# Trepenoid Biosynthesis Dominates among Secondary Metabolite Clusters in _Mucoromycotina_ Genomes
## 1 Introduction  
Early-diverging fungi were long considered to be devoid of secondary metabolite (SM) clusters; however, this perspective has gradually changed with the advancement of genome sequencing of selected representatives. The reviews by [PERSON], [PERSON] and colleagues [1, 2] showed that sequences similar to known secondary metabolite clusters (SMCs) can be identified in most analysed _Mucoromycota_ genomes. The identified SMCs harboured key enzymes involved in SM biosynthesis in _Dikarya_: polyketide synthases (PKS), nonribosomal peptide synthetases (NRPS), terpene cyclases/synthases (TC), and dimethylallyl tryptophan synthases (DMATS). One or several of the core genes are typically surrounded by accessory genes, most often encoding additional enzymes (e.g., transferases, hydroxylases), regulatory transcriptional factors and/or efflux transporters. The main classes of secondary metabolites in fungi include the respective compounds tied to the above core enzymes: polyketides, nonribosomal peptides, terpenoids and siderophores. The polyketides are produced by PKS clusters coding several proteins forming a multi-domain enzyme that condensates acyl-CoA precursors. Polyketides are typically modified by accessory enzymes, leading to the formation of complex structures. Aflatoxin, patulin and lovastatin belong to the best-studied fungal polyketides [3]. Nonribosomal peptides are catalysed without a mRNA template by a complex enzyme called NRPS. The peptide often includes noncanonical amino acids and is modified by accessory enzymes similar to polyketides. Well-known NRPS include \(\beta\)-lactam antibiotics, cyclosporine A and echinocandin [4]. Terpenes are isoprene polymers which often have multicyclic structures and can also be further modified, leading to the formation of terpenoids. Terpenes and terpenoids often possess scent, flavour or colour, like carotenes. Terpenoid compounds play diverse functional roles: they can serve as toxins (e.g., fusicoccin A of _Duporte amygdali_) or growth-promoting factors (e.g., gibberellin GA14 of _Fusarium fujikuro_) [5]. Siderophores are produced for the iron chelation needed for both storage and transport of this element. Iron is usually scarce, and many microorganisms produce siderophores to scavenge insoluble iron forms, e.g., fusarinines of _Fusarium_ spp., coprogen of _Pilobolus_ sp. and asperchromes B1-F3 of _Aspergillus ochraceus_[6]. Although siderophores are not a biosynthetic class of SMs on its own, they are biosynthesized by an NRPS in the case of hydroxamate-based siderophores (preferably in ascomycetes (e.g., triacetylfusarinine C) and basidiomycetes (e.g., basidioferrin)) or by NRPS-independent siderophore (NIS) biosynthetic enzymes in the case of polycarboxylate siderophores (preferably in early-diverging fungi such as _Mucoromycota_). For example, siderophore production has been confirmed in _Glamus_ (golomuferrin) [7], _Apophysomyces_[8] and _Rhizopus delmar_ (rhizoferrin) [9]. The latter has been further characterised. It belongs to the NIS family [9] and is likely to be regulated by glycosylation [10] (see the example in Figure 1). Experimental studies showed that different _Morierellomycin_ representatives produce diverse natural products with interesting properties e.g., malpinin acetylated hexapeptides and malpibaldin cyclic pentapeptides [11]. These compounds have been linked to the presence of several NRPS clusters, for example, in the mycelium of _Mortierella alpina_. The NRPS of _M. alpina_ are related to bacterial ones and contain atypical epimerase/condensation domains [12]. _Podila minutilsima_ (syn. _Mortierella minutilsima_) is used for an enantioselective bioconversion of limonee to perilla alcohol and perillaldehyde [13]. PKS and NRPS cluster presence was recently described in transcriptomes of five _Mucor_ species [14] and _Gigaspora margarita_[15]. The mycelium of _Mucor circinelloides_ was shown to produce carotenoids and terpenoids [1]. This property of _M. circinelloides_ is used in industrial settings.