Journal Article

FZJ-2020-02159

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Oxford Nanopore Sequencing: New opportunities for plant genomics?

Dumschott, K. (Corresponding author)FZJ* ; Schmidt, M.FZJ* ; Chawla, H. S. ; Snowdon, R. ; Usadel, B.FZJ*

2020
Oxford Univ. Press Oxford

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Please use a persistent id in citations: http://hdl.handle.net/2128/25768  doi:10.1093/jxb/eraa263

Abstract: DNA sequencing was dominated by Sanger’s chain-termination method until the mid-2000s, when it was progressively supplanted by new sequencing technologies that can generate much larger quantities of data in a shorter time. At the forefront of these developments, long-read sequencing technologies (third-generation sequencing) can produce reads that are several kilobases in length. This greatly improves the accuracy of genome assemblies by spanning the highly-repetitive segments that cause difficulty for second-generation short-read technologies. Third-generation sequencing is especially appealing for plant genomes, which can be extremely large with long stretches of highly-repetitive DNA. Until recently, the low basecalling accuracy of third-generation technologies meant that accurate genome assembly required expensive, highcoverage sequencing followed by computational analysis to correct for errors. However, today’s long-read technologies are more accurate and less expensive, making them the method of choice for the assembly of complex genomes. Oxford Nanopore Technologies (ONT), a thirdgeneration platform for the sequencing of native DNA strands, is particularly suitable for the generation of high-quality assemblies of highly-repetitive plant genomes. Here we discuss the benefits of ONT, especially for the plant science community, and describe the issues that remain to be addressed when using ONT for plant genome sequencing.

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Contributing Institute(s):

1. Bioinformatik (IBG-4)

Research Program(s):

1. 582 - Plant Science (POF3-582) (POF3-582)
2. 583 - Innovative Synergisms (POF3-583) (POF3-583)

Appears in the scientific report 2020

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Database coverage:
; ; ; BIOSIS Previews ; Biological Abstracts ; Clarivate Analytics Master Journal List ; Current Contents - Agriculture, Biology and Environmental Sciences ; Current Contents - Life Sciences ; Ebsco Academic Search ; Essential Science Indicators ; IF >= 5 ; JCR ; NCBI Molecular Biology Database ; National-Konsortium ; Nationallizenz ; PubMed Central ; SCOPUS ; Science Citation Index ; Science Citation Index Expanded ; Web of Science Core Collection

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