Genome Sequence of the Native Apiculate Wine Yeast Hanseniaspora vineae T02/19AF

The use of novel yeast strains for winemaking improves quality and provides variety including subtle characteristic differences in fine wines. Here we report the first genome of a yeast strain native to Uruguay, Hanseniaspora vineae T02/19AF, which has been shown to positively contribute to aroma and wine quality.Fil: Giorello, Facundo M.. Universidad de la República; UruguayFil: Berná, Luisa. Instituto Pasteur de Montevideo; UruguayFil: Greif, Gonzalo. Instituto Pasteur de Montevideo; UruguayFil: Camesasca, Laura. Inst. de Investigaciones Biológicas Clemente Estable; UruguayFil: Salzman, Valentina. Instituto Pasteur de Montevideo; Uruguay. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Medina, Karina. Universidad de la Republica. Facultad de Química; UruguayFil: Robello, Carlos. Instituto Pasteur de Montevideo; UruguayFil: Gaggero, Carina. Inst. de Investigaciones Biológicas Clemente Estable; UruguayFil: Aguilar, Pablo S.. Instituto Pasteur de Montevideo; UruguayFil: Carrau, Francisco. Sección Enología; Urugua

Draft genome sequence and gene annotation of the uropathogenic bacterium Proteus mirabilis Pr2921

Here, we report the genome sequence of Proteus mirabilis Pr2921, a uropathogenic bacterium that can cause severe complicated urinary tract infections. After gene annotation, we identified two additional copies of ucaA, one of the most studied fimbrial protein genes, and other fimbriae related-proteins that are not present in P. mirabilis HI4320

Analysis of the NCR Mechanisms in Hanseniaspora vineae and Saccharomyces cerevisiae During Winemaking

There is increasing interest in the use of non-Saccharomyces yeasts in winemaking due to their positive attributes. The non-Saccharomyces yeast Hanseniaspora vineae is an apiculate yeast that has been associated with the production of wine with good fermentation capacity and an increase in aromatic properties. However, this yeast represents a concern in mixed culture fermentation because of its nutrient consumption, especially nitrogen, as its mechanisms of regulation and consumption are still unknown. In this study, we analyzed the nitrogen consumption, as well as the nitrogen catabolism repression (NCR) mechanism, in two genome-sequenced H. vineae strains, using synthetic must fermentations. The use of synthetic must with an established nitrogen content allowed us to study the NCR mechanism in H. vineae, following the amino acid and ammonia consumption, and the expression of genes known to be regulated by the NCR mechanism in S. cerevisiae, AGP1, GAP1, MEP2, and PUT2. H. vineae exhibited a similar amino acid consumption and gene expression profile to S. cerevisiae. However, the wine strain of S. cerevisiae QA23 consumed ammonia and valine more quickly and, in contrast, tyrosine and tryptophan more slowly, than the H. vineae strains. Our results showed a similar behavior of nitrogen regulation in H. vineae and S. cerevisiae, indicating the presence of the NCR mechanism in this Hanseniaspora yeast differentiated before the whole genome duplication event of the Saccharomyces complex. Future study will elucidate if the NCR mechanism is the only strategy used by H. vineae to optimize nitrogen consumption

Caracterización del transcriptoma de riñón del ratón oliváceo sudamericano Abrothrix olivacea

Tribunal: Dr. Hugo Naya, Dr. Gustavo Guerberoff y Dr. Héctor Romero

Data from: An association between differential expression and genetic divergence in the Patagonian olive mouse (Abrothrix olivacea)

Recent molecular studies have found striking differences between desert-adapted species and model mammals regarding water conservation. In particular, aquaporin 4, a classical gene involved in water regulation of model species, is absent or not expressed in the kidneys of desert-adapted species. To further understand the molecular response to water availability we studied the Patagonian olive mouse Abrothrix olivacea, a species with an unusually broad ecological tolerance that exhibits a great urine concentration capability. The species is able to occupy both the arid Patagonian steppe and the Valdivian and Magellanic forests. We sampled 95 olive mouse specimens from four localities (two in the steppe, two in the forests) and analyzed both phenotypic variables and transcriptomic data to investigate the response of this species to the contrasting environmental conditions. The relative size of the kidney and the ratio of urine to plasma concentrations were, as expected, negatively correlated with annual rainfall. Expression analyses uncovered nearly 3,000 genes that were differentially expressed between steppe and forest samples and indicated that this species resorts to the “classical” gene pathways for water regulation. Differential expression across biomes also involves genes involved in immune and detoxification functions. Overall, genes that were differentially expressed showed a slight tendency to be more divergent and to display an excess of intermediate allele frequencies, relative to the remaining loci. Our results indicate that both differential expression in pathways involved in water conservation and geographical allelic variation are important in the occupation of contrasting habitats by the Patagonian olive mouse

The contribution of incomplete lineage sorting and introgression to the evolutionary history of the fast-evolving genus Ctenomys (Rodentia, Ctenomyidae)

