Taxogenomic analysis of a novel yeast species isolated from soil, Pichia galeolata sp. nov


D.A. Opulente et al. "Taxogenomic analysis of a novel yeast species isolated from soil, Pichia galeolata sp. Nov" Yeast 40:608 (2023) [DOI:10.1002/yea.3905]


A novel budding yeast species was isolated from a soil sample collected in the United States of America. Phylogenetic analyses of multiple loci and phylogenomic analyses conclusively placed the species within the genus Pichia. Strain yHMH446 falls within a clade that includes Pichia norvegensis, Pichia pseudocactophila, Candida inconspicua, and Pichia cactophila. Whole genome sequence data were analyzed for the presence of genes known to be important for carbon and nitrogen metabolism, and the phenotypic data from the novel species were compared to all Pichia species with publicly available genomes. Across the genus, including the novel species candidate, we found that the inability to use many carbon and nitrogen sources correlated with the absence of metabolic genes. Based on these results, Pichia galeolata sp. nov. is proposed to accommodate yHMH446(T) (=NRRL Y-64187 = CBS 16864). This study shows how integrated taxogenomic analysis can add mechanistic insight to species descriptions.

Data Access

All gene and genome sequence data have been deposited in GenBank under the accession numbers described above. All other data are contained within the manuscript and its supplements; Paired-end Illumina DNA sequencing reads were used to generate whole genome assemblies using the meta-assembler iWGS v1.1 (Zhou et al., 2016). The “best” assembly was chosen for each species based on genome size and N50 value (Supporting Information: Table S3). The genome assembly for strain yHMH446 is available at JANIWQ000000000. Genome quality was assessed by quantifying their completeness based on the expected gene content of the Benchmarking Universal Single-Copy Orthologs (BUSCO) (v5.2.2) (Simão et al., 2015; Waterhouse et al., 2017). We used a set of 1711 genes inferred by BUSCO to be universal in Saccharomycotina. GenBank numbers for the ITS, LSU, and TEF1 sequences for yHMH446 are OL583853, OL583873, and OM328112.

Phylogenetic relationships