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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{
  "description": "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\u2003bp to 10\u2003kb were sequenced using an Illumina genome analyzer. A de novo assembly, comprised exclusively of deep-coverage (approximately 94\u00d7 raw, approximately 69\u00d7 filtered) short-sequence reads (44-100\u2003bp), produced a set of scaffolds with N(50) \u2003=\u2003694\u2003kb, including contigs with N(50) \u2003=\u200320.1\u2003kb. The contig assembly contained 302\u2003Mb 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\u2003384 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\u2003MYA) 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.", 
  "license": "https://creativecommons.org/licenses/by/4.0/legalcode", 
  "creator": [
    {
      "@type": "Person", 
      "name": "Wang, Zhiwen"
    }, 
    {
      "@type": "Person", 
      "name": "Hobson, Neil"
    }, 
    {
      "@type": "Person", 
      "name": "Galindo, Leonardo"
    }, 
    {
      "@type": "Person", 
      "name": "Zhu, Shilin"
    }, 
    {
      "@type": "Person", 
      "name": "Shi, Daihu"
    }, 
    {
      "@type": "Person", 
      "name": "McDill, Joshua"
    }, 
    {
      "@type": "Person", 
      "name": "Yang, Linfeng"
    }, 
    {
      "@type": "Person", 
      "name": "Hawkins, Simon"
    }, 
    {
      "@type": "Person", 
      "name": "Neutelings, Godfrey"
    }, 
    {
      "@type": "Person", 
      "name": "Datla, Raju"
    }, 
    {
      "@type": "Person", 
      "name": "Lambert, Georgina"
    }, 
    {
      "@type": "Person", 
      "name": "Galbraith, David W."
    }, 
    {
      "@type": "Person", 
      "name": "Grassa, Christopher J."
    }, 
    {
      "@type": "Person", 
      "name": "Geraldes, Armando"
    }, 
    {
      "@type": "Person", 
      "name": "Cronk, Quentin C."
    }, 
    {
      "@type": "Person", 
      "name": "Cullis, Christopher"
    }, 
    {
      "@type": "Person", 
      "name": "Dash, Prasanta K."
    }, 
    {
      "@type": "Person", 
      "name": "Kumar, Polumetla A."
    }, 
    {
      "@type": "Person", 
      "name": "Cloutier, Sylvie"
    }, 
    {
      "@type": "Person", 
      "name": "Sharpe, Andrew G."
    }, 
    {
      "@type": "Person", 
      "name": "Wong, Gane K.-S."
    }, 
    {
      "@type": "Person", 
      "name": "Wang, Jun"
    }, 
    {
      "@type": "Person", 
      "name": "Deyholos, Michael K."
    }
  ], 
  "headline": "The genome of flax ( Linum usitatissimum ) assembled de novo from short shotgun sequence reads", 
  "image": "https://zenodo.org/static/img/logos/zenodo-gradient-round.svg", 
  "datePublished": "2012-07-03", 
  "url": "https://zenodo.org/record/897213", 
  "@context": "https://schema.org/", 
  "identifier": "https://doi.org/10.1111/j.1365-313x.2012.05093.x", 
  "@id": "https://doi.org/10.1111/j.1365-313x.2012.05093.x", 
  "@type": "ScholarlyArticle", 
  "name": "The genome of flax ( Linum usitatissimum ) assembled de novo from short shotgun sequence reads"
}
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