Bottle gourd (Lagenaria siceraria), a versatile member of the Cucurbitaceae family, holds considerable economic significance and a rich cultural history spanning multiple civilizations. As a medicinal plant, it has long been valued for its diverse therapeutic properties, while its fruiting body is widely consumed for its distinctive taste and exceptional nutritional profile, encompassing nearly all essential components conducive to good health. The plant is also a potential source of physiologically active polysaccharides, and various parts have been extensively studied for their anti-inflammatory and analgesic activities, making it a compelling subject for genomic research and crop improvement programmes.

BGCNVdb is a comprehensive database dedicated to copy number variations (CNVs) in bottle gourd, cataloguing genomic structural variation across 145 whole-genome sequencing (WGS) genotypes sourced from the NCBI BioProject PRJNA952543. A total of 26,660 CNVs (18,322 deletions and 8,338 duplications) and 1,024 CNV regions (CNVRs) were identified across all 11 chromosomes, using the bottle gourd reference genome BVRC_Lsic_1.0 (GCA_049863445.1) as the reference assembly. This resource is intended to serve the bottle gourd research community as a high-utility platform for a broad range of applications including genotype identification, assessment of genetic diversity, marker–trait association studies, and the utilisation of structural genomic variation in plant breeding programmes aimed at the acquisition of desirable agronomic traits.