AlliumDB: a central portal for comparative and functional genomics in Allium

Abstract

The genus Allium belongs to the botanical family Amaryllidaceae and includes economically important crops such as onion, garlic, bunching onion, and leek, used as vegetables, spices, and traditional medicines. The large sizes of Allium genomes hamper the genetic dissection of agronomically important traits and molecular breeding. With the growing accumulation of genomic, resequencing, transcriptome, and phenotypic data, the demand for an integrative Allium database is increasing. Here we present a user-friendly database, AlliumDB ( https://allium.qau.edu.cn ), as a functional genomics hub integrating public and in-house data. The database contains all currently available nuclear and organelle genomes for Allium species, with genes comprehensively annotated based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, orthology, gene families, protein families (Pfam), and non-coding RNA families (Rfam). Transcriptome and variation profiles are integrated into dynamic visualization tools. We took phenotypic photographs and generated trait records for hundreds of Allium germplasms collected worldwide, which are included in the database. We incorporated JBrowse for the visualization of gene structures, RNA sequencing data, and variation data. Analysis tools such as the basic local alignment search tool (BLAST), sequence fetch, enrichment, and motif analyses are available to explore potential gene functions. This database incorporates comprehensive Allium genotypic and phenotypic datasets. As the community assembles new genomes and generates resequencing data for Allium germplasms, the database will be improved and continuously updated with these multi-omics data and comparative genomic studies. We expect the AlliumDB database to become a key resource for the study of Allium crops.

Acknowledgements

We thank Professor Zhen Su and Ms Wenying Xu for their valuable comments and suggestions. This work was supported by grants from the National Natural Science Foundation of China (32002064, 32170313, and 32000458), the Youth Fund of Shandong Natural Science Foundation (ZR2020QC070), the Taishan Scholar Foundation of the People’s Government of Shandong Province, and Breeding Plan of Shandong Provincial Qingchuang Research Team (2021).

Author contributions

Z.Z. and Y.L. designed the project; Y.L., P.Y., Y.Y., Q.Y., and L.D. constructed the website; Y.L., B.L., C.Y., Y.J., and A.L. collected the data; Y.L. and P.Y. wrote the manuscript; B.L., Z.Z., and Y.L. revised the manuscript.

Data availability

The AlliumDB can be freely accessed at http://allium.qau.edu.cn and http://bioinformatics.nat300.top/Allium/. A reliable data management system has been developed, and all newly released information will be updated on this website. Enquiries concerning the database should be directed by e-mail to [e-mail].

Supplementary data

Supplementary data is available at Horticulture Research online.

Conflict of interest

None declared.

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