## 3 Results and Discussion
### Type I PKS Phylogeny  
Our maximum-likelihood phylogeny of TI-PKS with a total of 624 sequences recovered from twenty-three fungal genomes and supplemented with previously published sequences is the largest analysis of biosynthetic gene content of various TI-PKS genes in lichen-forming fungi to date. The TI-PKSs phylogenetic tree is divided into six main subgroups (Figure 3): Bacterial Type II PKS (including bacterial and mitochondrial ketoacyl-ACP-synthetases; used as outgroup), Bacterial Type I PKS (also including some fungal sequences), animal fatty acid synthase (FAS), PR-PKS, NR-PKS, and R-PKS. Lichen PKS genes are distributed across the three of these main subgroups, viz. PR-PKS, NR-PKS, and R-PKS. These groups were also recognized by [PERSON] et al. [14] and [PERSON] et al. [6], but both used the single KS domain for tree reconstruction, and the latter subsumed PR-PKS and R-PKS. \begin{table}
\begin{tabular}{l r r r r r r r r r r} \hline \hline
**Assembly** & \begin{tabular}{c} **No. of** \\ **Contigs** \\ \end{tabular} & \begin{tabular}{c} **Largest** \\ **Contig (bp)** \\ \end{tabular} & \begin{tabular}{c} **Total Length** \\ **(Mb)** \\ \end{tabular} & \begin{tabular}{c} **GC (\%)** \\ \end{tabular} & \begin{tabular}{c} **NS0 (bp)** \\ \end{tabular} & \begin{tabular}{c} **N75 (bp)** \\ \end{tabular} & \begin{tabular}{c} **BUSCO** \\ **Completeness (\%)** \\ \end{tabular} & \begin{tabular}{c} **Genes** \\ **Predicted** \\ \end{tabular} & \begin{tabular}{c} **Proteins** \\ **Predicted** \\ \end{tabular} \\ \hline \begin{tabular}{l} _Rananina_ \\ _intermedia_ \\ \end{tabular} & 196 & 898,913 & 26.2 & 51.89 & 273,318 & 142,876 & **97.5** & 7405 & 7355 \\ \hline \begin{tabular}{l} _Ranulina_ \\ _perviviana_ \\ \end{tabular} & 1657 & 694,821 & 26.9 & 50.75 & 40,431 & 15,829 & 90.0 & 6756 & 6706 \\ \hline \
\begin{tabular}{l} _Usnea_ \\ _hakonensis_ \\ \end{tabular} & 879 & 624,317 & 41.1 & 45.57 & 166,123 & 71,534 & **96.5** & 10,700 & 10,641 \\ \hline
\begin{tabular}{l} _Xanthoria_ \\ _elegans_ \\ \end{tabular} & 261 & 990,773 & 44.3 & 40.70 & 385,707 & 188,494 & **98.2** & 9033 & 8911 \\ \hline \hline \end{tabular}
\end{table} 
Table 4: _Cont._Figure 3: Maximum-likelihood phylogeny of Type I PKS genes inferred by IQ-TREE using Type II. Bacterial PKSs as outgroup. Clades containing lichen-forming fungi are highlighted and the corresponding Orthogroups (1 to 9, respectively) are indicated by different colors. PR-PKS corresponds  
to Orthogroup 1 (green); the nine NR-PKS groups (NR-I to NR-IX) belong to Orthogroups 2, 3 and 4 (dark blue, pink and light green, respectively); the ten R-PKS groups (R-I to R-X) belong to Orthogroups 5, 6, 7, 8, and 9 (light blue, red, peach, orange, and lilac, respectively). Characteristic secondary substances for the groupings are given in the corresponding colored boxes. Groups not containing lichen-forming fungal genes are indicated by grey boxes. For each group, the domain arrangement of PKS is highlighted with distinct colors: SAT--starter unit-ACP transacy-lase; KS--ketoacyl synthase; AT--acyltransferase; ACP--acyl carrier protein; KR--ketoreductase; DH--dehydratase; ER--enoyl reductase; CMeT--methyltransferase; TE--thioesterase; HTT--helix-to-helix; ADH--adhydrolase; NAD--NAD-binding; Carn--Choline/Carnitine O-acyltransferase domain. * _TI-PKS domain content mostly corresponds to phylogeny_ TI-PKS genes encode for multi-domain enzymes, with each domain executing a specific function. The order and domain content of the PKSs thus defines the class of polyketides produced by the corresponding BGC. The presence or absence of individual domains has led to the classification of fungal PKSs into three main subgroups. The first subgroup comprises NR-PKSs, which lack reductive domains. The generalized domain content of NR-PKS in fungi studied here is SAT-KS-AT-DH-ACP-[ACP]-HTH-CMeT-[TE or ADH or NAD]-[Peptidase S9] (NR-I to NR-IX; Figure 3). The second subgroup comprises PR-PKSs containing a single KR domain or KR and DH domains.