Comparative transcriptome-wide analysis of Polyketide Synthase (PKS) gene family amongst five Phalaenopsis species

In the present study, transcriptome-wide identification and characterization of polyketide synthase (PKS) also known as Chalcone synthase (CHS) genes which play a pivotal role in flavonoid biosynthesis in plants was done in five Phalaenopsis species (Phalaenopsis aphrodite, P. bellina, P. lueddemanniana, P. modesta and P. schilleriana). Three PKS genes were identified in each of the transcriptomes of P. bellina, P. lueddemanniana and P. modesta while P. aphrodite and P. schilleriana consisted of only one and two members, respectively. Domain and motif analysis depicted the conserved nature of this gene family. The enzymatically active residues and the signature sequence of PKS proteins were shown through a multiple sequence alignment. All the identified proteins were localized in the cytoplasm. Structure elucidation shows predominant alpha helices in the secondary structures. Molecular homology modelling depicted that these proteins showed structural similarity to PKS proteins of other plants. Phylogenetic analysis confirmed the clustering of these proteins into two separate clades, CHS and non-CHS. Variable expression was observed in the various vegetative and reproductive tissues which supported its role in overall growth and development. These studies provide a preliminary resource for future studies on understanding the pathway of flavonoid biosynthesis at a molecular level in orchids.