The genome sequence of a stonefly, <i>Nemurella pictetii</i> Klapalek, 1900

Author(s): Craig Macadam ¹ , Caleala Clifford ² , Benjamin W. Price ³ , 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): 25 February 2022

Journal: Wellcome Open Research

Publisher: F1000 Research Limited

Keywords: Nemurella pictetii, genome sequence, chromosomal, Plecoptera

Read this article at

ScienceOpen Publisher PMC

Bookmark

There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

Abstract

We present a genome assembly from an individual male Nemurella pictetii (Arthropoda; Insecta; Plecoptera; Nemouridae). The genome sequence is 257 megabases in span. The majority of the assembly (99.79%) is scaffolded into 12 chromosomal pseudomolecules, with the X sex chromosome assembled. The X chromosome was found at half coverage, but no Y chromosome was found. The mitochondrial genome was assembled, and is 16.0 kb in length.

Related collections

Most cited references 26

Record: found
Abstract: found
Article: not found

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.

0 comments Cited 2239 times – based on 0 reviews      Review now

Bookmark

Record: found
Abstract: found
Article: found

Is Open Access

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.

0 comments Cited 1395 times – based on 0 reviews      Review now

Bookmark

Record: found
Abstract: found
Article: not found

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.

0 comments Cited 1268 times – based on 0 reviews      Review now

Bookmark

All references

Author and article information

Contributors

Craig Macadam: Role: InvestigationRole: ResourcesRole: Writing – Original Draft Preparation

Caleala Clifford: Role: InvestigationRole: Resources

Benjamin W. Price: Role: 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): 25 February 2022

Publication date Collection: 2022

Volume: 7

Electronic Location Identifier: 56

Affiliations

[1 ]Buglife – The Invertebrate Conservation Trust, Stirling, UK

[2 ]South East Environmental Assessment and Advice Team, Natural Resources Wales, Cardiff, UK

[3 ]Department of Life Sciences, Natural History Museum, London, UK

[1 ]Manaaki Whenua Landcare Research, Lincoln, New Zealand

[1 ]Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA

[1 ]School of Biological Sciences, Washington State University, Pullman, WA, USA

Author notes

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

No competing interests were disclosed.

Competing interests: No competing interests were disclosed.

Article

DOI: 10.12688/wellcomeopenres.17684.2

PMC ID: 9086528

PubMed ID: 35592548

SO-VID: 2769ba13-17f8-45c9-a426-4d01bca10c58

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 : 22 February 2022

Funding

Funded by: Wellcome Trust

Award ID: 206194

Funded by: Wellcome Trust

Award ID: 218328

This work was supported by the Wellcome Trust 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 a stonefly, Nemurella pictetii Klapalek, 1900

Read this article at

Abstract

Related collections

Genome Integrity

Most cited references 26

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

Author and article information

Contributors

Journal

Affiliations

Author notes

Article

History

Funding

Categories

Comments

Comment on this article

Similar content 491

Cited by 1

Most referenced authors 259