CassavaDB: An integrated multi-omics resource for functional genomics and molecular breeding of cassava

Dear Editor,

Cassava (Manihot esculenta) is a vital tropical staple and economic crop for hundreds of millions of people across Africa, Asia, and Latin America. Improving its yield and quality is of great importance for food security and sustainable agriculture. Although several cassava databases, such as CassavaBase, TCOD, and TropiCODB, have been developed, a truly comprehensive platform that deeply integrates multi-omics data, along with powerful online analysis tools, is still lacking in the cassava research field. In contrast, soybean researchers have developed the SoyOmics database, enabling deep multi-omics integration and visualization from gene to phenotype.

To fill this critical gap in cassava research, we developed CassavaDB (https://nature.hainanu.edu.cn/CassavaDB/), a comprehensive multi-omics database platform dedicated to cassava. CassavaDB provides genomic, transcriptomic, and metabolomic data along with integrated analysis tools tailored for cassava research. The platform consolidates data from 50 cassava varieties, encompassing 2,370,477 genes, 13,187 microRNAs (miRNAs) (across 34 families), and over 50 million genetic variants (Figure 1A). It also integrates 1,538 bulk transcriptomic samples and two single-cell transcriptomic datasets comprising a total of 58,116 cells from root and leaf tissues, covering 24 distinct cell types and identifying 6,453 marker genes. In addition, the platform hosts metabolomic profiles covering 2,980 metabolic traits across 299 cultivated cassava varieties. Besides, CassavaDB provides comparative metabolite expression profiles for three representative cultivars (KU50, R11, and TME3) along with differential metabolite analyses under SLCMV infection. Built on the guiding concept of “multi-omics integration-functional mining-breeding support,” CassavaDB strives to accelerate functional gene discovery (Figure 1B) and the development of new cassava varieties through multilayered data connections (Figure 1C) and robust analytical capabilities (Figure 1D).

Genome module

CassavaDB provides access to 50 high-quality genome assemblies from diverse cassava accessions, including reference cultivars such as AM560 (v7/v8), and key African varieties like TME3 and TME7. Among these, one genome (XX048) has reached telomere-to-telomere (T2T) assembly level, and 49 are assembled at the chromosome level. The dataset includes 7 wild cassava accessions (e.g., A4011, A4041, A4047, A4111, A4144, A4160, and W14), while the remaining 43 are cultivated cassava. Of these, 30 genomes were obtained from our previous studies and published resources,7,8 and 20 novel high-quality assemblies were generated in this study. The genome module offers powerful tools for gene search, miRNA search, and gene family exploration. Specifically, the gene search function allows users to retrieve gene information across different cultivars using gene IDs, names, or relevant keywords (Figure 1E). The miRNA module compiles 13,187 cassava miRNAs belonging to 34 families. The gene family module, leveraging tools like PFAM, identifies 6,920 protein families, enabling researchers to browse genes by family or functional category with ease. CassavaDB integrates a suite of commonly used bioinformatics tools to accelerate data mining and functional exploration. An embedded BLAST tool enables rapid sequence similarity searches between user-provided sequences and cassava genomic data, the PCR Primer Designer automatically generates optimal primer sets based on gene sequences, and the Functional Enrichment module allows researchers to perform GO and KEGG pathway enrichment analyses on gene lists, uncovering the biological processes and pathways underlying gene sets of interest (Figures 1F and 1G). Additionally, the platform includes advanced visualization tools such as JBrowse2 for genome browsing, SynVisio for synteny visualization, and ID mapping utilities, offering a seamless, one-stop analytical experience for cassava researchers.