Incomplete lineage sorting (ILS) and introgression have been increasingly recognized as important processes involved in biological differentiation. Both ILS and introgression result in incongruences between gene trees and species trees, consequently causing difficulties in phylogenetic reconstruction. This is particularly the case for rapid radiations, as short internodal distances and incomplete reproductive isolation increase the likelihood of both ILS and introgression. Estimation of the relative frequency of these processes requires assessments across many genomic regions. We use transcriptomics to test for introgression and estimate the frequency of ILS in a set of three closely related and geographically adjacent South American tuco-tucos species (Ctenomys), a genus comprising 64 species resulting from recent, rapid radiation. After cleaning and filtering, 5764 orthologous genes strongly support paraphyly of C. pearsoni relative to C. brasiliensis (putatively represented by the population of Villa Serrana). In line with earlier phylogenetic work, the C. pearsoni - C. brasiliensis pair is closely related to C. torquatus, whereas C. rionegrensis is more distantly related to these three nominal species. Classical Patterson's d-statistic shows significant signals of introgression from C. torquatus into C. brasiliensis. However, a 5-taxon test shows no significant results. ILS was estimated to have involved about 9% of the loci, suggesting it represents an important process in the incipient diversification of tuco-tucos.Fil: Tomasco, Ivanna H.. Universidad de la Republica; UruguayFil: Giorello, Facundo M.. Universidad de la República; UruguayFil: Boullosa, Nicolás. Universidad de la Republica; UruguayFil: Feijoo, Matías. Universidad de la República; UruguayFil: Lanzone, Cecilia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Posadas | Universidad Nacional de Misiones. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Posadas; ArgentinaFil: Lessa, Enrique P.. Universidad de la República; Urugua

De novo synthesis of benzenoid compounds by the yeast hanseniaspora vineae increases the flavor diversity of wines

Benzyl alcohol and other benzenoid-derived metabolites of particular importance in plants confer floral and fruity flavors to wines. Among the volatile aroma components in Vitis vinifera grape varieties, benzyl alcohol is present in its free and glycosylated forms. These compounds are considered to originate from grapes only and not from fermentative processes. We have found increased levels of benzyl alcohol in red Tannat wine compared to that in grape juice, suggesting de novo formation of this metabolite during vinification. In this work, we show that benzyl alcohol, benzaldehyde, p-hydroxybenzaldehyde, and p-hydroxybenzyl alcohol are synthesized de novo in the absence of grape-derived precursors by Hanseniaspora vineae. Levels of benzyl alcohol produced by 11 different H. vineae strains were 20-200 times higher than those measured in fermentations with Saccharomyces cerevisiae strains. These results show that H. vineae contributes to flavor diversity by increasing grape variety aroma concentration in a chemically defined medium. Feeding experiments with phenylalanine, tryptophan, tyrosine, p-aminobenzoic acid, and ammonium in an artificial medium were tested to evaluate the effect of these compounds either as precursors or as potential pathway regulators for the formation of benzenoid-derived aromas. Genomic analysis shows that the phenylalanine ammonia-lyase (PAL) and tyrosine ammonia lyase (TAL) pathways, used by plants to generate benzyl alcohols from aromatic amino acids, are absent in the H. vineae genome. Consequently, alternative pathways derived from chorismate with mandelate as an intermediate are discussed.Fil: Martín, Valentina. Universidad de la República; Uruguay. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Giorello, Facundo. Universidad de la República; UruguayFil: Fariña, Laura. Universidad de la República; Uruguay. Instituto de Investigaciones Biológicas "Clemente Estable"; UruguayFil: Minteguiaga, Manuel. Universidad de la República; UruguayFil: Salzman, Valentina. Instituto Pasteur de Montevideo; Uruguay. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas; ArgentinaFil: Boido, Eduardo. Universidad de la República; UruguayFil: Aguilar, Pablo Sebastián. Instituto Pasteur de Montevideo; Uruguay. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas; ArgentinaFil: Gaggero, Carina. Instituto de Investigaciones Biológicas "Clemente Estable"; UruguayFil: Dellacassa, Eduardo. Universidad de la República; UruguayFil: Mas, Albert. Universitat Rovira I Virgili; EspañaFil: Carrau, Francisco. Universidad de la República; Urugua

Characterization of the Kidney Transcriptome of the Long-Haired Mouse <i>Abrothrix hirta</i> (Rodentia, Sigmodontinae) and Comparison with That of the Olive Mouse <i>A</i>. <i>olivacea</i>

<div><p>To understand how small mammals cope with the challenge of water homeostasis is a matter of interest for ecologists and evolutionary biologists. Here we take a step towards the understanding of the transcriptomic functional response of kidney using as a model the long–haired mouse (<i>Abrothrix hirta</i>) a species that distributes across Patagonian steppes and Austral temperate rainforests in Argentina and Chile. Specifically, we i) characterize the renal transcriptome of <i>A</i>. <i>hirta</i>, and ii) compare it with that—already available—of the co-generic and co-distributed <i>A</i>. <i>olivacea</i>. Renal mRNA transcripts from 16 specimens of <i>A</i>. <i>hirta</i> from natural populations were analyzed. Over 500 million Illumina paired-end reads were assembled <i>de novo</i> under two approaches, an individual assembly for each specimen, and a single <i>in-silico</i> normalized joint assembly including all reads from all specimens. The total number of annotated genes was similar with both strategies: an average of 14,956 in individual assemblies and 14,410 in the joint assembly. Overall, 15,463 distinct genes express in the kidney of <i>A</i>. <i>hirta</i>. Transcriptomes of <i>A</i>. <i>hirta</i> and <i>A</i>. <i>olivacea</i> were similar in terms of gene abundance and composition: 95.6% of the genes of <i>A</i>. <i>hirta</i> were also found in <i>A</i>. <i>olivacea</i> making their functional profiles also similar. However, differences in the transcriptome of these two species were observed in the set of highly expressed genes, in terms of private genes for each species and the functional profiles of highly expressed genes. As part of the novel transcriptome characterization, we provide distinct gene lists with their functional annotation that would constitute the basis for further research on these or any other species of the subfamily Sigmodontinae, which includes about 400 living species distributed from Tierra del Fuego to southern United States.</p></div