Asian giant hornet, Vespa mandarinia, genome assembly
<p>The Asian giant hornet, <em>Vespa mandarinia</em>, 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. </p> <p>The Primary and Haplotig assemblies, along with the HiFi reads have been archived at NCBI.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: <a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA649644/">PRJNA649644</a>, BioSample: <a href="https://www.ncbi.nlm.nih.gov/biosample/SAMN15675875/">SAMN15675875</a>, GenBank: <a href="https://www.ncbi.nlm.nih.gov/nuccore/JACHAV000000000">JACHAV000000000</a> - Primary contig assembly and mitochondrial genome BioProject: <a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA649643">PRJNA649643</a>, BioSample: <a href="https://www.ncbi.nlm.nih.gov/biosample/SAMN15675875/">SAMN15675875</a>, GenBank: <a href="https://www.ncbi.nlm.nih.gov/nuccore/JACHAW000000000">JACHAW000000000</a> - Alternate (Haplotigs) contig assembly </p> <div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: IPA contigs purged from haplotigs.</p> <p>File Name: ihVesMand1_IPA_purged_from_htig.fasta</p><p>Resource Description: IPA contigs purged from the haplotigs contig set by purge_dups. Fasta format.</p></li><br><li><p>Resource Title: Mitochondrial PacBio HiFi read set.</p> <p>File Name: ihVesMand1_mt_reads.fasta</p><p>Resource Description: Mitochondrial reads from the PacBio HiFi read set. Fasta format.</p></li><br><li><p>Resource Title: All mitochondrial genome VNTR variants.</p> <p>File Name: ihVesMand1_mtgenome_all_VNTR_variants.fasta</p><p>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.</p></li><br><li><p>Resource Title: Vespa mandarinia sequencing and assembly methods.</p> <p>File Name: Vespa_mandarinia_Sequencing_and_Assembly_Methods.docx</p></li></ul>
| Main Authors: | , , , , |
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| Format: | Dataset biblioteca |
| Published: |
2020
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| Subjects: | Crop and pasture protection (incl. pests, diseases and weeds), Genomics and transcriptomics, Genetics, Environmental sciences, Biosecurity science and invasive species ecology, ag100pest, genome assembly, Asian giant hornet, Vespa mandarinia, i5k, data.gov, ARS, |
| Online Access: | https://figshare.com/articles/dataset/Asian_giant_hornet_Vespa_mandarinia_genome_assembly/25234189 |
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