Sweetpotato Germplasm and Genome Resource Database

The Genome module collects genome assemblies from hexaploid sweetpotato cultivars and diploid relatives, and provides assembly archives, genome browsing, transcription-factor comparison, a curated functional gene catalogue, sequence and annotation search, synteny analysis, and orthology exploration.

An archive of 20 genome assemblies from 16 materials of 9 species. Records can be searched by keyword and filtered by species and ploidy. Assemblies can be sorted by source, N50, or genome size. The detail panel shows material photographs, genome size, N50, number of sequences, gene number, genome and transcriptome BUSCO scores, assembly and annotation methods, species description, source, and publications.

Genome Browse is powered by JBrowse2. Users can navigate to any genomic region by coordinate (e.g., Chr01:1000000..2000000) or gene ID. Gene annotation, repeat, and other feature tracks are preloaded. Synteny tracks between selected assembly pairs are also available for cross-genome comparison.

iTAK classifications are available for eight assemblies: Beauregard v4, Xushu 18 / IBA 1.0, Mx23Hm / Itr r2.2, NSP306 v3, NSP323 v3, New Kawogo v3, Tanzania v3, and Pasi3. The module contains 62,013 transcription-factor records in 69 families and 12,941 transcriptional-regulator records in 24 families. An assembly-by-family matrix supports comparative browsing, while the member table can be searched by genome, family, or gene/transcript identifier and exported as TSV.

A curated catalogue of 239 experimentally characterized sweetpotato genes in 51 functional categories, compiled from publications between 1985 and 2026. Each record lists the gene or locus, specific function or mechanism, validation system, alias, protein family, GenBank accession, gene or transcript ID, major phenotype, and a linked reference. The table supports keyword, category, and year filtering, sorting, pagination, and TSV download.

All gene models from 10 genome assemblies are indexed. Users can search by gene ID to retrieve gene coordinates, exon–intron structure, CDS and protein sequences, and functional annotation. Results include a structure diagram and downloadable FASTA sequences.

All gene models are functionally annotated based on homology with Arabidopsis thaliana, InterProScan domain assignments, GO terms, and KEGG pathway mappings. Users can search by keyword (e.g., "drought", "starch synthase") to retrieve candidate genes across all supported species.

Whole-genome synteny was constructed by pairwise alignment using minimap2 (asm5 preset). Alignment results are stored in PAF format. Users can compare any two supported assemblies and browse syntenic blocks as an interactive Plotly dotplot. Both inter-species and intra-species haplotype comparisons are supported.

Orthologous gene groups across all 10 assemblies were inferred by OrthoFinder v2 using DIAMOND all-vs-all protein comparisons. Users can input a gene ID to retrieve its orthogroup members across all genomes and view the phylogenetic gene tree rendered by ggtree.