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Orchids have a huge reservoir of secondary metabolites making these plants of immense therapeutic importance. Their potential as curatives has been realized since times immemorial and are extensively studied for their medicinal properties. Secondary metabolism is under stringent genetic control in plants and several molecular factors are involved in regulating the production of the metabolites. However, due to the complex molecular networks, a complete understanding of the specific molecular cues is lacking. High-throughput omics technologies have the potential to fill up this lacuna. The present study deals with comparative analysis of high-throughput transcript data involving gene identification, functional annotation, and differential expression in more than 30 orchid transcriptome data sets, with a focus to elucidate the role of various factors in alkaloid and flavonoid biosynthesis. Comprehensive analysis of the mevalonate (MVA) pathway, methyl-d-erythritol 4-phosphate (MEP) pathway, and phenylpropanoid pathway provide specific insights to the potential gene targets for drug discovery. It is envisaged that a positive stimulation of these pathways through regulation of pivotal genes and alteration of specific gene expression, could facilitate the production of secondary metabolites and enable efficient tapping of the therapeutic potential of orchids. This further would lay the foundation for developing strategies for genetic and epigenetic improvement of these plants for development of therapeutic products.

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Background: V. planifolia is of tremendous commercial importance as a source of an important flavor, vanilla, which is the backbone of the culinary and perfumery industry. Hence, efforts to ease cultivation and promote growth in this plant are need of the hour. Nuclear factor-Y (NF-Y) gene family, a class of vital transcription factors, plays a pivotal role in a large number of developmental processes. Objectives: The present study aims to identify and characterize NF-Y gene family in Vanilla planifolia which would bring insights to their role as key factors promoting growth and development in this orchid. Methods: Physico-chemical characterization, protein structure prediction and interaction, establishment of evolutionary relationship and expression profiling were attempted using various in silico tools. Results: Twenty five putative NF-Y members were identified in Vanilla planifolia, which were further classified into three sub-classes, NF-YA (13), NF-YB (7) and NF-YC (5), on the basis of specific domains and conserved regions. Prediction of three dimensional structure was done on the basis of structural similarity with NF-Y structure templates. Evolutionary analysis with the NF-Ys of Arabidopsis thaliana and Oryza sativa, classified these into three major clusters which indicated towards similarity of functions. Variable expression of VpNF-Y genes confirmed their role in diverse functions. VpNF-YA genes generally showed higher expression in vegetative tissues while a few VpNF-YBs showed seed specific expression. Protein-protein interaction indicated complex formation for optimum function. Conclusions: This work paves way for further functional characterization of NF-Y genes in Vanilla planfolia.