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Article

Whole-Genome Sequencing and Annotation of the Yeast Clavispora santaluciae Reveals Important Insights about Its Adaptation to the Vineyard Environment

by
Ricardo Franco-Duarte
1,2,*,
Neža Čadež
3,
Teresa Rito
1,2,
João Drumonde-Neves
4,
Yazmid Reyes Dominguez
5,
Célia Pais
1,2,
Maria João Sousa
1,2 and
Pedro Soares
1,2
1
CBMA, Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, 4710-057 Braga, Portugal
2
Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal
3
Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, 101, 1000 Ljubljana, Slovenia
4
IITAA—Institute of Agricultural and Environmental Research and Technology, University of Azores, 9700-042 Angra do Heroísmo, Portugal
5
Laimburg Research Centre, Laimburg 6, 39052 Vadena, Italy
*
Author to whom correspondence should be addressed.
J. Fungi 2022, 8(1), 52; https://doi.org/10.3390/jof8010052
Submission received: 6 December 2021 / Revised: 3 January 2022 / Accepted: 4 January 2022 / Published: 5 January 2022
(This article belongs to the Special Issue New Trends in Yeast Genomics)
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Abstract

Clavispora santaluciae was recently described as a novel non-Saccharomyces yeast species, isolated from grapes of Azores vineyards, a Portuguese archipelago with particular environmental conditions, and from Italian grapes infected with Drosophila suzukii. In the present work, the genome of five Clavispora santaluciae strains was sequenced, assembled, and annotated for the first time, using robust pipelines, and a combination of both long- and short-read sequencing platforms. Genome comparisons revealed specific differences between strains of Clavispora santaluciae reflecting their isolation in two separate ecological niches—Azorean and Italian vineyards—as well as mechanisms of adaptation to the intricate and arduous environmental features of the geographical location from which they were isolated. In particular, relevant differences were detected in the number of coding genes (shared and unique) and transposable elements, the amount and diversity of non-coding RNAs, and the enzymatic potential of each strain through the analysis of their CAZyome. A comparative study was also conducted between the Clavispora santaluciae genome and those of the remaining species of the Metschnikowiaceae family. Our phylogenetic and genomic analysis, comprising 126 yeast strains (alignment of 2362 common proteins) allowed the establishment of a robust phylogram of Metschnikowiaceae and detailed incongruencies to be clarified in the future.
Keywords: genomics; phylogenomics; functional gene analysis; Metschnikowiaceae; Azores; wine yeasts; biotechnology; adaptation genomics; phylogenomics; functional gene analysis; Metschnikowiaceae; Azores; wine yeasts; biotechnology; adaptation

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MDPI and ACS Style

Franco-Duarte, R.; Čadež, N.; Rito, T.; Drumonde-Neves, J.; Dominguez, Y.R.; Pais, C.; Sousa, M.J.; Soares, P. Whole-Genome Sequencing and Annotation of the Yeast Clavispora santaluciae Reveals Important Insights about Its Adaptation to the Vineyard Environment. J. Fungi 2022, 8, 52. https://doi.org/10.3390/jof8010052

AMA Style

Franco-Duarte R, Čadež N, Rito T, Drumonde-Neves J, Dominguez YR, Pais C, Sousa MJ, Soares P. Whole-Genome Sequencing and Annotation of the Yeast Clavispora santaluciae Reveals Important Insights about Its Adaptation to the Vineyard Environment. Journal of Fungi. 2022; 8(1):52. https://doi.org/10.3390/jof8010052

Chicago/Turabian Style

Franco-Duarte, Ricardo, Neža Čadež, Teresa Rito, João Drumonde-Neves, Yazmid Reyes Dominguez, Célia Pais, Maria João Sousa, and Pedro Soares. 2022. "Whole-Genome Sequencing and Annotation of the Yeast Clavispora santaluciae Reveals Important Insights about Its Adaptation to the Vineyard Environment" Journal of Fungi 8, no. 1: 52. https://doi.org/10.3390/jof8010052

APA Style

Franco-Duarte, R., Čadež, N., Rito, T., Drumonde-Neves, J., Dominguez, Y. R., Pais, C., Sousa, M. J., & Soares, P. (2022). Whole-Genome Sequencing and Annotation of the Yeast Clavispora santaluciae Reveals Important Insights about Its Adaptation to the Vineyard Environment. Journal of Fungi, 8(1), 52. https://doi.org/10.3390/jof8010052

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