OrchidMD: An Integrated and User-Interactive Orchid Multi-Omics Database for Mining Genes and Biological Research

The Orchidaceae family, with its unparalleled species diversity among angiosperms, is integral to ornamental, medicinal, cultural, and ecological value. Multi-omics techniques have proven invaluable for the identification of candidate genes and the advancement of functional genomics research. Nevertheless, the application of these technologies in Orchidaceae remains severely limited due to the lack of effective platforms that can integrate and analyze multi-omics data, especially in understanding the mechanisms underlying key traits such as distinctive floral morphology. In this study, we present OrchidMD, the Orchid Multi-omics Database (www.orchidcomics.com), a resource platform that integrates data from five omics layers: genomics, transcriptomics, proteomics, metabolomics, and phenomics, encompassing a total of 213 species. OrchidMD is equipped with 18 specialized statistical and analytical tools, and features a user-friendly interface that facilitates efficient gene mining, multi-omics data exploration, and integrative interactive analysis. A case study on the comprehensive identification of the pan-ARF gene family across Orchidaceae species demonstrates the effectiveness and convenience of OrchidMD. Furthermore, experimental validation further shows that transgenic overexpression of CsiARF04 promotes the differentiation and budding of orchid rhizomes. In addition, another case study using gene editing in orchids, CRISPR Design was employed to predict the CsiPDS target site in Cymbidium sinense. Effective editing was subsequently achieved via Agrobacterium-mediated delivery of the CRISPR/Cas9 vector into leaves. These results underscore OrchidMD's formidable capacity to discern candidate genes associated with salient traits and elucidate their regulatory mechanisms. Thus, OrchidMD serves as a pivotal platform advancing multi-dimensional biological research and functional genomics in orchids.