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ARS Home » Southeast Area » Stoneville, Mississippi » Pollinator Health in Southern Crop Ecosystems Research » Research » Publications at this Location » Publication #421597
Research Project: Ecological Assessment and Mitigation Strategies to Reduce the Risks of Bees to Stressors in Southern Crop Ecosystems

Location: Pollinator Health in Southern Crop Ecosystems Research

Title: Chromosome-level genome assembly of Protandrena (Anthemurgus) passiflorae (Hymenoptera: Andrenidae), a host-plant specialist bee

Author
item Parys, Katherine
item Schweizer, Rena
item BENAVIDES, LIGIA - Harvard University
item Geib, Scott
item Sim, Sheina
item Evans, Jay
item Branstetter, Michael

Submitted to: G3: Genes, genomics, genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/5/2025
Publication Date: N/A
Citation: N/A

Interpretive Summary: Scientists from the USDA-ARS' Beenome100 project report the genome assembly of the passionflower bee, Protandrena (Anthemurgus) passiflorae, a host-plant specialist of the passionflower plant, Passiflora lutea L. This genome is the first Protandrena species to be sequenced and assembled at a chromosome scale, and one of a few available in the bee family, Andrenidae. To better understand P. passiflorae biology and support future studies on host plant specialization, we sequenced and assembled the P. passiflorae genome from a single male bee. High-fidelity sequencing of the entire genome using PacBio, along with HiC sequencing, and short-read RNA sequencing data led to a comprehensive chromosome level assembly. This assembly successfully identified 12 chromosomes spread across the 249 Mb assembly with a Benchmarking Universal Single-Copy Ortholog (BUSCO) score indicating >97% completeness. This assembly showcases producing efficient, comprehensive, and continuous genome arrangements from a single specimen.

Technical Abstract: The passionflower bee, Protandrena (Anthemurgus) passiflorae (Robertson) is a monolectic, host-plant specialist of the passionflower plant Passiflora lutea L. Using a single adult male individual, we generated long-read PacBio HiFi, HiC, and short-read RNA sequencing data to build a well-annotated, chromosome-level genome assembly for this species. The final nuclear genome is 249 Mb with 150x coverage and with most of the genome scaffolding into 12 chromosomes. The scaffold N50 is 21.4 Mb and the genome has a Benchmarking Universal Single-Copy Ortholog (BUSCO) score of 97.2% for 5991 hymenopteran genes. BRAKER3 annotation of the genome identified 12,098 genes and 15,353 total transcripts, and found that 20.27 % of the genome is made up of repetitive elements. We resolved a mitochondrial genome of 12.7 kb. The P. passiflorae genome represents one of only a few published andrenid bee genomes and one of the first monolectic bees. This new high-quality genome will serve as a valuable resource for investigating the genomic basis of specialization and for providing a useful resource for studying pollinator health and conservation.