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      • Record: found
      • Abstract: found
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      Is Open Access

      The genome sequence of an ichneumonid wasp, Campoletis raptor (Zetterstedt, 1838)

      data-paper
      Author(s): 1 , 1 , 1 , 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, Darwin Tree of Life Consortium a ,
      Publication date (Electronic):
      Journal: Wellcome Open Research
      Publisher: F1000 Research Limited
      Keywords: Campoletis raptor, an ichneumonid wasp, genome sequence, chromosomal, Hymenoptera

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          Abstract

          We present a genome assembly from an individual female Campoletis raptor (an ichneumonid wasp; Arthropoda; Insecta; Hymenoptera; Ichneumonidae). The genome sequence is 218.6 megabases in span. Most of the assembly is scaffolded into 11 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 28.53 kilobases in length.

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          BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs.

          Felipe A. Simão, Robert Waterhouse, Panagiotis Ioannidis … (2015)
          Genomics has revolutionized biological research, but quality assessment of the resulting assembled sequences is complicated and remains mostly limited to technical measures like N50.
          Article 0 comments Cited 3442 times – based on 0 reviews     Review now
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            A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.

            Suhas Rao, Miriam H Huntley, Neva 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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              MITOS: improved de novo metazoan mitochondrial genome annotation.

              Matthias Bernt, Alexander Donath, Frank Jühling … (2013)
              About 2000 completely sequenced mitochondrial genomes are available from the NCBI RefSeq data base together with manually curated annotations of their protein-coding genes, rRNAs, and tRNAs. This annotation information, which has accumulated over two decades, has been obtained with a diverse set of computational tools and annotation strategies. Despite all efforts of manual curation it is still plagued by misassignments of reading directions, erroneous gene names, and missing as well as false positive annotations in particular for the RNA genes. Taken together, this causes substantial problems for fully automatic pipelines that aim to use these data comprehensively for studies of animal phylogenetics and the molecular evolution of mitogenomes. The MITOS pipeline is designed to compute a consistent de novo annotation of the mitogenomic sequences. We show that the results of MITOS match RefSeq and MitoZoa in terms of annotation coverage and quality. At the same time we avoid biases, inconsistencies of nomenclature, and typos originating from manual curation strategies. The MITOS pipeline is accessible online at http://mitos.bioinf.uni-leipzig.de. Copyright © 2012 Elsevier Inc. All rights reserved.
              Article 0 comments Cited 1817 times – based on 0 reviews     Review now
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                Author and article information

                Contributors
                Gavin R. Broad: Role: InvestigationRole: ResourcesRole: Writing – Original Draft PreparationRole: Writing – Review & Editing
                ORCID: https://orcid.org/0000-0001-7223-5333
                Chris Fletcher: Role: InvestigationRole: Resources
                ORCID: https://orcid.org/0000-0002-1944-5048
                Inez Januszczak: Role: InvestigationRole: Resources
                ORCID: https://orcid.org/0000-0003-3857-9989
                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): 20 July 2023
                Publication date Collection: 2023
                Volume: 8
                Electronic Location Identifier: 313
                Affiliations
                [1 ]Natural History Museum, London, England, UK
                [1 ]Museum of Natural History, University of Tartu, Tartu, Estonia
                [1 ]Serbia University of Belgrade, Belgrade, Serbia
                Author notes

                No competing interests were disclosed.

                Competing interests: No competing interests were disclosed.

                Competing interests: No competing interests were disclosed.

                Author information
                https://orcid.org/0000-0001-7223-5333
                https://orcid.org/0000-0002-1944-5048
                https://orcid.org/0000-0003-3857-9989
                Article
                DOI: 10.12688/wellcomeopenres.19738.1
                PMC ID: 11137483
                PubMed ID: 38818412
                SO-VID: dddc5ebc-8411-4da7-9f78-e2a53fe01e50
                Copyright © Copyright: © 2023 Broad GR 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 : 14 July 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) and the Darwin Tree of Life Discretionary Award (218328).
                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: campoletis raptor,an ichneumonid wasp,genome sequence,chromosomal,hymenoptera
                Data availability:
                Keywords: campoletis raptor, an ichneumonid wasp, genome sequence, chromosomal, hymenoptera

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