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Abstract We present the first chromosome-level genome assembly for Bombus pensylvanicus, a historically widespread native pollinator species that was distributed 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 role of genetic variation. Here we present a chromosome-level reference genome assembled using Pacific Biosciences singe-molecule HiFi sequences and Hi-C data and annotated using evidence derived from RNA sequencing of multiple tissue types. 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 Bombus genomes representing different subgenera and examine the distribution of repetitive regions of the genome relative to the distribution of genes and noncoding RNAs. 

Abstract Bumble bees (Bombus) exhibit exceptional diversity in setal body color patterns, largely as a result of convergence onto multiple Mullerian mimicry patterns globally. When multiple species cross the same sets of mimicry complexes, they can acquire the same color polymorphisms, providing replicates of phenotypic evolution. This study examines the genetic basis of parallel color pattern acquisition in three bumble bee taxon pairs in western North America that shift between orange-red and black mid-abdominal segmental coloration in Rocky Mountain and Pacific Coastal mimicry regions: polymorphic Bombus vancouverensis and B. melanopygus, and sister species B. huntii and B. vosnesenskii. Initial gene targets are identified using a genome-wide association study, while cross-developmental transcriptomics reveals genetic pathways leading to final pigmentation genes. The data show all three lineages independently target the regulatory region of a segmental-fate determining Hox gene, Abdominal B (Abd-B), for this color transition. For B. vancouverensis and B. melanopygus, this involves different deletions in the same location, and all mimicry pairs differentially express Abd-B and ncRNAs in this locus. Transcriptomics reveals a shared core gene network across species, where Abd-B interacts with nubbin and pigment enzyme ebony to decrease black melanin production in favor of paler, redder morphs. Expression of multiple genes in the melanin biosynthesis pathway is modified to promote this phenotype, with differing roles by taxon. Replicated morphologies unveil key genes and a Hox gene hotspot, while enabling evolutionary tracking of genetic changes to phenotypic changes and informing how gene regulatory networks evolve. 

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 Bombus huntii colonies for growers to deliver pollination services to crops. To better understand Bombus huntii biology and support population genetic studies and breeding decisions, we sequenced and assembled the Bombus 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 97.6% completeness. Synteny analysis demonstrates shared chromosome number (n = 18) with Bombus 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, the assembly outcome, alongside the minimal tissue sampled destructively, showcases efficient techniques for producing a comprehensive, highly contiguous genome.