Expanding the Yeast Genomic Resource: Structural and Functional Annotation of 27 Taxonomically Diverse Ascomycetous and Basidiomycetous Yeasts

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High-quality genome annotation is essential for unlocking the potential of comparative and functional genomics. Yet, despite the remarkable diversity of yeast species, many genomes remain poorly characterised, with limited functional annotation restricting their biological interpretation and biotechnological exploitation. This knowledge gap has contributed to the continued reliance on a small number of well-studied yeast models for industrial applications. Here, we present high-confidence structural and functional annotations for 27 previously unannotated yeast genomes, providing a foundation for broader exploration of yeast diversity and its industrial potential. The 27 yeasts in this dataset represent a taxonomically diverse collection of conventional and non-conventional yeasts spanning two major fungal phyla: Basidiomycota and Ascomycota. Basidiomycota is represented by the oleaginous red yeast Rhodotorula glutinis and Apiotrichum brassicae, while Ascomycota encompasses the remaining 25 species. Within Ascomycota, the taxa can be broadly categorized into distinct physiological and industrial groups. The first group includes model and fermentative yeasts within Saccharomycetaceae, comprising several Saccharomyces strains such as food-fermenting strains (S. cerevisiae Makgeolli, S. bayanus) and probiotic variants (S. boulardii strains), alongside related traditional fermentative taxa such as Kazachstania exigua, Zygosaccharomyces bailii, and Zygosaccharomyces parabailii. The dataset also features non-conventional, industrially relevant Ascomycetes known for specialized metabolic traits, including high-ester and aroma producers (Pichia kluyveri, P. fermentans, P. ethanolica, and Cyberlindnera species), amylolytic starch-degraders (Saccharomycopsis fibuligera), antimicrobial pulcherrimin producers (Metschnikowia pulcherrima), and halotolerant species (Millerozyma farinosa). Additionally, osmotolerant and fructophilic clades are represented by members of the Starmerella/Wickerhamiella clade (Starmerella bacillaris, S. etchellsii, S. stellata, and Wickerhamiella versatilis), which are frequently associated with high-sugar environments such as wine musts and floral nectar. Finally, the collection includes early-diverging Saccharomycotina and opportunistic yeasts, encompassing filamentous-like early-diverging ascomycetous yeasts (Ascoidea asiatica, Ascoidea tarda) as well as opportunistic human and environmental colonizers (Brettanomyces anomalus, Candida sake, and Candida zeylanoides). Each genome was annotated using a multi-evidence approach integrating independent prediction methods, providing consensus gene models supported by complementary evidence. Genome completeness, assessed using BUSCO, ranged from 65.9% to 95.9%. For each genome, the resulting annotations are provided in GFF3 and GenBank formats, enabling integration with genome browsers and downstream analyses, together with Excel-based protein catalogues containing gene identifiers, protein lengths, and functional annotations, including Pfam domains, Gene Ontology (GO) terms, and KEGG pathway assignments. Capturing a broad spectrum of metabolic traits, including alcoholic fermentation, lipogenesis, secondary metabolism, and extreme stress tolerance, this dataset provides a valuable resource for comparative phylogenomics, evolutionary biology, and the expanded exploitation of non-conventional yeasts in industrial biotechnology. Contents. For the 27 genomes, this record contains the annotations in GFF3 and GenBank, the Excel protein catalogues, an abstract-and-methods document, Figure 1.1 (annotation pipeline), Table 1.1 (per-genome metrics), and a README (with the funding acknowledgement). See README.txt for details. Funding. I.R.S., S.S., K.L.T., and T.S.W. are supported by the UK National Alternative Protein Innovation Centre (NAPIC), an Innovation and Knowledge Centre funded by the BBSRC and Innovate UK (Grant Ref: BB/Z516119/1). T.S.W. also receives support from the ISPF Institutional Support Grant (RE-CL-2025-06). A.H., J.S. and K.L. are supported by the PMUC, Ministry of Higher Education, Science, Research and Innovation, Thailand (Grant Ref: C10F640076 and C10F650231).

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