New Multi Omics Database Advances Chrysanthemum Research and Breeding

The Asteraceae family boasts more than 25,000 species, with chrysanthemums ranking among its most iconic and economically valuable members. Having been cultivated for over three millennia in China and beyond, these plants hold deep cultural, medicinal, and horticultural significance. Yet, despite a growing number of sequenced chrysanthemum genomes, researchers have struggled with fragmented data and limited tools for integrating multi-omics analyses. In contrast, crops like rice and tomato already benefit from powerful genomic databases that drive both discovery and breeding. Due to these limitations, there is a pressing need to develop an integrated database for in-depth multi-omics studies of Chrysanthemum.

In a advancement for ornamental plant science, researchers at the Sanya Institute of Nanjing Agricultural University have developed the Chrysanthemum Genome Database (CGD), the first centralized multi-omics resource tailored to chrysanthemums. Published (DOI: 10.1093/hr/uhae238) in Horticulture Research on August 21, 2024, CGD combines cutting-edge tools with rich genomic and transcriptomic datasets. The platform enables researchers worldwide to explore gene functions, visualize expression profiles, and design targeted CRISPR edits-laying the groundwork for next-generation chrysanthemum research and breeding.

CGD integrates reference genomes from six Chrysanthemum species, spanning wild, edible, and cultivated varieties. With over 540,000 protein-coding genes annotated across multiple functional databases (NR, SwissProt, GO, KEGG), the database provides a robust foundation for exploring gene evolution and regulatory pathways. Users can delve into expression profiles derived from nine plant organs, five floral stages, and stress treatments including cold exposure and pathogen infection. This spatiotemporal data is accessible through a visually driven 'RNA Data' module, complete with interactive tools like an eFP browser.

The database also includes a synteny analysis module, helping researchers trace conserved gene families and explore polyploidy dynamics. A particularly innovative feature is the CRISPR search module, which supports both generic and paralog-specific sgRNA design-crucial for editing genes in the complex genomes of polyploid chrysanthemums. Beyond genomics, CGD hosts a suite of auxiliary tools-from GO/KEGG enrichment analysis to co-expression networks-that empower users to conduct in-depth functional studies. Altogether, CGD is more than a database-it's a comprehensive bioinformatics ecosystem for chrysanthemum science.

Our mission with CGD was to bring chrysanthemum research into the multi-omics era. We've combined the latest genomic insights with intuitive tools to help researchers uncover gene functions, streamline breeding, and accelerate innovation. We believe CGD will serve not just as a data hub, but as a global collaboration platform that enables deeper exploration into the biology and improvement of this important plant."

Professor Aiping Song, study's senior author

CGD is poised to become the go-to platform for molecular breeding, functional genomics, and evolutionary studies in Chrysanthemum. Its unified design supports efficient marker discovery, trait mapping, and CRISPR-based genetic engineering-all essential for developing improved varieties with better yield, resilience, and ornamental value. Looking ahead, the team plans to continuously expand CGD by incorporating proteomics, epigenomics, metabolomics, and high-throughput phenotype data. With its commitment to open access and global collaboration, CGD is set to power the next wave of innovation in chrysanthemum biology and beyond.