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Data from: Genome assembly of the ragweed leaf beetle, a step forward to better predict rapid evolution of a weed biocontrol agent to environmental novelties

Bouchemousse, Sarah; Falquet, Laurent; Müller-Schärer, Heinz


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  <identifier identifierType="URL">https://zenodo.org/record/3866426</identifier>
  <creators>
    <creator>
      <creatorName>Bouchemousse, Sarah</creatorName>
      <givenName>Sarah</givenName>
      <familyName>Bouchemousse</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0001-5283-5112</nameIdentifier>
      <affiliation>University of Fribourg</affiliation>
    </creator>
    <creator>
      <creatorName>Falquet, Laurent</creatorName>
      <givenName>Laurent</givenName>
      <familyName>Falquet</familyName>
      <affiliation>University of Fribourg</affiliation>
    </creator>
    <creator>
      <creatorName>Müller-Schärer, Heinz</creatorName>
      <givenName>Heinz</givenName>
      <familyName>Müller-Schärer</familyName>
      <affiliation>University of Fribourg</affiliation>
    </creator>
  </creators>
  <titles>
    <title>Data from: Genome assembly of the ragweed leaf beetle, a step forward to better predict rapid evolution of a weed biocontrol agent to environmental novelties</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2020</publicationYear>
  <subjects>
    <subject>Biological control agent</subject>
    <subject>Ophraella communa</subject>
    <subject>Chrysomelidae</subject>
    <subject>Whole genome sequence</subject>
    <subject>SMRT-Cell sequencing</subject>
    <subject>de novo Assembly</subject>
  </subjects>
  <dates>
    <date dateType="Issued">2020-05-29</date>
  </dates>
  <resourceType resourceTypeGeneral="Dataset"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/3866426</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsSupplementTo">10.1093/gbe/evaa102</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsIdenticalTo">10.5061/dryad.1ns1rn8qt</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsPartOf">https://zenodo.org/communities/dryad</relatedIdentifier>
  </relatedIdentifiers>
  <rightsList>
    <rights rightsURI="https://creativecommons.org/publicdomain/zero/1.0/legalcode">Creative Commons Zero v1.0 Universal</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;&lt;span&gt;Rapid evolution of weed biological control agents (BCAs) to new biotic and abiotic conditions is poorly understood and so far, only little considered both in pre-release and post-release studies, despite potential major negative or positive implications for risks of non-targeted attacks or for colonizing yet unsuitable habitats, respectively. Provision of genetic resources, such as assembled and annotated genomes, is essential to assess potential adaptive processes by identifying underlying genetic mechanisms. Here, we provide the first sequenced genome of a phytophagous insect used as a BCA, &lt;i&gt;i.e.&lt;/i&gt; the leaf beetle &lt;i&gt;Ophraella communa&lt;/i&gt;, a promising BCA of common ragweed, recently and accidentally introduced into Europe. A total 33.98 Gb of raw DNA sequences, representing c. 43-fold coverage, were obtained using the PacBio SMRT-Cell sequencing approach. Among the five different assemblers tested, the SMARTdenovo assembly displaying the best scores was then corrected with Illumina short reads. A final genome of 774 Mb containing 7,003 scaffolds was obtained. The reliability of the final assembly was then assessed by benchmarking universal single-copy orthologous genes (&amp;gt; 96.0% of the 1,658 expected insect genes) and by remapping tests of Illumina short reads (average of 98.6% ± 0.7% without filtering). The number of protein-coding genes of 75,642, representing 82% of the published antennal transcriptome, and the phylogenetic analyses based on 825 orthologous genes placing &lt;i&gt;O. communa &lt;/i&gt;in the monophyletic group of Chrysomelidae, confirm the relevance of our genome assembly. Overall, the genome provides a valuable resource for studying potential risks and benefits of this BCA facing environmental novelties.&lt;/span&gt;&lt;/p&gt;</description>
    <description descriptionType="Other">&lt;div class="o-metadata__file-usage-entry"&gt;
Proteome and annotation files

&lt;p&gt;The "GenePrediction_Ophraella_communa_Augustus.aa" (fasta format) contains the 75,642 protein-coding genes predicted with Augustus (v3.2.3), using parameters "--gff3=on --species=tribolium2012". The preliminary annotation of each 75,642 predicted proteins, performed with Pannzer2, is described in the "Annotation_Ophraella_communa.out" file (text format). Details of the meaning of columns are provided on the Pannzer2 website (http://ekhidna2.biocenter.helsinki.fi/sanspanz/). An interactive html file can be generated using the command line below.&lt;/p&gt;

&lt;pre class="moz-quote-pre"&gt;perl anno2html.pl &amp;lt; Annotation_Ophraella_communa.out &amp;gt; Annotation_Ophraella_communa.html
&lt;/pre&gt;
&lt;/div&gt;
&lt;p&gt;Funding provided by: Swiss National Science Foundation*&lt;br&gt;Crossref Funder Registry ID: &lt;br&gt;Award Number: 31003A_166448 to HMS&lt;/p&gt;</description>
  </descriptions>
</resource>
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