Modular control of orchid beauty: co-expression networks orchestrate organ development and evolution in Phalaenopsis flower

The Orchidaceae family is known for its extraordinary floral diversity and unique ecological adaptations. Beyond their scientific relevance, orchids represent a major component of the ornamental plant industry due to their high commercial value. Therefore, understanding the complex molecular networks that govern orchid flower development is a fascinating and relevant challenge. Despite extensive molecular knowledge, crucial gaps remain regarding the unique developmental programs of orchids. This work aims to present a transcriptomic analysis to investigate differential gene expression across floral tissues during the early stage of flower development in Phalaenopsis aphrodite, in order to uncover new orchid-specific patterns. The identification of co-expression networks, combined with Gene Ontology enrichment analysis, revealed key biological pathways active across distinct floral organs. We found tissue-specific enrichment of functions related to photosynthesis, lipid metabolism, and carbohydrate metabolism. Particular emphasis was placed on genes associated with labellum traits, including pigmentation and morphology, features that are crucial for pollinator attraction and central to orchid floral evolution. The expression patterns of selected genes were validated by qPCR in both wild-type and peloric Phalaenopsis mutants at early developmental stages. Overall, our findings advance the understanding of the molecular regulation underlying orchid flower development and provide new insights into the evolutionary mechanisms shaping floral diversity in orchids.