The genome sequence of the common green lacewing, <i>Chrysoperla carnea </i>(Stephens, 1836)

Author(s): Liam M. Crowley ¹ , 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): 9 December 2021

Journal: Wellcome Open Research

Publisher: F1000 Research Limited

Keywords: Chrysoperla carnea, common green lacewing, genome sequence, chromosomal, Chrysopidae

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Abstract

We present a genome assembly from an individual female Chrysoperla carnea (a common green lacewing; Arthropoda; Insecta; Neuroptera; Chrysopidae). The genome sequence is 560 megabases in span. The majority of the assembly (95.70%) is scaffolded into six chromosomal pseudomolecules, with the X sex chromosome assembled. Gene annotation of this assembly by the NCBI Eukaryotic Genome Annotation Pipeline has identified 12,985 protein coding genes.

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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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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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Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm

Haoyu Cheng, Gregory Concepcion, Xiaowen Feng … (2021)

Haplotype-resolved de novo assembly is the ultimate solution to the study of sequence variations in a genome. However, existing algorithms either collapse heterozygous alleles into one consensus copy or fail to cleanly separate the haplotypes to produce high-quality phased assemblies. Here we describe hifiasm, a de novo assembler that takes advantage of long high-fidelity sequence reads to faithfully represent the haplotype information in a phased assembly graph. Unlike other graph-based assemblers that only aim to maintain the contiguity of one haplotype, hifiasm strives to preserve the contiguity of all haplotypes. This feature enables the development of a graph trio binning algorithm that greatly advances over standard trio binning. On three human and five nonhuman datasets, including California redwood with a ~30-Gb hexaploid genome, we show that hifiasm frequently delivers better assemblies than existing tools and consistently outperforms others on haplotype-resolved assembly.

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Author and article information

Contributors

Liam M. Crowley: Role: InvestigationRole: ResourcesRole: Writing – Original Draft PreparationRole: Writing – Review & Editing

ORCID: https://orcid.org/0000-0001-6380-0329

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): 9 December 2021

Publication date Collection: 2021

Volume: 6

Electronic Location Identifier: 334

Affiliations

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

[1 ]University of Liverpool, Liverpool, UK

[1 ]University of Guelph, Guelph, Canada

[1 ]George Washington University, Washington, DC, USA

Author notes

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

No competing interests were disclosed.

Competing interests: No competing interests were disclosed.

Author information

Liam M. Crowley https://orcid.org/0000-0001-6380-0329

Article

DOI: 10.12688/wellcomeopenres.17455.1

PMC ID: 10116181

PubMed ID: 37089663

SO-VID: 62d180e1-4937-4ddb-adca-a145ec3a45e3

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 : 2 December 2021

Funding

Funded by: Wellcome

Award ID: 218328

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.

The genome sequence of the common green lacewing, Chrysoperla carnea (Stephens, 1836)

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Abstract

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Arabidopsis genomics

Most cited references 16

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

Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm

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