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      The genome sequence of the black clock beetle, Pterostichus madidus (Fabricius, 1775)

      data-paper
      Author(s): 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):
      Journal: Wellcome Open Research
      Publisher: F1000 Research Limited
      Keywords: Pterostichus madidus, black clock beetle, genome sequence, chromosomal

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          Abstract

          We present a genome assembly from an individual female Pterostichus madidus (the black clock beetle; Arthropoda; Insecta; Coleoptera; Carabidae). The genome sequence is 705 megabases in span. The majority (99.96%) of the assembly is scaffolded into 19 chromosomal pseudomolecules, with the X sex chromosome assembled.

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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): 8 November 2021
                Publication date Collection: 2021
                Volume: 6
                Electronic Location Identifier: 301
                Affiliations
                [1 ]Department of Zoology, University of Oxford, Oxford, UK
                [1 ]Institute of Biology, University of Graz, Graz, Austria
                [1 ]Department of Integrative Biology, Oregon State University, Corvallis, OR, USA
                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/0000-0001-6380-0329
                Article
                DOI: 10.12688/wellcomeopenres.17347.1
                PMC ID: 9315234
                SO-VID: 7bcf224e-eff1-4f84-a3de-bad2ef637cfe
                Copyright statement: Copyright: © 2021 Crowley LM 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 : 2 November 2021
                Product
                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.
                Categories
                Subject: Data Note
                Subject: Articles

                Keywords: pterostichus madidus,black clock beetle,genome sequence,chromosomal
                Data availability:
                Keywords: pterostichus madidus, black clock beetle, genome sequence, chromosomal

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