A Chromosome-scale Assembly of the Sorghum Genome Using Nanopore Sequencing and Optical Mapping

Overview

Journal Nat Commun

Specialty Biology

Date 2018 Nov 20

PMID 30451840

Citations 85

Authors

Stephane Deschamps

Yun Zhang

Victor Llaca

Liang Ye

Abhijit Sanyal

Matthew King

Gregory May

Haining Lin

Affiliations

Soon will be listed here.

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 N 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.

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