Drivers of genetic diversity in secondary metabolic gene clusters within a fungal species

Abstract

Filamentous fungi produce a diverse array of secondary metabolites (SMs) critical for defense, virulence, and communication. The metabolic pathways that produce SMs are found in contiguous gene clusters in fungal genomes, an atypical arrangement for metabolic pathways in other eukaryotes. Comparative studies of filamentous fungal species have shown that SM gene clusters are often either highly divergent or uniquely present in one or a handful of species, hampering efforts to determine the genetic basis and evolutionary drivers of SM gene cluster divergence. Here, we examined SM variation in 66 cosmopolitan strains of a single species, the opportunistic human pathogen Aspergillus fumigatus. Investigation of genome-wide within-species variation revealed 5 general types of variation in SM gene clusters: nonfunctional gene polymorphisms; gene gain and loss polymorphisms; whole cluster gain and loss polymorphisms; allelic polymorphisms, in which different alleles corresponded to distinct, nonhomologous clusters; and location polymorphisms, in which a cluster was found to differ in its genomic location across strains. These polymorphisms affect the function of representative A. fumigatus SM gene clusters, such as those involved in the production of gliotoxin, fumigaclavine, and helvolic acid as well as the function of clusters with undefined products. In addition to enabling the identification of polymorphisms, the detection of which requires extensive genome-wide synteny conservation (e.g., mobile gene clusters and nonhomologous cluster alleles), our approach also implicated multiple underlying genetic drivers, including point mutations, recombination, and genomic deletion and insertion events as well as horizontal gene transfer from distant fungi. Finally, most of the variants that we uncover within A. fumigatus have been previously hypothesized to contribute to SM gene cluster diversity across entire fungal classes and phyla. We suggest that the drivers of genetic diversity operating within a fungal species shown here are sufficient to explain SM cluster macroevolutionary patterns.

Whole-genome sequencing of Aspergillus tubingensis G131 and overview of its secondary metabolism potential

“…It seems that genomic variability between strains and thus their potential to produce specific metabolites were only caused by genomic mutations or genes acquisition / deletion but not chromosomal re-arrangement. This result is in agreement with Lind et al (2017) which argued that the identity and total number of SM clusters can vary between very closely related species, as for the four studied Aspergillus sp., whose genomes exhibit very high sequence and synteny conservation [37]. SM clusters prediction in A. tubingensis G131 was done using two available software packages: AntiSMASH and SMURF [38,39].…”

Orthologous peramine and pyrrolopyrazine‐producing biosynthetic gene clusters in Metarhizium rileyi, Metarhizium majus and Cladonia grayi

“…The large genetic distance separating the Cladonia and Metarhizium lineages indicates that these larger clusters represent the ancestral state of the PPZ locus, rather than the single perA gene found in Epichloë species. Degenerative processes such as gene deletion and inactivation are common mechanisms generating secondary metabolite diversity in fungal species (Lind et al ., ). For example, Epichloë elymi contains a functional four‐gene EAS cluster encoding for chanoclavine I biosynthesis (Schardl et al ., ), yet the common ancestor of all Epichloë spp.…”

“…However, fungal SM clusters often contain additional ‘accessory’ genes that innovate on these core structural motifs. Accessory gene content variation is one of the primary mechanisms generating within‐class SM diversity between different fungal strains and species (Lind et al ., ; Schardl et al ., ). The SM repertoire of a pathogenic fungus is one of the primary determinants for virulence and host specificity (Macheleidt et al ., ).…”

Biosynthesis of abscisic acid in fungi: identification of a sesquiterpene cyclase as the key enzyme in Botrytis cinerea

“…One of the main outcomes of this study was the enrichment in TEs within horizontally transferred clusters, clusters that change in genomic locations, and idiomorphic clusters. One hypothesis to explain this observation is that TEs may be responsible for repeat‐driven recombination and gene rearrangements (Lind et al ., ). In the case of ABA in B. cinerea , it would be interesting to investigate whether TEs could be responsible for the dual localization of the Bcaba genes.…”

“…Enzymes that are involved in the biosynthesis of one fungal secondary metabolite and its derivatives are usually clustered at one genomic locus (Hoffmeister and Keller, ; Wisecaver and Rokas, ; Lind et al ., ). The main counterexample is the biosynthesis of the DHN (dihydroxynaphthalene) melanin that is produced by almost all fungi.…”