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Genomics

Genomics

Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...

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

Yonglu Wei¹, Zengyu Lin¹, Qi Xie¹

¹Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China.

Plant Biotechnology Journal

|November 11, 2025

Summary

A new database, OrchidMD, integrates five omics layers for 213 orchid species. This resource aids in identifying genes for traits like floral morphology and advancing orchid functional genomics.

Keywords:

ARF Orchidaceae database functional genomics multi‐omics

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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.