AmDB: functional genomics database of Astragalus membranaceus

Astragalus membranaceus (A. membranaceus) belongs to the genus Astragalus within the family Leguminosae. Astragalus membranaceus var. mongholicus (A. mongholicus) is a variety of A. membranaceus. Its dried root is a Chinese herbal medicine, also known as "Huang Qi". Sequencing technology has made a large amount of high-quality transcriptomics data for A. mongholicus and A. membranaceus publicly available. Their whole genomes were sequenced in 2022 and 2024, respectively. Despite the increasing availability of genomic and transcriptomic data, a reliable platform for comparing and mining gene function information remains unavailable. To fill this gap, this study aimed to develop AmDB ( http://bioinformatics.nwnu.edu.cn/AmDB/ ), a functional genomics database of A. membranaceus. First, functional and structural annotations were performed for 27,245 genes based on genomic data, using algorithms and software tools. Second, 62 transcriptome samples were collected from the SRA database. A co-expression network was constructed using the Pearson correlation coefficient and the Mutual Rank method, containing 224,615 positive and 116,806 negative gene pairs, covering 94.87% of the coding genes. The network analysis revealed that the phenylalanine ammonia-lyase function was closely related to phenylpropanoid metabolism, and the positively co-expressed genes in the network exhibited similar expression patterns. These findings validated the reliability of the network. Finally, AmDB implemented easy-to-use bioinformatics tools, including gene set enrichment analysis, BLAST, sequence extraction, orthologue identification, JBrowse, and expression data extraction.