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Chromosome-level reference genome of the European wasp spider Argiope bruennichi: a resource for studies on range expansion and evolutionary adaptation

View ORCID ProfileMonica M. Sheffer, View ORCID ProfileAnica Hoppe, View ORCID ProfileHenrik Krehenwinkel, View ORCID ProfileGabriele Uhl, Andreas W. Kuss, Lars Jensen, Corinna Jensen, View ORCID ProfileRosemary G. Gillespie, View ORCID ProfileKatharina J. Hoff, View ORCID ProfileStefan Prost
doi: https://doi.org/10.1101/2020.05.21.103564
Monica M. Sheffer
1Zoological Institute and Museum, University of Greifswald, Germany
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  • For correspondence: monica.sheffer@uni-greifswald.de
Anica Hoppe
2Institute of Mathematics and Computer Science, University of Greifswald, Germany
3Center for Functional Genomics of Microbes, University of Greifswald, Germany
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Henrik Krehenwinkel
4Department of Biogeography, University of Trier, Germany
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Gabriele Uhl
1Zoological Institute and Museum, University of Greifswald, Germany
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Andreas W. Kuss
5Interfaculty Institute for Genetics and Functional Genomics, University of Greifswald, Germany
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Lars Jensen
5Interfaculty Institute for Genetics and Functional Genomics, University of Greifswald, Germany
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Corinna Jensen
5Interfaculty Institute for Genetics and Functional Genomics, University of Greifswald, Germany
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Rosemary G. Gillespie
6Department of Environmental Science Policy and Management, University of California Berkeley, USA
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Katharina J. Hoff
2Institute of Mathematics and Computer Science, University of Greifswald, Germany
3Center for Functional Genomics of Microbes, University of Greifswald, Germany
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Stefan Prost
7LOEWE-Centre for Translational Biodiversity Genomics, Germany
8South African National Biodiversity Institute, National Zoological Gardens of South Africa, South Africa
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Abstract

Background Argiope bruennichi, the European wasp spider, has been studied intensively as to sexual selection, chemical communication, and the dynamics of rapid range expansion at a behavioral and genetic level. However, the lack of a reference genome has limited insights into the genetic basis for these phenomena. Therefore, we assembled a high-quality chromosome-level reference genome of the European wasp spider as a tool for more in-depth future studies.

Findings We generated, de novo, a 1.67Gb genome assembly of A. bruennichi using 21.5X PacBio sequencing, polished with 30X Illumina paired-end sequencing data, and proximity ligation (Hi-C) based scaffolding. This resulted in an N50 scaffold size of 124Mb and an N50 contig size of 288kb. We found 98.4% of the genome to be contained in 13 scaffolds, fitting the expected number of chromosomes (n = 13). Analyses showed the presence of 91.1% of complete arthropod BUSCOs, indicating a high quality of the assembly.

Conclusions We present the first chromosome-level genome assembly in the class Arachnida. With this genomic resource, we open the door for more precise and informative studies on evolution and adaptation in A. bruennichi, as well as on several interesting topics in Arachnids, such as the genomic architecture of traits, whole genome duplication and the genomic mechanisms behind silk and venom evolution.

Competing Interest Statement

The authors have declared no competing interest.

  • List of abbreviations

    Abd-A
    Abdominal-A;
    Abd-B
    Abdominal-B;
    AcSp
    aciniform spidroin;
    AgSp
    aggregate spidroin;
    Antp
    Antennapedia;
    AT
    adenine thymine;
    bp
    basepairs;
    BUSCO
    Benchmarking Universal Single Copy Orthologs;
    DDBJ
    DNA Data Bank of Japan;
    Dfd
    Deformed;
    DNA
    deoxyribonucleic acid;
    Flag
    flagelliform spidroin;
    ftz
    fushi tarazu;
    Gb
    gigabase pairs;
    GC
    guanine cytosine;
    kb
    kilobase pairs;
    lab
    labial;
    LINE
    long interspersed nuclear element;
    LTR
    long terminal repeat;
    MaSp
    major ampullate spidroin;
    Mb
    megabase pairs;
    MiSp
    minor ampullate spidroin;
    NCBI
    National Center for Biotechnology Information;
    PacBio
    Pacific Biosciences;
    pb
    proboscipedia;
    PCR
    polymerase chain reaction;
    PiSp
    piriform spidroin;
    RNA
    ribonucleic acid;
    scr
    sex combs reduced;
    SINE
    short interspersed nuclear element;
    TuSp
    tubuliform spidroin;
    Ubx
    Ultrabithorax;
    WGD
    whole genome duplication
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    Chromosome-level reference genome of the European wasp spider Argiope bruennichi: a resource for studies on range expansion and evolutionary adaptation
    Monica M. Sheffer, Anica Hoppe, Henrik Krehenwinkel, Gabriele Uhl, Andreas W. Kuss, Lars Jensen, Corinna Jensen, Rosemary G. Gillespie, Katharina J. Hoff, Stefan Prost
    bioRxiv 2020.05.21.103564; doi: https://doi.org/10.1101/2020.05.21.103564
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    Chromosome-level reference genome of the European wasp spider Argiope bruennichi: a resource for studies on range expansion and evolutionary adaptation
    Monica M. Sheffer, Anica Hoppe, Henrik Krehenwinkel, Gabriele Uhl, Andreas W. Kuss, Lars Jensen, Corinna Jensen, Rosemary G. Gillespie, Katharina J. Hoff, Stefan Prost
    bioRxiv 2020.05.21.103564; doi: https://doi.org/10.1101/2020.05.21.103564

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