The genome sequence of an ichneumon wasp, <i>Clistopyga incitator</i> (Fabricius, 1793)

Author(s): Lucy Broad ¹ , Gavin R. Broad ² , 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): 12 May 2023

Journal: Wellcome Open Research

Publisher: F1000 Research Limited

Keywords: Clistopyga incitator, ichneumon wasp, genome sequence, chromosomal, Hymenoptera

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Abstract

We present a genome assembly from an individual female Clistopyga incitator (an ichneumon wasp; Arthropoda; Insecta; Hymenoptera; Ichneumonidae). The genome sequence is 260.7 megabases in span. Most of the assembly is scaffolded into 21 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 25.0 kilobases in length.

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Most cited references 26

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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.

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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.

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Author and article information

Contributors

Lucy Broad: Role: InvestigationRole: ResourcesRole: Writing – Review & Editing

ORCID: https://orcid.org/0009-0002-7215-3711

Gavin R. Broad: Role: InvestigationRole: ResourcesRole: Writing – Original Draft PreparationRole: Writing – Review & Editing

ORCID: https://orcid.org/0000-0001-7223-5333

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): 12 May 2023

Publication date Collection: 2023

Volume: 8

Electronic Location Identifier: 215

Affiliations

[1 ]Independent researcher, Tonbridge, England, UK

[2 ]Natural History Museum, London, England, UK

[1 ]Centro de investigacion de Estudios Avanzados del Maule, Universidad Catolica del Maule, Talca, Maule, Chile

[1 ]Purdue University, West Lafayette, Indiana, USA

Author notes

[a ] mark.blaxter@ 123456sanger.ac.uk

No competing interests were disclosed.

Competing interests: No competing interests were disclosed.

Author information

Lucy Broad https://orcid.org/0009-0002-7215-3711

Gavin R. Broad https://orcid.org/0000-0001-7223-5333

Article

DOI: 10.12688/wellcomeopenres.19302.1

PMC ID: 11191966

PubMed ID: 38911280

SO-VID: fad168f0-28f6-471e-acc8-52fe9a3784d7

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 : 27 March 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.

The genome sequence of an ichneumon wasp, Clistopyga incitator (Fabricius, 1793)

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Abstract

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Hymenoptera

Most cited references 26

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

A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.

MITOS: improved de novo metazoan mitochondrial genome annotation.

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