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A chromosome-scale assembly of the sorghum genome using nanopore sequencing and optical mapping

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Listed:
  • Stéphane Deschamps

    (Corteva Agriscience™, Agriculture Division of DowDuPont™)

  • Yun Zhang

    (Corteva Agriscience™, Agriculture Division of DowDuPont™)

  • Victor Llaca

    (Corteva Agriscience™, Agriculture Division of DowDuPont™)

  • Liang Ye

    (Corteva Agriscience™, Agriculture Division of DowDuPont™)

  • Abhijit Sanyal

    (Corteva Agriscience™, Agriculture Division of DowDuPont™)

  • Matthew King

    (Corteva Agriscience™, Agriculture Division of DowDuPont™)

  • Gregory May

    (Corteva Agriscience™, Agriculture Division of DowDuPont™)

  • Haining Lin

    (Corteva Agriscience™, Agriculture Division of DowDuPont™)

Abstract

Long-read sequencing technologies have greatly facilitated assemblies of large eukaryotic genomes. In this paper, Oxford Nanopore sequences generated on a MinION sequencer are combined with Bionano Genomics Direct Label and Stain (DLS) optical maps to generate a chromosome-scale de novo assembly of the repeat-rich Sorghum bicolor Tx430 genome. The final assembly consists of 29 scaffolds, encompassing in most cases entire chromosome arms. It has a scaffold N50 of 33.28 Mbps and covers 90% of the expected genome length. A sequence accuracy of 99.85% is obtained after aligning the assembly against Illumina Tx430 data and 99.6% of the 34,211 public gene models align to the assembly. Comparisons of Tx430 and BTx623 DLS maps against the public BTx623 v3.0.1 genome assembly suggest substantial discrepancies whose origin remains to be determined. In summary, this study demonstrates that informative assemblies of complex plant genomes can be generated by combining nanopore sequencing with DLS optical maps.

Suggested Citation

  • Stéphane Deschamps & Yun Zhang & Victor Llaca & Liang Ye & Abhijit Sanyal & Matthew King & Gregory May & Haining Lin, 2018. "A chromosome-scale assembly of the sorghum genome using nanopore sequencing and optical mapping," Nature Communications, Nature, vol. 9(1), pages 1-10, December.
    • Handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-07271-1
    DOI: 10.1038/s41467-018-07271-1
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