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ARS Home » Pacific West Area » Logan, Utah » Pollinating Insect-Biology, Management, Systematics Research » Research » Publications at this Location » Publication #401675
Research Project: Sustainable Crop Production and Wildland Preservation through the Management, Systematics, and Conservation of a Diversity of Bees

Location: Pollinating Insect-Biology, Management, Systematics Research

Title: Chromosome-scale genome assembly of the rusty patched bumble bee, Bombus affinis (Cresson)(Hymenoptera: Apidae), an endangered North American pollinator

Author
item Koch, Jonathan
item Sim, Sheina
item Scheffler, Brian
item Geib, Scott
item SMITH, TAMARA - U.S. FISH AND WILDLIFE SERVICE

Submitted to: G3, Genes/Genomes/Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/5/2023
Publication Date: 6/20/2023
Citation: Koch, J., Sim, S.B., Scheffler, B.E., Geib, S.M., Smith, T.A. 2023. Chromosome-scale genome assembly of the rusty patched bumble bee, Bombus affinis (Cresson)(Hymenoptera: Apidae), an endangered North American pollinator. G3, Genes/Genomes/Genetics. 13(8). Article jkad119. https://doi.org/10.1093/g3journal/jkad119.
DOI: https://doi.org/10.1093/g3journal/jkad119

Interpretive Summary: The rusty patched bumble bee, Bombus affinis, is an important pollinator in North America and a federally protected endangered species. Due to habitat loss and large declines in population size, B. affinis is facing imminent extinction unless human intervention and recovery efforts are implemented. To better understand B. affinis biology and population genetic and genomic landscapes, we sequenced and assembled the B. affinis genome. Whole genome sequencing (PacBio HiFi) and HiC library preparation was performed from tissue collected from the same partial abdomen of one male. From this limited material, a contiguous and complete genomic resources for a rare and endangered species was developed.

Technical Abstract: The rusty patched bumble bee, Bombus affinis, is an important pollinator in North America and a 24 federally listed endangered species. Due to habitat loss and large declines in population size, B. 25 affinis is facing imminent extinction unless human intervention and recovery efforts are 26 implemented. To better understand B. affinis biology and population genetic and genomic 27 landscapes, we sequenced and assembled the B. affinis genome from a single male. Whole 28 genome HiFi sequencing on PacBio coupled with HiC sequencing resulted in a complete and 29 highly contiguous contig assembly that was scaffolded into a chromosomal context, resolving 18 30 chromosomes for this species. All material for both HiFi and HiC sequencing was derived from a 31 single abdominal tissue segment from the one male. These assembly results, coupled with the 32 minimal amount of tissue destructively sampled, demonstrates methods for generating 33 contiguous and complete genomic resources for a rare and endangered species with limited 34 material available and highlights the importance of sample preservation. Precise methods and 35 applications of these methods are presented for potential applications in other species with 36 similar limitations in specimen availability and curation considerations.