Diversity and evolution of polyketide biosynthesis gene clusters in the Ceratocystidaceae

Abstract

Polyketides are low-molecular weight secondary metabolites with diverse biological activities. Polyketide synthase (PKS) and other proteins responsible for producing these compounds are often encoded from genes that are clustered in the same genomic region. Functional analyses and recent genomic studies are increasingly showing that most fungi are capable of producing a repertoire of PKS compounds. In this study, we considered the potential of Ceratocystidaceae for producing polyketides by making use of a comparative genomics approach. The fungi in this family have diverse lifestyles ranging from being saprotrophs, insect associates through to plant pathogens. Our specific aims were to identify the putative polyketide biosynthesis gene clusters, to characterize them at the structural and phylogenetic levels and to predict the types of polyketide compounds they might produce. For this purpose, we used the whole genome sequences from nineteen species in the genera, Ceratocystis, Endoconidiophora, Davidsoniella, Huntiella, Thielaviopsis and Bretziella, to identify and characterise PKS gene clusters, by employing a range of bioinformatics and phylogenetic tools. Our results showed that all of the examined genomes contained putative clusters containing a non-reducing type I PKS and a type III PKS. Phylogenetic analyses suggested that these genes were already present in the ancestor of the Ceratocystidaceae after which they diverged together with the species harbouring them. By contrast, the various reducing type I PKS-containing clusters identified in these genomes, appeared to have distinct origins during the evolution of this family. Although one of the identified clusters potentially allows for the production of melanin, their functional characterization will undoubtedly reveal many novel and important compounds implicated in the biology of the Ceratocystidaceae.