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Asian giant hornet, Vespa mandarinia, genome assembly

Metadata Updated: March 30, 2024

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 The Primary and Haplotig assemblies, along with the HiFi reads have been archived at NCBI.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.fastaResource 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.fastaResource 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.fastaResource 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

Access & Use Information

Public: This dataset is intended for public access and use. License: us-pd

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Dates

Metadata Created Date March 30, 2024
Metadata Updated Date March 30, 2024

Metadata Source

Harvested from USDA JSON

Additional Metadata

Resource Type Dataset
Metadata Created Date March 30, 2024
Metadata Updated Date March 30, 2024
Publisher Agricultural Research Service
Maintainer
Identifier 10.15482/USDA.ADC/1519179
Data Last Modified 2024-02-21
Public Access Level public
Bureau Code 005:18
Metadata Context https://project-open-data.cio.gov/v1.1/schema/catalog.jsonld
Schema Version https://project-open-data.cio.gov/v1.1/schema
Catalog Describedby https://project-open-data.cio.gov/v1.1/schema/catalog.json
Harvest Object Id f4759eb1-f310-4fab-a2fe-542f5bdffa4f
Harvest Source Id d3fafa34-0cb9-48f1-ab1d-5b5fdc783806
Harvest Source Title USDA JSON
License https://www.usa.gov/publicdomain/label/1.0/
Old Spatial {"type": "Point", "coordinates": -123.943125, 49.152809}
Program Code 005:040
Source Datajson Identifier True
Source Hash 58a491644b66e48997d4de592363be2837552df5fe743410fbbcb43658372b67
Source Schema Version 1.1
Spatial {"type": "Point", "coordinates": -123.943125, 49.152809}

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