New reference genome assembly for the declining American Bumble Bee, Bombus pensylvanicus

Authors: LOZIER, JEFFREY - University Of Alabama; Schweizer, Rena; Sim, Sheina; Koch, Jonathan; Branstetter, Michael; BENAVIDES, LIGIA - Harvard University; Geib, Scott; Evans, Jay

Submitted to: G3: Genes, Genomes, Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/31/2025
Publication Date: 8/11/2025
Citation: Lozier, J.D., Schweizer, R.M., Sim, S.B., Koch, J., Branstetter, M.G., Benavides, L.R., Geib, S.M., Evans, J.D. 2025. New reference genome assembly for the declining American Bumble Bee, Bombus pensylvanicus. G3: Genes, Genomes, Genetics. Volume 15, Issue 10. https://doi.org/10.1093/g3journal/jkaf181.
DOI: https://doi.org/10.1093/g3journal/jkaf181

Interpretive Summary: In collaboration with the University of Alabama and Harvard University, ARS scientists created a high-quality map of the DNA (genome) for the bumble bee species the American bumble bee, Bombus pensylvanicus. This bumble bee used to be common across eastern North America, but its numbers and the areas where it lives have gone down over time. Scientists are interested in this bee because it may help us understand why bumble bees are disappearing, and whether genes play a role in that. The final genome is very complete and well-organized. It is about 352.6 million base pairs long and was put together into 224 pieces, with 19 large sections that are likely the bee’s chromosomes. Genome assembly analysis confirmed 11,411 genes, including over 10,000 that make proteins. The genome assembly is about 99% complete, which means it’s a reliable resource for research.

Technical Abstract: We present a new chromosome-level genome assembly for Bombus pensylvanicus, a historically widespread native pollinator species that ranges across eastern North America but has subsequently undergone declines in range area and local relative abundance. This species has been of significant interest as a model for understanding both patterns and possible causes of bumble bee decline in the region, including the possible role of genetic variation. Using a combination of long read Pacific Biosciences Revio HiFi sequencing, HiC sequencing, and RNA sequencing of multiple tissue types, we have assembled an intact and complete genome with high quality annotations. The B. pensylvanicus genome has a total length of ~352.6 Mb and was assembled into a total of 224 scaffolds, with 19 primary pseudomolecules representing putative chromosomes and an N50 = 14.872 Mb. Annotation with the Eukaryotic Genome Annotation Pipeline – External (EGAPx) identified 11,411 genes (10,263 protein coding), and BUSCO analysis of 5,991 Hymenoptera-specific BUSCO groups indicated a completeness for the proteins of 99.0% (98.6% single-copy, 0.5% duplicated) and for the genome of 98.5% (98.2% single-copy, 0.3% duplicated). We present synteny analyses with other recently-assembled genomes for other Thoracobombus subgenus taxa to examine the distribution of repetitive regions of the genome relative to the distribution of genes and non-coding RNAs.