Are there conserved biosynthetic genes in lichens? Genome-wide assessment of terpene biosynthetic genes suggests conserved evolution of the squalene synthase cluster

Abstract Lichen-forming fungi (LFF) are prolific producers of functionally and structurally diverse secondary metabolites, most of which are taxonomically exclusive delivering lineage-specific roles. But are there evolutionary conserved biosynthetic pathways in lichens? Based on the current evidence it seems there aren’t any. This notion is derived from polyketide-derivatives as most biochemical investigations on lichens focused on PKSs whereas the other class of compounds remain mostly unexplored. Here we present first systematic identification and comparison of lichenized fungal terpene synthases which are ever-present in the LFF, however, they have never been systematically analyzed. We gathered 111 genomes of LFF representing 60 genera and 23 families and implemented genome mining and gene clustering approaches to identify and group the clusters into networks of similar biosynthetic clusters. Our large-scale analysis led to the identification of 733 terpene BGCs with varying degrees of mutual similarity, most of them were unique. Remarkably, we found two widely distributed and homologous networks – both squalene/phytoene clusters - putatively involved in sterol/ergosterol biosynthesis. These clusters contain the same core gene, but different sets of accessory genes. This indicates an early gene duplication event, followed by gene losses and gains of accessory genes, leading to different architecture of the two clusters. We show that sequence divergence, gene duplications, losses and rearrangement and are the major factors driving the evolution of this cluster across LFF. Our study shows lichenized fungi do have a core biosynthetic cluster, bringing the first indication that a biosynthetic gene may form an essential gene content in lichens.