The transcriptome of Paraphelidium tribonemae illuminates the ancestry of Fungi and Opisthosporidia

SUMMARY Aphelids constitute a group of diverse, yet poorly known, parasites of algae [1, 2]. Their life cycle and morphology resemble those of zoosporic fungi (chytrids) and rozellids (Cryptomycota/Rozellosporidia), another specious group of parasites of fungi and oomycetes [3, 4]. Unlike fungi, which are osmotrophs, aphelids and rozellids are phagotrophs, feeding on the host’s cytoplasm. Combined RNA polymerase and rRNA gene trees [5] suggested that aphelids and rozellids relate to Microsporidia, extremely reduced parasites with remnant mitochondria [6]. Accordingly, aphelids, rozellids and Microsporidia were proposed to form a monophyletic clade, called Opisthosporidia, sister to Fungi [1]. Microsporidia would have subsequently lost the ancestral opisthosporidian phagotrophy. However, the limited phylogenetic signal of those genes combined with microsporidian fast-evolving sequences have resulted in incongruent tree topologies, showing either rozellids [5, 7] or aphelids [8] as the earliest-branching lineages of Opisthosporidia. We have generated the first transcriptome data for one aphelid species, Paraphelidium tribonemae [2]. In-depth multi-gene phylogenomic analyses using various protein datasets place aphelids in a deep, pivotal position as a sister group to Fungi, making Opisthosporidia paraphyletic. We infer a rich, free-living-like proteome for P. tribonemae, which includes cellulases likely involved in algal cell-wall penetration, enzymes involved in chitin biosynthesis and several metabolic pathways that were lost in the comparatively reduced Rozella allomycis genome [9]. Our results suggest that Fungi evolved from a complex phagotrophic opisthosporidian ancestor, likely a specialized endobiotic predator, which became osmotrophic at the fungal root and evolved towards phagotrophic parasitism in the rozellid/microsporidian line.