## 3 Results and Discussion
### Type I PKS Phylogeny
The generalized domain content in PR-PKS according to our phylogeny is KS-AT-[DH]-KR-ACP (PR-PKS; Figure 3). Finally, the third subgroup--R-PKSs--contains a complete set of reductive domains, viz. KR, DH, and ER and thus exhibit the following domain structure: KS-AT-DH-CMeT-ER-KR-ACP-[Carn] (R-I to R-X; Figure 3). Additional domains, such as helix-to-helix (HTH), anhydrorolase (ADH), NAD-binding (NAD), Peptide S9, and Choline/Carnitine O-acyltransferase domain (Carn) were not shown in the previous studies of TI-PKS in lichen-forming fungi. We discuss them in detail below in the corresponding sections. * _The discrepancy of grouping PKS genes_ Assigning PKS genes to different groups in fungi on the account of gene domain composition and their synthesized products was introduced by [PERSON] et al. [14] and later refined based on DH-domain pocket sizes by [PERSON] et al. [69] and [PERSON] et al. [70]. This classification was used in several studies investigating PKS gene diversity in lichen-forming fungi, e.g., [29; 71]. Despite this existing classification, it remains unclear if all groups indeed form monophyletic clades and if all genes from one group synthesize the same (or at least chemically similar) substances. In our phylogeny, previously proposed groups were not always monophyletic (e.g., NR-II; Figure 3), and experimentally characterized genes from one group have been shown to produce different substances (e.g., PKS81 and AGNPKS1 in NR-V; Figure 3). Additionally, we performed an ortholog clustering using Orthofinder on all TI-PKS sequences to provide an objective way of identifying groups of sequences. This resulted in nine orthogroups (Figure 3: colored clades), named Orthogroup 1 to Orthogroup 9, respectively. Orthogroup 1 corresponds to the PR-PKSs (Figure 3). NR-PKSs are spread across Orthogroups 2, 3, and 4 but none of them correspond explicitly to any of the nine groups identified before by [PERSON] et al. [71] and [PERSON] et al. [29]. Orthogroups 5, 6, 7, 8, and 9 contain R-PKSs, where only Orthogroup 6 (R-IV) and 7 (R-V) agree with groups defined in [PERSON] et al. [14] and [PERSON] et al. [72]. However, all Orthogroups identified here form well supported clades in the PKS phylogeny (Figure 3). The discrepancy between our results and previous studies needs to be investigated in subsequent studies. In our phylogeny, several groups of the NR-PKS and R-PKS showed differences in the PKS domains present corresponding to the supported clades; these groups do contain support from different sources and thus merit discussion (see below). 3.1. Lichen-Forming Fungi Contain Only a Few Partially Reducing PKSs in the Phylogenetic Neighbourhood to Bacterial PKSs  
The PR-PKS sequences formed a well-supported clade sister to bacterial Type I PKS sequences with other fungal PKSs (PR-PKS; Figure 3). Their domain configuration is KS-AT-[DH]-KR-ACP, including only a single reductase domain (KR). In contrast to the large NR- and R-PKS groups, PR-PKS contains genes mainly from _Aspergillus_ and _Penicillium_, and only a few genes from lichen-forming fungi. Genes from the studied fungal genomes have the typical PR-PKS domain composition, but in two genes from two _Ramalina_ (ram-intpred_001715 and ramperpred_002012), the DH domain was missing. PR-PKS genes form a sister clade to Bacterial Type I PKSs (Figure 2). Bacterial T1-PKSs often possess a KR domain catalyzing the first step in the reductive modification of beta-carbonyl centers in the growing polyketide chain. This domain requires NADPH to reduce the keto- to a hydroxy group [73]. The \"simple\" domain configuration of Bacterial and PR-PKS genes compared to NR- and R-PKSs has not escaped our attention. Our study was not designed to specifically test how PKS genes in Ascomycetes were acquired and how they diversified. However, the placement of Bacterial and NR-PKS sequences as the earliest branches in our phylogeny supports the hypothesis suggested by [PERSON] et al.