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

Area of Science:

• Plant genomics
• Functional genomics
• Bioinformatics

Background:

• Orchidaceae family exhibits high species diversity and significant ornamental, medicinal, cultural, and ecological value.
• Multi-omics approaches are crucial for gene discovery and functional genomics but are underutilized in orchids due to a lack of integrated data platforms.
• Understanding key traits, such as floral morphology, requires integrated multi-omics data analysis.

Purpose of the Study:

• To develop OrchidMD, an integrated multi-omics database for Orchidaceae research.
• To provide a platform for efficient gene mining and analysis of multi-omics data in orchids.
• To facilitate the understanding of genetic mechanisms underlying important orchid traits.

Main Methods:

• Integration of genomics, transcriptomics, proteomics, metabolomics, and phenomics data for 213 orchid species.
• Development of a user-friendly platform with 18 specialized statistical and analytical tools.
• Case studies involving pan-ARF gene family identification and gene editing (CRISPR/Cas9) for trait analysis.

Main Results:

• OrchidMD successfully integrates diverse omics data, offering tools for gene mining and interactive analysis.
• Identification of the pan-ARF gene family across Orchidaceae species was demonstrated.
• Experimental validation showed that CsiARF04 overexpression promotes rhizome differentiation, and CRISPR/Cas9 enabled gene editing in Cymbidium sinense.

Conclusions:

• OrchidMD is a valuable resource for identifying candidate genes related to orchid traits and elucidating regulatory mechanisms.
• The platform significantly advances multi-dimensional biological research and functional genomics in orchids.
• OrchidMD facilitates comprehensive analysis and experimental validation in orchid research.