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      The genome sequence of the Lesser Hornet Hoverfly, Volucella inanis (Linnaeus, 1758)

      data-paper
      Author(s): 1 , 2 , University of Oxford and Wytham Woods Genome Acquisition Lab, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, 3 , 3 , Darwin Tree of Life Consortium a ,
      Publication date (Electronic):
      Journal: Wellcome Open Research
      Publisher: F1000 Research Limited
      Keywords: Volucella inanis, lesser hornet hoverfly, genome sequence, chromosomal, Diptera

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          Abstract

          We present a genome assembly from an individual female Volucella inanis (the Lesser Hornet Hoverfly; Arthropoda; Insecta; Diptera; Syrphidae). The genome sequence is 961 megabases in span. Most of the assembly is scaffolded into six chromosomal pseudomolecules, including the assembled X sex chromosome. The mitochondrial genome has also been assembled and is 16.0 kilobases in length. Gene annotation of this assembly on Ensembl has identified 11,616 protein coding genes.

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          Most cited references24

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          UniProt: a worldwide hub of protein knowledge

          (2018)
          Abstract The UniProt Knowledgebase is a collection of sequences and annotations for over 120 million proteins across all branches of life. Detailed annotations extracted from the literature by expert curators have been collected for over half a million of these proteins. These annotations are supplemented by annotations provided by rule based automated systems, and those imported from other resources. In this article we describe significant updates that we have made over the last 2 years to the resource. We have greatly expanded the number of Reference Proteomes that we provide and in particular we have focussed on improving the number of viral Reference Proteomes. The UniProt website has been augmented with new data visualizations for the subcellular localization of proteins as well as their structure and interactions. UniProt resources are available under a CC-BY (4.0) license via the web at https://www.uniprot.org/.
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            A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.

            Suhas S.P. Rao, Miriam H Huntley, Neva C Durand … (2014)
            We use in situ Hi-C to probe the 3D architecture of genomes, constructing haploid and diploid maps of nine cell types. The densest, in human lymphoblastoid cells, contains 4.9 billion contacts, achieving 1 kb resolution. We find that genomes are partitioned into contact domains (median length, 185 kb), which are associated with distinct patterns of histone marks and segregate into six subcompartments. We identify ∼10,000 loops. These loops frequently link promoters and enhancers, correlate with gene activation, and show conservation across cell types and species. Loop anchors typically occur at domain boundaries and bind CTCF. CTCF sites at loop anchors occur predominantly (>90%) in a convergent orientation, with the asymmetric motifs "facing" one another. The inactive X chromosome splits into two massive domains and contains large loops anchored at CTCF-binding repeats. Copyright © 2014 Elsevier Inc. All rights reserved.
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              BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes

              Mosè Manni, Matthew Berkeley, Mathieu Seppey … (2021)
              Methods for evaluating the quality of genomic and metagenomic data are essential to aid genome assembly procedures and to correctly interpret the results of subsequent analyses. BUSCO estimates the completeness and redundancy of processed genomic data based on universal single-copy orthologs. Here, we present new functionalities and major improvements of the BUSCO software, as well as the renewal and expansion of the underlying data sets in sync with the OrthoDB v10 release. Among the major novelties, BUSCO now enables phylogenetic placement of the input sequence to automatically select the most appropriate BUSCO data set for the assessment, allowing the analysis of metagenome-assembled genomes of unknown origin. A newly introduced genome workflow increases the efficiency and runtimes especially on large eukaryotic genomes. BUSCO is the only tool capable of assessing both eukaryotic and prokaryotic species, and can be applied to various data types, from genome assemblies and metagenomic bins, to transcriptomes and gene sets.
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                Author and article information

                Contributors
                Liam M. Crowley: Role: InvestigationRole: ResourcesRole: Writing – Review & Editing
                ORCID: https://orcid.org/0000-0001-6380-0329
                Ryan Mitchell: Role: InvestigationRole: Resources
                Scarlett T. Weston: Role: Writing – Original Draft Preparation
                Karl R. Wotton: Role: Writing – Original Draft PreparationRole: Writing – Review & Editing
                Journal
                Journal ID (nlm-ta): Wellcome Open Res
                Journal ID (iso-abbrev): Wellcome Open Res
                Title: Wellcome Open Research
                Publisher: F1000 Research Limited (London, UK )
                ISSN (Electronic): 2398-502X
                Publication date (Electronic): 10 February 2023
                Publication date Collection: 2023
                Volume: 8
                Electronic Location Identifier: 69
                Affiliations
                [1 ]Department of Biology, University of Oxford, Oxford, UK
                [2 ]Natural History Museum, London, UK
                [3 ]Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, Cornwall, UK
                [1 ]University of Georgia, Athens, Georgia, USA
                [1 ]National University of La Plata, Argentina, Argentina
                [1 ]Universidade Estadual de Santa Cruz, Ilhéus, State of Bahia, Brazil
                Author notes

                No competing interests were disclosed.

                Competing interests: No competing interests were disclosed.

                Competing interests: No competing interests were disclosed.

                Competing interests: No competing interests were disclosed.

                Author information
                https://orcid.org/0000-0001-6380-0329
                Article
                DOI: 10.12688/wellcomeopenres.18897.1
                PMC ID: 10620480
                PubMed ID: 37928210
                SO-VID: aec0b24b-94a2-4593-bc27-9e464b3c398d
                Copyright © Copyright: © 2023 Crowley LM et al.
                License:

                This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Date accepted : 18 January 2023
                Funding
                Funded by: Wellcome Trust
                Award ID: 218328
                Funded by: Wellcome Trust
                Award ID: 206194
                This work was supported by Wellcome through core funding to the Wellcome Sanger Institute (206194, <a href=https://doi.org/10.35802/206194>https://doi.org/10.35802/206194</a>) and the Darwin Tree of Life Discretionary Award (218328, <a href=https://doi.org/10.35802/218328>https://doi.org/10.35802/218328</a>).
                The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Subject: Data Note
                Subject: Articles

                Keywords: volucella inanis,lesser hornet hoverfly,genome sequence,chromosomal,diptera
                Data availability:
                Keywords: volucella inanis, lesser hornet hoverfly, genome sequence, chromosomal, diptera

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