Improvement of Torulaspora delbrueckii Genome Annotation: Towards the Exploitation of Genomic Features of a Biotechnologically Relevant Yeast

Abstract

Saccharomyces cerevisiae is the most commonly used yeast in wine, beer, and bread fermentations. However, Torulaspora delbrueckii has attracted interest in recent years due to its properties, ranging from its ability to produce flavor- and aroma-enhanced wine to its ability to survive longer in frozen dough. In this work, publicly available genomes of T. delbrueckii were explored and their annotation was improved. A total of 32 proteins were additionally annotated for the first time in the type strain CBS1146, in comparison with the previous annotation available. In addition, the annotation of the remaining three T. delbrueckii strains was performed for the first time. eggNOG-mapper was used to perform the functional annotation of the deduced T. delbrueckii coding genes, offering insights into its biological significance, and revealing 24 clusters of orthologous groups (COGs), which were gathered in three main functional categories: information storage and processing (28% of the proteins), cellular processing and signaling (27%), and metabolism (23%). Small intraspecies variability was found when considering the functional annotation of the four available T. delbrueckii genomes. A comparative study was also conducted between the T. delbrueckii genome and those from 386 fungal species, revealing a high number of homologous genes with species from the Zygotorulaspora and Zygosaccharomyces genera, but also with Lachancea and S. cerevisiae. Lastly, the phylogenetic placement of T. delbrueckii was clarified using the core homologs that were found across 204 common protein sequences of 386 fungal species and strains.

Cold Adaptation Strategies and the Potential of Psychrophilic Enzymes from the Antarctic Yeast, Glaciozyma antarctica PI12

“…strain UV9 (4.25 Mb) [18] and Pseudomonas sp. MPC6 (7.22 Mb) [19] and the mesophilic yeast Torulaspora delbrueckii (9.52 Mb) [20], whereas it is smaller as compared to other psychrophilic fungi such as Cryomyces antarcticus (24.32 Mb) [21] and Rachicladosporium antarcticum CCFEE 5527 (47.4 Mb) [22]. However, the genome size of this yeast is considered moderate as compared to other psychrophilic yeasts such as Candida psychrophile (11.2 Mb) [14], Dioszegia cryoxerica (39.5 Mb) and Mrakia psychrophila (27.8 Mb) [23] (Table 1).…”

Biotechnological Importance of Torulaspora delbrueckii: From the Obscurity to the Spotlight

“…In addition, both these genera-Torulaspora and Zygotorulaspora-formed an isolated group, separated from the one containing Zygosaccharomyces species (highlighted in blue in Figure 2). [25]. The phylogenetic reconstruction was obtained using the following parameters: maximum likelihood in IQ-TREE (http://www.iqtree.org, accessed on 28 July 2021), the model of amino acid evolution JTT (Jones-Taylor-Thornton), and four gamma-distributed rates.…”

“…Bootstrapping provided values of 100% for most nodes. [25]. The phylogenetic reconstruction was obtained using the following parameters: maximum likelihood in IQ-TREE (http://www.iqtree.org, accessed on 28 July 2021), the model of amino acid evolution JTT (Jones-Taylor-Thornton), and four gamma-distributed rates.…”

“…Even though T. delbrueckii possesses lower tolerance to low-oxygen conditions [14,34], its metabolism is usually associated with several positive characteristics, mainly regarding the wine industry, related to high osmotic and sulphur dioxide resistance [23][24][25][26][27][28]35], enhanced capacity for biotransformation of terpenes [28,36,37], or high competence to produce lactic and succinic acids [28,36].…”

“…Figure 2. Phylogenetic placement of Torulaspora delbrueckii, showing the relationship of 15 strains with publicly available genomes, in relation to its closely related species, chosen from[25]. The phylogenetic reconstruction was obtained using the following parameters: maximum likelihood in IQ-TREE (http://www.iqtree.org, accessed on 28 July 2021), the model of amino acid evolution JTT (Jones-Taylor-Thornton), and four gamma-distributed rates.…”