In a phylogenetic tree of type III polyketide synthases (PKS), the amino acid sequences from angiosperms diverge into two clusters. One group consists of chalcone synthases (CHS). CHS is ubiquitously distributed in higher plants. The second cluster is formed by PKSs, which functionally diverge from CHS, such as benzophenone synthase (BPS) and biphenyl synthase (BIS).
The two clusters originate from the duplication of a common ancestral gene prior to the speciation of the angiosperms. One gene after the duplication event retained the CHS function which is indispensable for plants (UV protection, flower pigmentation etc.). Due to the functional redundancy, the other gene after the duplication event was free to undergo remarkable functional diversification during the speciation of the angiosperms. Under the environmental selection pressure, mutagenic amino acid exchanges generated functional modifications which resulted in the formation of new defence compounds against herbivores and pathogens
The functionally diverse PKS phenotypes include BIS and BPS which group together closely in the phylogenetic tree. BIS and BPS are subbranches of the same higher branch, indicating that these two benzoic acid-specific type III PKSs result from a relatively recent functional divergence of a common ancestral gene.
A phylogenetic tree of CoA ligases also consists of two large, evolutionarily different clusters. One group comprises CoA ligases of benzenoid metabolism including cinnamate:CoA ligase and benzoate:CoA ligase, which points to their origin from a common ancestral gene. The second group comprises 4-coumarate:CoA ligases from angiosperms, gymnosperms, ferns and mosses, which arise from another ancestral gene. Thus, the two large clusters appear to have separated before the diversification of the evolutionary lines of higher plants.
