Phylogenetic relationships among ascomycetes: evidence from an RNA polymerse II subunit

TLDR

RPB2 is a single‑copy, large gene with a modest evolutionary rate that provides strong phylogenetic resolution for Ascomycota. The study aimed to develop a viable alternative to the 18S rRNA system for fungal systematics by examining the nuclear RPB2 gene. The authors generated phylogenies from RPB2, encoding the second largest subunit of RNA polymerase II, and compared them with 18S rDNA trees. The RPB2 phylogeny matched the 18S rDNA tree but yielded markedly higher bootstrap support for deeper branches, identified three major Ascomycota lineages (Archiascomycetes, Saccharomycetales, Euascomycetes), confirmed Neolecta’s placement, and demonstrated RPB2’s effectiveness for resolving fungal relationships.

Abstract

In an effort to establish a suitable alternative to the widely used 18S rRNA system for molecular systematics of fungi, we examined the nuclear gene RPB2, encoding the second largest subunit of RNA polymerase II. Because RPB2 is a single-copy gene of large size with a modest rate of evolutionary change, it provides good phylogenetic resolution of Ascomycota. While the RPB2 and 18S rDNA phylogenies were highly congruent, the RPB2 phylogeny did result in much higher bootstrap support for all the deeper branches within the orders and for several branches between orders of the Ascomycota. There are several strongly supported phylogenetic conclusions. The Ascomycota is composed of three major lineages: Archiascomycetes, Saccharomycetales, and Euascomycetes. Within the Euascomycetes, plectomycetes, and pyrenomycetes are monophyletic groups, and the Pleosporales and Dothideales are distinct sister groups within the Loculoascomycetes. We confirm the placement of Neolecta within the Archiascomycetes, suggesting that fruiting body formation and forcible discharge of ascospores were characters gained early in the evolution of the Ascomycota. These findings show that a slowly evolving protein-coding gene such as RPB2 is useful for diagnosing phylogenetic relationships among fungi.