Lichens are known producers of a variety of secondary metabolites. Fungal polyketides constitute a large family of these secondary metabolites that have a high degree of struc-tural diversity. Usnic acid is a lichen metabolite that has a broad range of biological ac-tivities. However the use of usnic acid in medical applications is limited due to the slow growth of the lichen in nature. In order to conduct in depth studies on compounds such as usnic acid it will be necessary to express their gene clusters in fast growing organisms. To achieve this goal, polyketide biosynthesis in the lichen fungi Cladonia uncialis has been investigated to identify the gene clusters that are responsible for secondary metabo-lites production. This thesis reports the de novo whole-genome sequencing of the lichen Cladonia un-cialis, in silico analysis of polyketide biosynthetic gene clusters, and putative identifica-tion and annotation of 56 different secondary metabolite gene clusters. The identified gene clusters include thirty two different type I polyketide synthase genes (non-reducing, partly reducing and highly reducing PKS genes) gene clusters besides two gene clusters of type III PKS gene, three independent, novel non-ribosomal peptide synthetases (NRPS) biosynthetic gene clusters, as well as seven noncanonical NRPS genes that did not contain condensation (C) domains, three polyketide non-ribosomal (PKS-NRP) hy-brid gene clusters, one lanthipeptide synthase gene and six different terpene synthase gene clusters. Out of 32 candidate genes a single PKS has been identified as being re-sponsible for usnic acid biosynthesis. The structure of one of the lichen non-reducing PKS genes that is responsible for produc-tion of a halogenated lichen metabolite was also studied. Based on the biosynthetic opera-tions of the gene cluster as well as catalogued examples of halogenated polyketides iso-lated from lichen fungi to date, this study suggests that the gene cluster is a biosynthetic gene for an unidentified anthraquinone. The ketosynthase and the acyltransferase do-mains among two different non reducing PKS genes from Cladonia uncialis genome se-quence are also studied. The amino acid sequences of the domains are confirmed by us-ing mass spectrometry. Protein homology modeling was performed using the Swiss-Model server. The generated protein models were visualized using LASERGENE Pro-tean 3D molecular visualization system. / May 2015