Whole-genome based phylogeny and comparative genomics of Sporidiobolales and related taxa of Basidiomycetes.

Abstract

Sporidiobolales is a fungal order of Basidiomycota within the subphylum Pucciniomycotina. This order encompasses significant yeasts, such as the oleaginous species Rhodotorulatoruloides and the opportunistic pathogen R.mucilaginosa. We present the sequencing and comparative analysis of 35 Sporidiobolales strains from 27 species, alongside a Leucosporidium strain (Leucosporidiales), and incorporating publicly available genomic data for related fungi. Based on the phylogenomics data, we found that the topologies obtained were relatively similar and in line with previous reports. A comparison between genomic makeup and previously described phenotypes revealed that the ability to utilize nitrate, raffinose, rhamnose, or sucrose clearly correlated with the existence of key enzymes involved in the corresponding metabolic pathways. However, similar associations could not be established for other carbon sources, such as maltose, galactose, or xylose. We further identified orthologs that are specifically present or absent in each taxon. These results and the genomic sequencing data will help in gaining a better understanding of these non-model yeast species.