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

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 for the querying of genes, functional annotations, protein domains, homologs, and other gene-related functional information of more than 500 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.

Acknowledgements

We thank Bo Yuan at Lianzhi Technology Co., Ltd for assistance with computing acceleration. This work was supported by grants from the Beijing University of Agriculture (Start-up fund) to Y.Z., Young Teachers’ Research and Innovation Capacity Enhancement Program QJKC2022044 and Beijing Municipal Education Commission Scientific Research Plan Project KM202310020010 to S.Wang. The computing power was supported by the Alibaba Cloud.

Author contributions

Z.F. and Y.Z. designed the project. S.Wei, Y.D., S.Wu, H.P., X.Z., S.Z., J.L., H.L., Y.F., Y.Yi, R.L., H.Z., Y.W., R.Z., L.N., and Y.Z. performed data collection. S.Wei, Y.Q., H.P., and S.Wang performed data analysis. S.Wei and Y.Z. wrote the code for database construction. Y.Yao, Z.F., and Y.Z. supervised the project and wrote the manuscript. All authors read and approved the final manuscript.

Data availability

All datasets have been made publicly available at http://hort.moilab.net/.

Conflict of interest statement

The authors declare that they have no conflict of interest.

Supplementary data

Supplementary data is available at Horticulture Research online.

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