Silva Margarida, Pontes Ana, Franco-Duarte Ricardo, Soares Pedro, Sampaio José Paulo, Sousa Maria João, Brito Patrícia H
Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, UCIBIO, Universidade Nova de Lisboa, Caparica, Portugal.
Faculdade de Ciências e Tecnologia, Associate Laboratory i4HB - Institute for Health and Bioeconomy, Universidade Nova de Lisboa, Caparica, Portugal.
Mol Ecol. 2023 May;32(10):2396-2412. doi: 10.1111/mec.16428. Epub 2022 Mar 28.
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.
微生物驯化具有重要的应用价值，但从进化角度来看，人们对其仍知之甚少。德氏有孢圆酵母（Torulaspora delbrueckii）在生物技术领域正变得越来越重要，但对其种群结构、基因含量变异或可能的驯化途径却知之甚少。在这里，我们表明德氏有孢圆酵母由五个主要分支组成。在欧洲的三个分支中，一个与野生树栖生态位相关的谱系是另外两个与人类环境相关谱系的姐妹谱系，其中一个与葡萄酒发酵相关，另一个与包括乳制品和面包面团在内的多种来源相关（混合人类环境分支）。我们使用64个基因组组装了德氏有孢圆酵母的泛基因组和可变基因组。与酿酒酵母（Saccharomyces cerevisiae）的比较表明，德氏有孢圆酵母泛基因组中可变基因组的权重要小得多。基因含量与生态学的关联支持了这样的假设，即混合人类环境分支具有最特殊化的基因组，并表明一些独特基因与半乳糖和麦芽糖利用有关。更详细的分析追踪了与乳制品相关菌株中GAL基因簇的获得，以及从面包面团中分离出的菌株中MAL基因的扩增和功能多样化。与酿酒酵母不同，德氏有孢圆酵母的驯化并非主要由酒精发酵驱动，而是由对乳制品和面包生产生态位的适应驱动。这项研究扩展了我们对微生物驯化过程以及导致适应人类生态位轨迹的看法。
