Author(s):
Silva, Margarida ; Pontes, Ana ; Franco-Duarte, Ricardo ; Soares, Pedro ; Sampaio, José Paulo ; Sousa, Maria João ; Brito, Patrícia H
Date: 2023
Persistent ID: https://hdl.handle.net/1822/91145
Origin: RepositóriUM - Universidade do Minho
Project/scholarship:
info:eu-repo/grantAgreement/FCT/3599-PPCDT/PTDC%2FBIA-MIC%2F30785%2F2017/PT;
info:eu-repo/grantAgreement/FCT/OE/SFRH%2FBD%2F136462%2F2018/PT;
info:eu-repo/grantAgreement/FCT/6817 - DCRRNI ID/UIDP%2F04378%2F2020/PT;
info:eu-repo/grantAgreement/FCT/6817 - DCRRNI ID/UIDB%2F04378%2F2020/PT;
info:eu-repo/grantAgreement/FCT/6817 - DCRRNI ID/UID%2FBIA%2F04050%2F2019/PT;
info:eu-repo/grantAgreement/FCT/9471 - RIDTI/PTDC%2FBIA-MIC%2F32059%2F2017/PT;
Subject(s): Saccharomyces cerevisiae; Domestication; Fermentation; Torulaspora; Wine; galactose metabolization gene; maltose metabolization gene; microbe domestication; microbial genomics; pangenome and variable genome; Torulaspora delbrueckii; Science & Technology; Produção e consumo sustentáveis; Ciências Naturais::Ciências Biológicas
Description
Microbe domestication has a major applied relevance but is still poorly understood from an evolutionary perspective. The yeast Torulaspora delbrueckii is gaining importance for biotechnology but little is known about its population structure, variation in gene content or possible domestication routes. Here, we show that T. delbrueckii is composed of five major clades. Among the three European clades, a lineage associated with the wild arboreal niche is sister to the two other lineages that are linked to anthropic environments, one to wine fermentations and the other to diverse sources including dairy products and bread dough (Mix-Anthropic clade). Using 64 genomes we assembled the pangenome and the variable genome of T. delbrueckii. A comparison with Saccharomyces cerevisiae indicated that the weight of the variable genome in the pangenome of T. delbrueckii is considerably smaller. An association of gene content and ecology supported the hypothesis that the Mix-Anthropic clade has the most specialized genome 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. In contrast to S. cerevisiae, domestication in T. delbrueckii is not primarily driven by alcoholic fermentation but rather by adaptation to dairy and bread-production niches. This study expands our views on the processes of microbe domestication and on the trajectories leading to adaptation to anthropic niches.
This research was funded by grants PTDC/BIA-MIC/30785/2017, SFRH/BD/136462/2018, UIDP/04378/2020 and UIDB/04378/2020 (UCIBIO), and LA/P/0140/2020 (i4HB). This work was supported by the strategic programme UID/BIA/04050/2019, and by the project PTDC/BIA-MIC/32059/2017 funded by national funds through FCT, I.P. and by the ERDF through the COMPETE2020 – Programa Operacional Competitividade e Internacionalização (POCI) and Sistema de Apoio à Investigação Científica e Tecnológica (SAICT). This work was carried out with support of INCD funded by FCT and FEDER under the project 22153-01/SAICT/2016.