Comparative genomics including the early-diverging smut fungus Ceraceosorus bombacis reveals signatures of parallel evolution within plant and animal pathogens of fungi and oomycetes

Ceraceosorus bombacis is an early-diverging lineage of smut fungi and a pathogen of cotton trees (Bombax ceiba). To study the evolutionary genomics of smut fungi in comparison with other fungal and oomycete pathogens, genome of Ce. bombacis was sequenced and comparative genomic analyses were performed. The genome of 26.09 megabases encodes for 8024 proteins, of which 576 are putative secreted effector proteins (PSEPs). Orthology analysis revealed 30 ortholog PSEPs among six Ustilaginomycotina genomes, the largest groups of which are lytic enzymes, such as aspartic peptidase and glycoside hydrolase. Positive selection analyses revealed the highest percentage of positively selected PSEPs in Ce. bombacis compared to other Ustilaginomycotina genomes. Metabolic pathway analyses reveal the absence of genes encoding for nitrite and nitrate reductase in the genome of human skin pathogen Malassezia globosa, but these enzymes are present in the sequenced plant pathogens in smut fungi. Interestingly, these genes are also absent in cultivable oomycete animal pathogens, but only nitrate reductase has been lost in cultivable oomycete plant pathogens. Similar patterns were also observed in obligate biotrophs and hemi-biotrophs of fungal and oomycete pathogens. Furthermore, it was also found that both fungal and oomycete animal pathogen genomes are lacking cutinases and pectinesterases. Overall, these findings highlight the parallel evolution of certain genomic traits, revealing potential common evolutionary trajectories within smuts, but also among fungal and oomycete pathogens, shaping the pathogen genomes according to their lifestyle.