Saccharomycotina phylogeny visualizing genomes sequenced as part of Opulente et al., 2024, colored by Order. Image by Abigail Leavitt LaBella.

Saccharomycotina is an ancient subphylum of fungi with evolutionary diversity rivaling that of other eukaryotic kingdoms (Shen et al., 2018). It contains several species of vital importance to the bioeconomy (e.g. Saccharomyces cerevisiae) and human health (e.g. Candida albicans). Towards a more comprehensive understanding of their genetics, evolution and metabolic capabilities, the Y1000+ Project sequenced over 1000 diverse lineages representing nearly all known species across the subphylum (Opulente et al., 2024). The Starmerella sorbosivorans NCYC 2938 genome was sequenced, assembled and annotated as part of that effort and imported into MycoCosm for comparative purposes.

All published models are available as ExternalModels. In order to ensure this genome is comparable to those sequenced and annotated by the JGI, we applied standard filters to ExternalModels to produce the initial GeneCatalog. Models were excluded based on one of the following classifications: 1) association with repetitive elements, 2) pseudogenes with internal stop codons, 3) alternative isoforms or overlapping transcript models, 4) alleles on secondary scaffolds, and 5) short models lacking functional annotation. The JGI Annotation Pipeline was used to add functional annotation to the genes. Please note that this copy of the genome is not maintained by the Y1000+ Team and is not automatically updated.

References:

• Shen, Xing-Xing, et al. "Tempo and mode of genome evolution in the budding yeast subphylum." Cell 175.6 (2018): 1533-1545.
• Opulente, Dana A., et al. "Genomic factors shape carbon and nitrogen metabolic niche breadth across Saccharomycotina yeasts." Science 384.6694 (2024): eadj4503.