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\begin{document}

\title{A glimpse at an early stage of microbe domestication revealed in the
variable genome of Torulaspora delbrueckii, an emergent industrial yeast}



\author[1]{Margarida  Silva}%
\author[1]{Ana Pontes}%
\author[1]{Ricardo Franco-Duarte}%
\author[2]{Pedro Soares}%
\author[3]{Jose Paulo Sampaio}%
\author[2]{Maria Sousa}%
\author[3]{Patrícia Brito}%
\affil[1]{Affiliation not available}%
\affil[2]{CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Braga, Portugal}%
\affil[3]{UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal}%


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  \date{May 19, 2024}


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\begin{abstract}
The yeast Torulaspora delbrueckii is gaining importance for
biotechnology due to its ability to increase wine sensorial complexity
and for enhancing pre-frozen bread dough leavening. However, little is
known about its population structure, variation in gene content, or
possible domestication routes. Here, we address these issues and update
the delimitation of T. delbrueckii along five major clades. Among the
three European clades, a basal lineage is associated with the wild
arboreal niche, while the two other lineages are linked with anthropic
environments, one to wine fermentations and the other to diverse sources
including dairy products and bread dough (Mix- Anthropic clade). Using
62 genomes we identified 5629 genes in the pangenome of T. delbrueckii
and 270 genes in the cloud genome. A pangenome tree analysis showed that
wine strains have a genome composition more similar to European wild
arboreal strains than to those of the Mix Anthropic clade, in
contradiction with the phylogenetic analysis. An association of gene
content and ecology gave further support to the hypothesis that the Mix
- Anthropic clade has the most specialized genome content and indicated
that some of the exclusive genes were implicated in galactose and
maltose utilization. More detailed analyses traced the acquisition of a
cluster of GAL genes in strains associated with dairy products and the
expansion and functional diversification of MAL genes in strains
isolated from bread dough. Contrary to S. cerevisiae, domestication in
T. delbrueckii is not primed by alcoholic fermentation and appears to be
a recent event.%
\end{abstract}%



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\verb`Tdelbrueckii genomics_v10.doc`  available at \url{https://authorea.com/users/434956/articles/538309-a-glimpse-at-an-early-stage-of-microbe-domestication-revealed-in-the-variable-genome-of-torulaspora-delbrueckii-an-emergent-industrial-yeast}\selectlanguage{english}
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