Journal article Open Access

The genome of flax ( Linum usitatissimum ) assembled de novo from short shotgun sequence reads

Wang, Zhiwen; Hobson, Neil; Galindo, Leonardo; Zhu, Shilin; Shi, Daihu; McDill, Joshua; Yang, Linfeng; Hawkins, Simon; Neutelings, Godfrey; Datla, Raju; Lambert, Georgina; Galbraith, David W.; Grassa, Christopher J.; Geraldes, Armando; Cronk, Quentin C.; Cullis, Christopher; Dash, Prasanta K.; Kumar, Polumetla A.; Cloutier, Sylvie; Sharpe, Andrew G.; Wong, Gane K.-S.; Wang, Jun; Deyholos, Michael K.


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    <creator>
      <creatorName>Wang, Zhiwen</creatorName>
      <givenName>Zhiwen</givenName>
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    <creator>
      <creatorName>Hobson, Neil</creatorName>
      <givenName>Neil</givenName>
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      <creatorName>Galindo, Leonardo</creatorName>
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      <creatorName>Zhu, Shilin</creatorName>
      <givenName>Shilin</givenName>
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      <creatorName>Shi, Daihu</creatorName>
      <givenName>Daihu</givenName>
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      <creatorName>McDill, Joshua</creatorName>
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      <creatorName>Yang, Linfeng</creatorName>
      <givenName>Linfeng</givenName>
      <familyName>Yang</familyName>
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      <creatorName>Hawkins, Simon</creatorName>
      <givenName>Simon</givenName>
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      <creatorName>Neutelings, Godfrey</creatorName>
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      <creatorName>Datla, Raju</creatorName>
      <givenName>Raju</givenName>
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      <creatorName>Lambert, Georgina</creatorName>
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      <creatorName>Galbraith, David W.</creatorName>
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      <creatorName>Grassa, Christopher J.</creatorName>
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      <creatorName>Geraldes, Armando</creatorName>
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      <creatorName>Cronk, Quentin C.</creatorName>
      <givenName>Quentin C.</givenName>
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      <creatorName>Cullis, Christopher</creatorName>
      <givenName>Christopher</givenName>
      <familyName>Cullis</familyName>
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      <creatorName>Dash, Prasanta K.</creatorName>
      <givenName>Prasanta K.</givenName>
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      <creatorName>Kumar, Polumetla A.</creatorName>
      <givenName>Polumetla A.</givenName>
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      <creatorName>Cloutier, Sylvie</creatorName>
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      <creatorName>Sharpe, Andrew G.</creatorName>
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      <creatorName>Wong, Gane K.-S.</creatorName>
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      <creatorName>Wang, Jun</creatorName>
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    <creator>
      <creatorName>Deyholos, Michael K.</creatorName>
      <givenName>Michael K.</givenName>
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  <titles>
    <title>The genome of flax ( Linum usitatissimum ) assembled de novo from short shotgun sequence reads</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2012</publicationYear>
  <dates>
    <date dateType="Issued">2012-07-03</date>
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  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/897213</alternateIdentifier>
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    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsIdenticalTo">10.1111/j.1365-313x.2012.05093.x</relatedIdentifier>
  </relatedIdentifiers>
  <rightsList>
    <rights rightsURI="https://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">Flax (Linum usitatissimum) is an ancient crop that is widely cultivated as a source of fiber, oil and medicinally relevant compounds. To accelerate crop improvement, we performed whole-genome shotgun sequencing of the nuclear genome of flax. Seven paired-end libraries ranging in size from 300 bp to 10 kb were sequenced using an Illumina genome analyzer. A de novo assembly, comprised exclusively of deep-coverage (approximately 94× raw, approximately 69× filtered) short-sequence reads (44-100 bp), produced a set of scaffolds with N(50)  = 694 kb, including contigs with N(50)  = 20.1 kb. The contig assembly contained 302 Mb of non-redundant sequence representing an estimated 81% genome coverage. Up to 96% of published flax ESTs aligned to the whole-genome shotgun scaffolds. However, comparisons with independently sequenced BACs and fosmids showed some mis-assembly of regions at the genome scale. A total of 43 384 protein-coding genes were predicted in the whole-genome shotgun assembly, and up to 93% of published flax ESTs, and 86% of A. thaliana genes aligned to these predicted genes, indicating excellent coverage and accuracy at the gene level. Analysis of the synonymous substitution rates (K(s) ) observed within duplicate gene pairs was consistent with a recent (5-9 MYA) whole-genome duplication in flax. Within the predicted proteome, we observed enrichment of many conserved domains (Pfam-A) that may contribute to the unique properties of this crop, including agglutinin proteins. Together these results show that de novo assembly, based solely on whole-genome shotgun short-sequence reads, is an efficient means of obtaining nearly complete genome sequence information for some plant species.</description>
  </descriptions>
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