Chromosome-scale genome assembly of the Hunt bumble bee, Bombus huntii Greene, 1860, a species of agricultural interest

Authors: Koch, Jonathan; Sim, Sheina; Scheffler, Brian; LOZIER, JEFFREY - University Of Alabama; Geib, Scott

Submitted to: G3, Genes/Genomes/Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/2/2024
Publication Date: 7/19/2024
Citation: Koch, J., Sim, S.B., Scheffler, B.E., Lozier, J.D., Geib, S.M. 2024. Chromosome-scale genome assembly of the Hunt bumble bee, Bombus huntii Greene, 1860, a species of agricultural interest. G3, Genes/Genomes/Genetics. https://academic.oup.com/g3journal/advance-article/doi/10.1093/g3journal/jkae160/7716913.
DOI: https://doi.org/10.1093/g3journal/jkae160

Interpretive Summary: The Hunt bumble bee, Bombus huntii, is a widely distributed pollinator in western North America. To better understand B. huntii biology and support population genetic studies and breeding decisions, we sequenced and assembled the B. huntii genome from a single haploid male. High-fidelity sequencing of the entire genome using PacBio, along with HiC sequencing, led to a comprehensive contig assembly of high continuity. This assembly was further organized into a chromosomal arrangement, successfully identifying 18 chromosomes spread across the 317.4 Mb assembly with a BUSCO score indicating >98% completeness. These assembly outcomes, alongside the minimal tissue sampled destructively, showcase techniques for producing efficient, comprehensive, and continuous genome arrangements.

Technical Abstract: The Hunt bumble bee, Bombus huntii, is a widely distributed pollinator in western North America. The species produces large colony sizes in captive rearing conditions, experiences low parasite and pathogen loads, and has been demonstrated to be an effective pollinator of tomatoes grown in controlled environment agriculture systems. These desirable traits have galvanized producer efforts to develop commercial B. huntii colonies for growers to deliver pollination services to crops. To better understand B. huntii biology and support population genetic studies and breeding decisions, we sequenced and assembled the B. huntii genome from a single haploid male. High-fidelity sequencing of the entire genome using PacBio, along with HiC sequencing, led to a comprehensive contig assembly of high continuity. This assembly was further organized into a chromosomal arrangement, successfully identifying 18 chromosomes spread across the 317.4 Mb assembly with a BUSCO score indicating >98% completeness. Synteny analysis demonstrates shared chromosome number (n = 18) with B. terrestris, a species belonging to a different subgenus, matching the expectation that presence of 18 haploid chromosomes is an ancestral trait at least between the subgenera Pyrobombus and Bombus sensu stricto. In conclusion, these assembly outcomes, alongside the minimal tissue sampled destructively, showcase techniques for producing efficient, comprehensive, and continuous genome arrangements.