A novel Arabidopsis phyllosphere resident Protomyces sp. and a re-examination of genus Protomyces based on genome sequence data

Protomyces is a genus of yeast-like fungi that is currently defined as plant pathogens of only Umbelliferae (Apiaceae) and Compositae (Asteraceae) family plants. Many Protomyces species have been proposed; however, there is a lack of molecular data and available specimens for Protomyces spp., just over ten species are officially accepted and only six species are preserved and available in public culture collections for examination. Phylogenetic relationships and species boundaries within this genus remain largely controversial. Recently, we isolated Protomyces strains from wild Arabidopsis thaliana (Arabidopsis), a Brassicaceae family plant only distantly related to the accepted Protomyces hosts. We have previously sequenced the genomes of all the currently publicly available Protomyces species, together with a strain (SC29) we isolated from the Arabidopsis phyllosphere. Genome-wide phylogenetic analysis suggests that SC29 occupies a unique phylogenetic position in the genus Protomyces. The SC29 genome has low average nucleotide identity values in comparison with other species genomes. As physiological evidence, SC29 has morphological characteristics and carbon assimilation patterns that distinguish it from the other six Protomyces species. Analysis with several nuclear gene phylogenetic markers further confirms SC29 as a novel Protomyces species and suggests the act1 gene DNA sequences can be used together with ITS sequences for the rapid identification of Protomyces species. In our previous study, SC29 could persist on the Arabidopsis phyllosphere in both short term laboratory and overwinter outdoor garden experiments and Protomyces spp. (or OTUs) were found in the Arabidopsis phyllosphere at multiple sites in both Finland and Germany. We conclude that SC29 is a novel Protomyces species isolated from Arabidopsis and propose the name of Protomyces arabidopsidicola sp. nov. Additionally, the genus Protomyces may not be strictly associated with only Compositae or Umbelliferae family host plants, as evidenced by SC29 and Protomyces strains previously isolated from plants in other families. The merging of two Protomyces species found to have high genomic similarity (P. inouyei and P. lactucaedebilis) is also proposed.