Whole-genome sequencing and annotation of the yeast Clavispora santaluciae reveals important insights about its adaptation to the vineyard environment

Franco-Duarte, Ricardo (author), Čadež, Neža (author), Rito, Teresa (author), Drumonde-Neves, João (author), Reyes Domínguez, Yazmid (author), Pais, Célia (author), Sousa, Maria João (author), Soares, Pedro (author)

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 noncoding 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.

• Language: English
• Keywords: genomics, phylogenomics, functional gene analysis, Metschnikowiaceae, Azores, wine yeasts, biotechnology, adaptation
• Work type: Article
• Typology: 1.01 - Original Scientific Article
• Organization: BF - Biotechnical Faculty
• Publication status: Published
• Publication version: Version of Record
• Year: 2022
• Number of pages: 18 str.
• Numbering: Vol. 8, iss. 1, art. 52
• PID: 20.500.12556/RUL-136749
• UDC: 579.25.065:582.28
• ISSN on article: 2309-608X
• DOI: 10.3390/jof8010052
• COBISS.SI-ID: 92329987
• Publication date in RUL: 19.05.2022

Record is a part of a journal

• Title: Journal of Fungi
• Shortened title: J. Fungi
• Publisher: MDPI
• ISSN: 2309-608X
• COBISS.SI-ID: 525300761

Licences

• License: CC BY 4.0, Creative Commons Attribution 4.0 International
• Link: http://creativecommons.org/licenses/by/4.0/
• Description: This is the standard Creative Commons license that gives others maximum freedom to do what they want with the work as long as they credit the author.
• Licensing start date: 05.01.2022

Secondary language

• Language: Slovenian
• Keywords: kvasovke, Clavispora santaluciae, filogenomika, sekvenciranje genoma