The genome sequence of the large yellow underwing, <i>Noctua pronuba </i>(Linnaeus, 1758)

Author(s): Douglas Boyes ¹ , Peter W.H. Holland ² , University of Oxford and Wytham Woods 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): 1 April 2022

Journal: Wellcome Open Research

Publisher: F1000 Research Limited

Keywords: Noctua pronuba, large yellow underwing, genome sequence, chromosomal, Lepidoptera

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Abstract

We present a genome assembly from an individual female Noctua pronuba (the large yellow underwing; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 529 megabases in span. The complete assembly is scaffolded into 32 chromosomal pseudomolecules, with the W and Z sex chromosome assembled. The mitochondrial genome was also assembled and is 15.3 kilobases in length.

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Most cited references 18

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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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Identifying and removing haplotypic duplication in primary genome assemblies

Dengfeng Guan, Shane A. McCarthy, Jonathan Wood … (2020)

Abstract Motivation Rapid development in long-read sequencing and scaffolding technologies is accelerating the production of reference-quality assemblies for large eukaryotic genomes. However, haplotype divergence in regions of high heterozygosity often results in assemblers creating two copies rather than one copy of a region, leading to breaks in contiguity and compromising downstream steps such as gene annotation. Several tools have been developed to resolve this problem. However, they either focus only on removing contained duplicate regions, also known as haplotigs, or fail to use all the relevant information and hence make errors. Results Here we present a novel tool, purge_dups, that uses sequence similarity and read depth to automatically identify and remove both haplotigs and heterozygous overlaps. In comparison with current tools, we demonstrate that purge_dups can reduce heterozygous duplication and increase assembly continuity while maintaining completeness of the primary assembly. Moreover, purge_dups is fully automatic and can easily be integrated into assembly pipelines. Availability and implementation The source code is written in C and is available at https://github.com/dfguan/purge_dups. Supplementary information Supplementary data are available at Bioinformatics online.

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Author and article information

Contributors

Douglas Boyes: Role: InvestigationRole: Resources

Peter W.H. Holland: Role: SupervisionRole: Writing – Original Draft PreparationRole: Writing – Review & Editing

ORCID: https://orcid.org/0000-0003-1533-9376

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): 1 April 2022

Publication date Collection: 2022

Volume: 7

Electronic Location Identifier: 119

Affiliations

[1 ]UK Centre for Ecology and Hydrology, Wallingford, Oxfordshire, UK

[2 ]Department of Zoology, University of Oxford, Oxford, UK

[1 ]Laboratory of Genetics, Wageningen University & Research, Wageningen, The Netherlands

[1 ]Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada

Author notes

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

⁺Deceased author

No competing interests were disclosed.

Competing interests: No competing interests were disclosed.

Author information

Peter W.H. Holland https://orcid.org/0000-0003-1533-9376

Article

DOI: 10.12688/wellcomeopenres.17747.1

PMC ID: 9975414

PubMed ID: 36874564

SO-VID: b6c91681-9408-4575-b0eb-efff09a80022

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 : 28 February 2022

Funding

Funded by: Wellcome Trust

Award ID: 206194

Funded by: Wellcome Trust

Award ID: 218328

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.

The genome sequence of the large yellow underwing, Noctua pronuba (Linnaeus, 1758)

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Abstract

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Most cited references 18

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

BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes

Identifying and removing haplotypic duplication in primary genome assemblies

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