High Diversity of Type I Polyketide Genes in Bacidia rubella as Revealed by the Comparative Analysis of 23 Lichen Genomes

Abstract

Fungi involved in lichen symbioses produce a large array of secondary metabolites that are often diagnostic in the taxonomic delimitation of lichens. The most common lichen secondary metabolites—polyketides—are synthesized by polyketide synthases, particularly by Type I PKS (TI-PKS). Here, we present a comparative genomic analysis of the TI-PKS gene content of 23 lichen-forming fungal genomes from Ascomycota, including the de novo sequenced genome of Bacidia rubella. Firstly, we identify a putative atranorin cluster in B. rubella. Secondly, we provide an overview of TI-PKS gene diversity in lichen-forming fungi, and the most comprehensive Type I PKS phylogeny of lichen-forming fungi to date, including 624 sequences. We reveal a high number of biosynthetic gene clusters and examine their domain composition in the context of previously characterized genes, confirming that PKS genes outnumber known secondary substances. Moreover, two novel groups of reducing PKSs were identified. Although many PKSs remain without functional assignments, our findings highlight that genes from lichen-forming fungi represent an untapped source of novel polyketide compounds.