Reference genome assemblies for the North American bumble bees Bombus flavifrons and Bombus fervidus, two phenotypically polymorphic species from distinct phylogenetic lineages.

We present genome assemblies for 2 bumble bee (Hymenoptera: Apidae: Bombus) species: Bombus (Pyrobombus) flavifrons and Bombus (Thoracobombus) fervidus. These species are widespread pollinators across North America and both exhibit intraspecific color pattern variation across their ranges due to Müllerian mimicry. These genomes will thus be a useful resource both for studies of native pollinator biology and the evolution of phenotypic variation. We used a combination of single molecule HiFi sequencing and Hi-C sequencing in each species to produce highly contiguous and complete genome assemblies. Utilizing publicly available data, the Eukaryotic Genome Annotation Pipeline was used to generate gene annotations. The B. flavifrons genome was assembled into a total of 483 scaffolds, with 18 primary assembled molecules representing putative chromosomes (scaffold N50 = 15.6 Mb), with a total length of 310.5 Mb. Annotation identified 12,476 genes (10,137 protein coding) with a Benchmark of Single-Copy Orthologs (BUSCO) protein score of 97.9% complete (97.6% complete and single copy). The B. fervidus genome was assembled into a total of 181 scaffolds, with 19 assembled chromosomes (scaffold N50 = 15.3 Mb, contig N50 = 10.3 Mb), and a total length of 314.3 Mb. Annotation revealed 13,353 genes (10,599 protein coding), with a BUSCO protein score of 98.8% complete (98.3% complete and single copy). We present summaries of gene and repetitive element distributions across the putative chromosome scaffolds and synteny analyses of both species to closely related chromosome-scale Bombus genomes.