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

<jats:title>Abstract</jats:title> <jats:p> 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 <jats:italic>Sorghum bicolor Tx430</jats:italic> genome. The final assembly consists of 29 scaffolds, encompassing in most cases entire chromosome arms. It has a scaffold N <jats:sub>50</jats:sub> 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 <jats:italic>Tx430</jats:italic> data and 99.6% of the 34,211 public gene models align to the assembly. Comparisons of <jats:italic>Tx430</jats:italic> and <jats:italic>BTx623</jats:italic> DLS maps against the public <jats:italic>BTx623</jats:italic> 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. </jats:p>