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

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

doi:10.3390/jof8010052

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.

Highlights

Introduction iationsIn our previous surveys on the yeast diversity of Azorean vineyards, in 2009 and [1,2,3], we described a new yeast species Clavispora santaluciae [4], isolated from grapes.It was characterized on the basis of the sequences of the internal transcribed spacer (ITS)region (ITS1-5.8S–ITS2), the sequences of the D1/D2 domain of the large subunit (LSU)ribosomal RNAs (rRNA) gene, and particular physiological characteristics
Even though the Clavispora lusitaniae genome was used as a query to compare between all the genomes, no species belonging to the Clavispora genus were considered, with the analysis focused on only the Metschnikowia genus
Strain NBLB-3.3 showed a surprisingly high number of unique genes (298), not shared by any of the other strains, reflecting its adaptation to a different ecological niche, as this strain was isolated from Italian grapes infected with Drosophila suzukii

Summary

Introduction

Introduction iationsIn our previous surveys on the yeast diversity of Azorean vineyards, in 2009 and [1,2,3], we described a new yeast species Clavispora santaluciae [4], isolated from grapes.It was characterized on the basis of the sequences of the internal transcribed spacer (ITS)region (ITS1-5.8S–ITS2), the sequences of the D1/D2 domain of the large subunit (LSU)rRNA gene, and particular physiological characteristics. That study described this species as being isolated from grapes infected with Drosophila suzukii in Italy This showed identical D1/D2 sequences and very similar ITS regions (five nucleotide substitutions) to the Azorean strains. The new species was obtained from particular viticultural environments, typical of the Azores archipelago, which result from the interaction between specific climatic conditions, autochthonous grapevine cultivars, and local viticultural practices. Phenotypic characterization of this new species revealed some interesting features that

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