Nucleotide composition bias of rDNA sequences as a source of phylogenetic artifacts in Basidiomycota—a case of a new lineage of a uredinicolous Ramularia-like anamorph with affinities to Ustilaginomycotina

Abstract

A Ramularia-like hyphomycete was discovered on uredinia of Phakopsora ampelopsidis on leaves of wild Ampelopsis brevipedunculata and cultivated Parthenocissus tricuspidata in several cities in Taiwan. The micromorphology of this fungicolous fungus is similar to that of species of the genus Ramularia which are mostly plant parasites but some species grow on rust fungi. Analyses of SSU and LSU rDNA and RPB2 gene sequence data and of ultrastructural features observed by scanning and transmission electron microscopy revealed that the fungus represents a novel lineage within the Ustilaginomycotina. The name Quasiramularia phakopsoricola is proposed for this new species in a new genus, a new family, and a new order. Sequence data obtained for ITS1, 5.8S, and ITS2 rDNA, however, did not match to any known fungal lineage. Bioinformatics analyses showed that these sequence data are extremely GC poor, but most probably do not represent a pseudogene. Extreme deviations of GC content can be observed in several lineages of Basidiomycota. Such variations affect the results of phylogenetic analyses and are an important source of artifacts.

Mycoparasitism in Basidiomycota

“…Mycoparasitism remains largely unknown in Ustilaginomycotina, a group dominated by phytoparasites and animal-associated yeasts. Only recently, Quasiramularia phakopsoricola was described as a mycoparasite of the rust Phakopsora ampelopsidis (Pucciniales) (Kolařík et al 2021). Quasiramularia phakopsoricola is known to reproduce asexually only, and morphologically this species displays more similarities to other mycoparasites from the genus Ramularia (Ascomycota) than to other members of Basidiomycota.…”

“…Mycoparasites among Basidiomycota comprise a heterogenous, phylogenetically diverse group of fungi, most of them belonging to subphyla Agaricomycotina and Pucciniomycotina (Aime et al 2014, Weiß et al 2014. Clear examples of mycoparasitic interactions in Ustilaginomycotina are rare, e.g., Kolařík et al (2021) introduced Quasiramulariales to accommodate a recently discovered mycoparasite of a phytoparasitic rust fungus. In Pucciniomycotina, mycoparasitism is phylogenetically widely distributed and occurs in at least six out of ten classes, whereas in Agaricomycotina, the majority of mycoparasites is restricted to Tremellomycetes.…”