Haplotype-resolved chromosome-level genome assembly of Alpinia officinarum Hance

Alpinia officinarum Hance is a medicinal and edible plant whose secondary metabolites possess significant pharmacological value. However, the lack of genomic resources has hindered a comprehensive understanding of this species and constrained its breeding efforts. In this study, we integrated PacBio HiFi, Illumina paired-end (PE), and high-throughput chromosome conformation capture (Hi-C) sequencing data to construct the first haplotype-resolved, chromosome-level reference genome of A. officinarum Hance. The resulting assembly achieved a contig N50 of 51.42 Mb, with the two haplotypes spanning 2.08 Gb and 2.00 Gb, respectively, and anchored onto 48 chromosomes. Repetitive sequences accounted for 82.04% and 81.02% of the two haplotypes, within which 34,601 and 33,642 protein-coding genes were annotated in the non-repetitive regions, respectively. This high-quality genomic resource provides a solid foundation for genomic and genetic studies of A. officinarum Hance and related Zingiberaceae species, and also facilitates future haplotype-based breeding efforts.