Taxogenomic Analysis of a Novel Yeast Species, Lachancea rosae Sp. Nov. F.A., Isolated From the Wild Rose Rosa californica.

A novel Saccharomycotina yeast strain, yHQL494, was isolated from the rose hip of the wild rose Rosa californica from Castle Crags State Park, California, USA. Phylogenetic analyses of both whole genome data and the sequences from the D1/D2 region of the large ribosomal subunit (LSU) rRNA gene placed strain yHQL494 within the genus Lachancea and grouped it into a clade with Lachancea lanzarotensis and Lachancea meyersii. Taxogenomic analyses were conducted on publicly available genome sequences to gain a deeper insight into the carbon and nitrogen gene-trait associations across the Lachancea clade.

Genomic factors limiting the diversity of Saccharomycotina plant pathogens.

The Saccharomycotina fungi have evolved to inhabit a vast diversity of habitats over their 400-million-year evolution. There are, however, only a few known fungal pathogens of plants in this subphylum, primarily belonging to the genera Eremothecium and Geotrichum. We compared the genomes of 12 plant-pathogenic Saccharomycotina strains to 360 plant-associated strains to identify features unique to the phytopathogens.

A taxogenomic view of the genus : an expansion from ten to twenty-two species.

The yeast genus (subphylum , family ) is mostly known from its type species, , a frequent colonizer of wine and sourdough bread fermentations. The genus currently contains 10 species that are typically found in various natural terrestrial environments in temperate and tropical climates. Here we employ taxogenomic analyses to investigate a large collection of strains obtained in multiple surveys we carried out in Asia, Australasia, North America, South America, and Europe, and to which we added several strains maintained in culture collections.

Machine learning identifies novel signatures of antifungal drug resistance in yeasts.

Antifungal drug resistance is a major challenge in fungal infection management. Numerous genomic changes are known to contribute to acquired drug resistance in clinical isolates of specific pathogens, but whether they broadly explain natural resistance across entire lineages is unknown. We leveraged genomic, ecological, and phenotypic trait data from naturally sampled strains from nearly all known species in subphylum to examine the evolution of resistance to eight antifungal drugs.

Convergent expansions of keystone gene families drive metabolic innovation in Saccharomycotina yeasts.

Many remarkable phenotypes have repeatedly occurred across vast evolutionary distances. When convergent traits emerge on the tree of life, they are sometimes driven by the same underlying gene families, while other times, many different gene families are involved. Conversely, a gene family may be repeatedly recruited for a single trait or many different traits.