Detection of Polyketide Synthase Genes in lichen Cladonia spp. by specific primers

Abstract

Lichens are well known for producing a great variety of secondary metabolites such as polyketides which have diverse biological roles and potential uses in pharmaceutical application. To attain a comprehensive understanding of polyketide synthase (PKS) gene diversity of lichen species from polar regions, thirty-two Cladonia samples were selected from Chile, the Artic and the Antarctic regions. The β-ketosynthase (KS) domains of putative PKS genes were amplified and sequenced using degenerate primers. We obtained 16 KS sequence fragments from direct sequencing and 40 fragments from cloning. Phylogenetic analyses of these 56 KS sequences showed that distinct 12 PKS types were retrieved, of which all belonged to non-reducing (NR) PKS. Three and eight kinds of types were included in NR clade I and clade II, respectively. The last type of PKS was basal to NR type I and type II. Tests for hypotheses between KS domains and their ITS-26S phylogeny showed that the relationships were not significantly different in the most OTUs belonged to type 9 and type 10. To make sure the existence of each type in Cladonia, type 4, 9 and 10 were especially selected and their primers were designed by KS domain sequences. These type-specific primers were not detected from clones except for their own clones of type 4, 9 and 10. Type10 were detected from all samples, but type 4 and 9 were detected 15 and 30 samples, respctively. Among the samples, 13 cladonia had all of the type4, 9 and 10.