínas Bacterianas/genética , Brotes de Enfermedades , Filogenia , Infecciones por Salmonella , Salmonella enteritidis/genética , Humanos , Tipificación de Secuencias Multilocus , Infecciones por Salmonella/epidemiología , Infecciones por Salmonella/genética , Salmonella enteritidis/aislamiento & purificación , Uruguay/epidemiologíaRESUMEN
Salmonella enterica serovar Enteritidis is a major agent of foodborne diseases worldwide. In Uruguay, this serovar was almost negligible until the mid 1990s but since then it has become the most prevalent. Previously, we characterized a collection of strains isolated from 1988 to 2005 and found that the two oldest strains were the most genetically divergent. In order to further characterize these strains, we sequenced and annotated eight genomes including those of the two oldest isolates. We report on the identification and characterization of a novel 44 kbp Salmonella prophage found exclusively in these two genomes. Sequence analysis reveals that the prophage is a mosaic, with homologous regions in different Salmonella prophages. It contains 60 coding sequences, including two genes, gogB and sseK3, involved in virulence and modulation of host immune response. Analysis of serovar Enteritidis genomes available in public databases confirmed that this prophage is absent in most of them, with the exception of a group of 154 genomes. All 154 strains carrying this prophage belong to the same sequence type (ST-1974), suggesting that its acquisition occurred in a common ancestor. We tested this by phylogenetic analysis of 203 genomes representative of the intraserovar diversity. The ST-1974 forms a distinctive monophyletic lineage, and the newly described prophage is a phylogenetic signature of this lineage that could be used as a molecular marker. The phylogenetic analysis also shows that the major ST (ST-11) is polyphyletic and might have given rise to almost all other STs, including ST-1974.
