Genomic and phenotypic comparison of Terrestrial and Aquatic Rhodotorula yeasts

Genomic and phenotypic comparison of Terrestrial and Aquatic Rhodotorula yeasts at  Fungal Genetics Conference, Pacific Grove, CA, Asilomar Conference Grounds

Abstract: 

Aquatic and marine environments can harbor specialist and generalist fungi exhibiting filamentous and yeast morphologies. Rhodotorula yeasts are red and orange pigmented basidiomycetes found in a broad range of environments including terrestrial biomes, marine and freshwater aquatic environments. Their near ubiquity in most biomes is intriguing as to whether it is a generally resilient fungus or is adept at rapid and specific adaptation to new environments. Isolation of these fungi from environments is straightforward with semi-selective media and easy to identify pigmented colonies. We have curated a set of strains for genomic and phenotypic exploration benefiting from extensive culture collections of Rhodotorula strains from at least 10 described species. These isolates have origins spanning food spoilage, soils, plants, rocks, and aquatic environments. Particular efforts were performed to isolate strains from brackish, mangrove, and tidal flat areas in China to identify species diversity and distribution among several similar environments. We have sequenced genomes of these strains to produce a set of 300 draft genomes and 10 reference quality genomes for type strains for most species. These efforts are intended to test how environmental origin, genomic composition and allelic diversity relate to phenotypes including carotenoid production, sensitivity to osmotic, UV, and heavy metal stresses. We used automated robotic approaches to image colony growth on solid media in the UCR ExFAB BioFoundry to test whether phenotype traits of aquatic isolates differ from those collected in terrestrial environments. Genome comparative approaches included population genomics of strains within a species complex and gene content and synteny between species. Our approaches to isolate these fungi from aquatic and terrestrial environments have produced a rich collection of fungal diversity and the comparisons will help identify adaptations to aquatic or marine environments and further test the hypothesis about these fungi resilience and adaptability.