Abstract Horticultural crops comprising fruit, vegetable, ornamental, beverage, medicinal and aromatic plants play essential roles in food security and human health, as well as landscaping. With the advances of sequencing technologies, genomes for hundreds of horticultural crops have been deciphered in recent years, providing a basis for understanding gene functions and regulatory networks and for the improvement of horticultural crops. However, these valuable genomic data are scattered in warehouses with various complex searching and displaying strategies, which increases learning and usage costs and makes comparative and functional genomic analyses across different horticultural crops very challenging. To this end, we have developed a lightweight universal search engine, HortGenome Search Engine (HSE; http://hort.moilab.net ), which allows querying genes, functional annotations, protein domains, homologs, and other gene-related functional information of more than 400 horticultural crops. In addition, four commonly used tools, including ‘BLAST’, ‘Batch Query’, ‘Enrichment analysis’, and ‘Synteny Viewer’, have been developed for efficient mining and analysis of these genomic data.

HortGenome Search Engine, a universal genomic search engine for horticultural crops