Kingdom-wide analysis of the evolution of the plant type III polyketide synthase superfamily

Figure 3.

Figure 3. Phylogenetic tree of type III PKSs with information on syntenic cluster membership, and type of the sequence according to pPAP-classification. The phylogenetic tree, based on amino acid sequences, indicates that the LAP ortholog containing clade and the 'R-4-C'-containing clade evolved by an early duplication event (early GD). The 'R-4-C'-containing syntenic clusters 2/14, 4 and 5 containing clades form highly related but mostly distinct clades in the phylogenetic tree indicating that cluster 2/14, 4 and 5 evolved by duplication events. The LAP5/6 clade contains orthologs of LAP5 and 6 from Arabidopsis thaliana (Supplementary Table S4). Blue arrows indicate 'R-4-A' sequences that evolved independently several times. Blue arrows with star (*) indicate STS sequences of Vitis vinifera, Arachis duranensis, Arachis ipaensis and from Gymnosperms. Magenta arrows indicate duplication events involving (proto) 'R-4-C'-type PKS sequences. Magenta arrows with a star indicate the origin of 'R-4-C' sequences from these events. The gene tree containing 1607 unique sequences was build using RAxML using 1000 bootstrap replications. Supplementary Figure 3 and 4 show information on the taxonomy. The tree shows high transfer bootstrap expectation values (Lemoine et al., 2018) for all major clades (cf. Supplementary Figure 5). Experimentally validates sequences are indicated by numbers. 1: triketide and tetraketide pyrone synthase, PKS18; 2: phloroglucinol synthase; 3: RppA; 4: quinolone synthase; 5: β-ketoacyl carrier protein synthase III; 6: 2'-oxoalkylresorcylic acid synthase, ORAS; 7: CsyB; 8: 2'-oxoalkylresorcinol synthase, ORS; 9: hydroxyalkyl α-pyrone synthase, LAP; 10: hydroxyalkyl α-pyrone synthase, LAP5; 11: hydroxyalkyl α-pyrone synthase, LAP6; 12: stilbenecarboxylate synthase, SCS; 13: valerophenone synthase, VPS, VPS annotated with 'R-4-C' also show prenylflavonoid synthase function; 14: diketide-CoA synthase, DCS; 15: curcuminoid synthase, CS/CURS; 16: octaketide synthase, OS; 17: chromone synthase; 18: aleosone synthase; 19: pyrrolidine ketide synthase; 20: alkylresorcylic acid synthase, ARS; 21: acridone synthase, ACS; 22: benzalacetone synthase, BAS; 23: olivetol synthase, OLS: 24: 2-pyrone synthase, 2-PS; 25: orcinol synthase; 26: benzophenone synthase, BPS.