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Chromosome-level genome assembly and annotation of two Asian bumble bees
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  • Published: 09 January 2026

Chromosome-level genome assembly and annotation of two Asian bumble bees

  • Jixiang Cui1,
  • Ye Xu2,
  • Jiyao Liu1,
  • Xinyang Zhang1,
  • Zhaoyang Chen1,
  • Wanhu Yang1,
  • Jin Ge3 nAff8,
  • Cheng Sun  ORCID: orcid.org/0000-0001-7476-92244,
  • Yifan Zhai5,
  • Zhimin Chang6,
  • Lixia Tian7,
  • Yuange Duan  ORCID: orcid.org/0000-0003-2311-98591,
  • Fan Song1,
  • Wanzhi Cai1,
  • Hu Li1 &
  • …
  • Li Tian  ORCID: orcid.org/0000-0002-7288-96761 

Scientific Data , Article number:  (2026) Cite this article

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We are providing an unedited version of this manuscript to give early access to its findings. Before final publication, the manuscript will undergo further editing. Please note there may be errors present which affect the content, and all legal disclaimers apply.

Subjects

  • Comparative genomics
  • Entomology

Abstract

The bumblebee Bombus patagiatus Nylander, 1848 and Bombus lantschouensis Vogt, 1908 (Hymenoptera: Apidae) are ecologically important bumble bee species native to East Asia, with considerable value for agricultural pollination and domestication. Despite their ecological and economic relevance, the lack of high-quality genomic resources has hindered in-depth investigations into their genetic architecture and evolutionary adaptations. Here, we present chromosome-level genome assemblies for both species, generated using a combination of PacBio HiFi long-read sequencing, Illumina short-read resequencing, and Hi-C scaffolding. The assembled genomes span 240.28 Mb (B. patagiatus) and 241.30 Mb (B. lantschouensis), with 94.38% and 94.00% of sequences anchored to 18 chromosomes, respectively. Genome annotation identified 17,351 and 16,023 protein-coding genes in B. patagiatus and B. lantschouensis, along with comprehensive repetitive element characterization. Both assemblies exhibit exceptional completeness, with BUSCO scores exceeding 99%, confirming their high quality and reliability. These genomic resources provide a critical foundation for future research on bumble bee evolution, population genetics, and the molecular basis of domestication traits.

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Data availability

All data generated in this study have been deposited in public repositories and are publicly available. The chromosome-level genome assemblies of Bombus patagiatus and Bombus lantschouensis are available in NCBI GenBank under the accession numbers JBSRNJ00000000037 and JBSRNK00000000038, respectively. Raw sequencing data, including PacBio HiFi, Hi-C, Illumina short reads, and transcriptome data, have been deposited in the Genome Sequence Archive (GSA) under the accession number CRA02799942. The corresponding genome annotation files are publicly available in the Figshare repository53. The assembled genomes are also archived in the Genome Warehouse (GWH)51,52.

Code availability

All analyses in this study were conducted using established bioinformatics tools available in the public domain. We exclusively employed published software packages, with each program’s specific version, parameters, and implementation details comprehensively described in the respective Methods sections. No custom scripts or in-house developed software were utilized during any phase of the genome assembly, annotation, or analysis pipeline.

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Acknowledgements

We thank Dr. Ling Ma from China Agricultural University for assisting data analyses; This work was supported by National Natural Science Foundation of China (32370487), China National Tobacco Corporation of Science and Technology Major Projects (110202201018 [LS-02]), the project of the Northeast Asia Biodiversity Research Center (2572022DS09) and the 2115 Talent Development Program of China Agricultural University.

Author information

Author notes

  1. Jin Ge

    Present address: Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, China

Authors and Affiliations

  1. Department of Entomology, State Key Laboratory of Agricultural and Forestry Biosecurity, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China

    Jixiang Cui, Jiyao Liu, Xinyang Zhang, Zhaoyang Chen, Wanhu Yang, Yuange Duan, Fan Song, Wanzhi Cai, Hu Li & Li Tian

  2. International Research Center of Cross-Border Pest Management in Central Asia, Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, College of Life Sciences, Xinjiang Normal University, Urumqi, China

    Ye Xu

  3. State Key Laboratory of Animal Biodiversity Conservation and Integrated Pest Management, Institute of Zoology, Chinese Academy of Sciences, Beijing, China

    Jin Ge

  4. College of Life Sciences, Capital Normal University, Beijing, China

    Cheng Sun

  5. Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, China

    Yifan Zhai

  6. Institute of Entomology, Provincial Special Key Laboratory for Developing and Utilizing of Insect Resources, Guizhou University, Guiyang, China

    Zhimin Chang

  7. Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China

    Lixia Tian

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Contributions

W.C., H.L. and L.T. contributed to the research design. J.C., W.Y., J.G. and L.T. collected the samples. J.C. and X.Z. performed the experiments. J.C., Z.C. and L.T. took photos of specimens. J.C., Y.X. and C.S. analyzed the data. J.C. and L.T. wrote the draft manuscript. J.C., J.L., L.T., Y.Z., Z.C., Y.D., F.S. and L.T. revised the manuscript. All authors contributed to this manuscript and agreed to the current version.

Corresponding authors

Correspondence to Hu Li or Li Tian.

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Cui, J., Xu, Y., Liu, J. et al. Chromosome-level genome assembly and annotation of two Asian bumble bees. Sci Data (2026). https://doi.org/10.1038/s41597-026-06568-x

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  • Received: 29 July 2025

  • Accepted: 06 January 2026

  • Published: 09 January 2026

  • DOI: https://doi.org/10.1038/s41597-026-06568-x

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