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Type III polyketide synthases (PKSs) catalyse the formation of an array of polyketides with diverse structures that play an important role in secondary metabolism in plants. This group of enzymes is encoded by a multigene family, the Type III  polyketide synthase (PKS)  gene family. Vast reserves of secondary metabolites in orchids make these plants suitable candidates for research in the area. In this study, genome-wide searches lead to the identification of five  PeqPKS , eight  DcaPKS  and six  AshPKS  genes in  Phalaenopsis equestris ,  Dendrobium catenatum  and  Apostasia shenzhenica,  respectively. All the members showed the presence of two characteristic conserved domains (Chal_sti_synt_N and Chal_sti_synt_C) and were generally localised in the cytoplasm. The phylogenetic analysis led to the classification of these proteins into two groups: CHS (chalcone synthase (CHS) and non-CHS. A single protein in  P. equestris  and two proteins each in  D. catenatum  and  A. shenzhenica  clustered within the CHS clade. The majority of the genes exhibited similar structural patterns with a single intron. Expression profiling revealed the tissue-specific expression of these genes with high expression in reproductive tissues for most genes. A number of stress-responsive  cis -regulatory elements were predicted, noteworthy amongst these are, ABRE and CGTCA that are chiefly responsible for responding to abscisic acid and methyl jasmonate, respectively. Our study provides a reference framework for future studies involving functional elucidation of  PKS  genes and biotechnological production of polyketides. Communicated by Ramaswamy H. Sarma

Polyketide synthases (PKSs) of secondary metabolism: in silico identification and characterization in orchids