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.
Highlights
Long-read sequencing technologies have greatly facilitated assemblies of large eukaryotic genomes
Libraries were prepared with the Oxford Nanopore Technologies (ONT) Ligation Sequencing Kit 1D (SQK-LSK108), except for three long-read libraries prepared with the ONT Rapid Sequencing Kit 1D (SQKRAD002), sequenced for 48 h using MinION R9.4 and R9.5 flow cells
This study demonstrates that the Oxford Nanopore sequencing technology, combined with the Direct Label and Stain (DLS) optical mapping technology recently developed by Bionano Genomics, can generate chromosome-scale assemblies of large and repeat-rich plant genomes
Summary
Long-read sequencing technologies have greatly facilitated assemblies of large eukaryotic genomes. 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. Numerous genomic assembly projects, including maize[9] and Aegilops tauschii[10], have generated chromosome-scale scaffolds when combining long-read PacBio sequences with complementary long-range scaffolding technologies, such as Bionano Genomics optical maps or Hi-C proximity ligation[11]. Results shown here suggest that the ONT technology can be used to quickly and cost-effectively generate informative assemblies and, in combination with longrange DLS optical maps from Bionano Genomics, can generate chromosome-scale assemblies to assess the overall structural integrity of large and repeat-rich plant genomes
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