Abstract
Piptanthus nepalensis (Hook.) Sweet is a leguminous shrub native to the Himalayan region and is valued for its medicinal uses and ornamental yellow flowers. Here, we report a chromosome-scale genome assembly of P. nepalensis generated using PacBio HiFi long reads, Illumina short reads, and Hi-C chromatin interaction data. The assembled genome spans approximately 1.04 Gb, with a contig N50 of 39.5 Mb and a scaffold N50 of 111.5 Mb. Benchmarking universal single-copy orthologs (BUSCO) analysis indicated high completeness for both the genome (99.3%) and predicted protein set (99.2%). Approximately 99.0% of the assembled sequences were anchored onto nine pseudo-chromosomes. We annotated 26,035 protein-coding genes, and repetitive elements were estimated to comprise ~75.2% of the genome. This high-quality genome assembly provides a foundational genomic resource for P. nepalensis and supports future studies on its biology and utilization.
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Data availability
The raw Illumina, PacBio, Hi-C, and RNA-seq sequencing data are available in the NCBI Sequence Read Archive (SRA) under accession number SRP679460. The final chromosome-level genome assembly is available in NCBI GenBank under accession number JBVQTV000000000. The genome annotation files are available in Figshare (https://doi.org/10.6084/m9.figshare.30416158.v1).
Code availability
All software and pipelines were implemented in full compliance with the manuals and protocols specified by the respective published bioinformatics tools. No custom programming or coding was employed.
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Acknowledgements
The computations in this research were performed using the CFFF platform of Fudan University. This work was supported by the Science and Technology Projects of Xizang Autonomous Region, China (Project Nos. XZ202402ZD0005, XZ202402ZY0023, XZ202402JX0003, XZ202401ZR0028, and XZ202303ZY0002G), and by the Open Project of the Key Laboratory of Biodiversity and Environment on the Qinghai-Tibet Plateau, Ministry of Education (Project No. KLBE2025003).
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Y.W., J.W., and L.Q. conceived and designed the research framework. J.Z., and Z.Z. collected the samples, prepared experimental materials, and conducted laboratory work. N.B., N.N., N.T., and X.T. contributed to data acquisition, curation, and preliminary analyses. Z.Z. and J.Z. performed the formal data analysis and drafted the initial manuscript, including figures and tables. Y.W., J.W., and L.Q. critically revised the manuscript for intellectual content and provided guidance throughout the study. All authors contributed to improving the manuscript and approved the final version for publication.
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Zhang, J., Zeng, Z., Bonjor, N. et al. Chromosome-Level Genome Assembly and Annotation of Piptanthus nepalensis (Hook.) Sweet. Sci Data (2026). https://doi.org/10.1038/s41597-026-07134-1
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DOI: https://doi.org/10.1038/s41597-026-07134-1
