Ag Data Commons
4 files

Asian giant hornet, Vespa mandarinia, genome assembly

posted on 2024-02-21, 20:20 authored by Anna ChildersAnna Childers, Scott M. Geib, Timothy P.L. Smith, Leonard J. Foster, Jonas Korlach

The Asian giant hornet, Vespa mandarinia, has a native range that extends from northern India to East Asia. In 2019, the hornet was confirmed for the first time in North America, posing an invasive threat to honey bees and human health. In September 2019, local beekeepers, tracked down a nest in a park in Nanaimo on Vancouver Island, British Columbia, Canada and exterminated it. The specimen we used for genome sequencing was obtained from that nest, the first one found in North America. DNA was extracted from the thorax for PacBio HiFi sequencing on two cells and data were assembled using IPA to yield a contig assembly of 248 Mb with a 3.14 Mb N50. The assembly was generated by the Agricultural Research Service's Ag100Pest Initiative in collaboration with Pacific Biosciences. This high-quality genome assembly is being released prior to publication in scientific journals as a public service to the research community.

The Primary and Haplotig assemblies, along with the HiFi reads have been archived at NCBI. Relevant accessions include: SRA: SRR12366675 - PacBio HiFi reads for both cells BioProject: PRJNA649644, BioSample: SAMN15675875, GenBank: JACHAV000000000 - Primary contig assembly and mitochondrial genome BioProject: PRJNA649643, BioSample: SAMN15675875, GenBank: JACHAW000000000 - Alternate (Haplotigs) contig assembly

Resources in this dataset:

  • Resource Title: IPA contigs purged from haplotigs.

    File Name: ihVesMand1_IPA_purged_from_htig.fasta

    Resource Description: IPA contigs purged from the haplotigs contig set by purge_dups. Fasta format.

  • Resource Title: Mitochondrial PacBio HiFi read set.

    File Name: ihVesMand1_mt_reads.fasta

    Resource Description: Mitochondrial reads from the PacBio HiFi read set. Fasta format.

  • Resource Title: All mitochondrial genome VNTR variants.

    File Name: ihVesMand1_mtgenome_all_VNTR_variants.fasta

    Resource Description: Multiple contigs of the mitochondrial genome were obtained due to the presence of an extended variable number tandem repeat (VNTR) region corresponding to the control region, with different copy numbers (ranging from 5 to 9) of an 823 bp repeat unit. We designated the most abundant mitochondrial genome variant (6 repeat copies) as the mitochondrial genome sequence and included it with the primary assembly deposited in GenBank.

  • Resource Title: Vespa mandarinia sequencing and assembly methods.

    File Name: Vespa_mandarinia_Sequencing_and_Assembly_Methods.docx




Data contact name

Childers, Anna

Data contact email


Ag Data Commons

Intended use

Supporting data for the Asian giant hornet, Vespa mandarinia, de novo genome assembly.

Temporal Extent Start Date



  • Not specified

Geographic Coverage


Geographic location - description

Specimen collected in Nanaimo on Vancouver Island, British Columbia, Canada (49.152809 N 123.943125 W)

ISO Topic Category

  • biota

Ag Data Commons Group

  • Insects - i5K

National Agricultural Library Thesaurus terms

social wasps; Vespa; genome assembly; India; East Asia; honey bees; human health; beekeepers; nests; British Columbia; DNA; thorax; Agricultural Research Service; mitochondrial genome; mitochondria; minisatellite repeats; invasive species; insect pests

OMB Bureau Code

  • 005:18 - Agricultural Research Service

OMB Program Code

  • 005:040 - National Research

Pending citation

  • No

Public Access Level

  • Public

Preferred dataset citation

Childers, Anna; Geib, Scott M.; Smith, Timothy P.L.; Foster, Leonard J.; Korlach, Jonas (2020). Asian giant hornet, Vespa mandarinia, genome assembly. Ag Data Commons.