Chromosome-level genome assembly of the large carpenter bee Xylocopa dejeanii Lepeletier, 1841 (Hymenoptera: Apidae)

• Published in: Scientific data Vol. 12; no. 1; pp. 1280 - 7
• Main Authors: Zhang, Dan, Jin, Jianfeng, Niu, Zeqing, Orr, Michael C., Zhang, Feng, Ferrari, Rafael R., Wu, Qingtao, Zhou, Qingsong, Da, Wa, Zhu, Chaodong, Luo, Arong
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 23.07.2025; Nature Publishing Group; Nature Portfolio
• Subjects: 631/181/2480; 631/208; Animals; Bees - genetics; Chromosomes; Chromosomes, Insect; Data Descriptor; Evolution; Genes; Genome, Insect; Genomes; Genomics; Humanities and Social Sciences; Molecular Sequence Annotation; multidisciplinary; Plant reproduction; Pollination; Pollinators; Proteins; Quality control; Science; Science (multidisciplinary); Social behavior; Xylocopa dejeanii; Xylocopinae
• ISSN: 2052-4463; 2052-4463
• DOI: 10.1038/s41597-025-05641-1

Xylocopinae, a diverse bee subfamily comprising over 1,000 bee species, and also a major model system for studying the pollination and evolution of sociality. The lack of chromosome-level genome assembly resources for the Xylocopinae limits our research of their biology and evolution. Here, we provided the first pseudo-chromosomes genome assembly of the Xylocopa dejeanii combined PacBio CLR long reads, Illumina sequences, and Hi-C data. The final genome is 194.44 Mb located in 16 chromosomes. Our assembly includes 141 scaffolds, with a scaffold N50 length of 13.15 Mb. BUSCO analysis revealed 99.00% completeness. Genome annotation identified 28.27 Mb of repetitive elements, 10,970 protein-coding genes, and 432 ncRNAs. This high-quality X. dejeanii assembly advances our understanding of Xylocopinae genomics and provides new insights into bee evolution.