Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2020 Sep 19;71(18):5313-5322.
doi: 10.1093/jxb/eraa263.

Oxford Nanopore sequencing: new opportunities for plant genomics?

Kathryn Dumschott  1   2 , Maximilian H-W Schmidt  1   2 , Harmeet Singh Chawla  3 , Rod Snowdon  3 , Björn Usadel  1   2   4
Affiliations

Oxford Nanopore sequencing: new opportunities for plant genomics?

Kathryn Dumschott et al. J Exp Bot. .

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, high-coverage 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 third-generation 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.

Keywords: de novo assembly; Basecalling; MinION flow cell; Oxford Nanopore; gene annotation; third-generation sequencing.

PubMed Disclaimer

Figures

Fig. 1.
Fig. 1.
ONT offers a variety of important advantages to the wider plant genomics community.
Fig. 2.
Fig. 2.
From plant tissue to genome assembly: the main steps in ONT sequencing. Optimizing each step can significantly increase the sequencing output and assembly quality.
Fig. 3.
Fig. 3.
Difference in read lengths between an untreated sample and a sample treated with the Circulomics Short Read Eliminator kit. DNA was extracted from rapeseed (Brassica napus) and sequenced on an ONT MinION (image created using NanoComp by De Coster et al. (2018).
See this image and copyright information in PMC

References

    1. Belser C, Istace B, Denis E, et al. . 2018. Chromosome-scale assemblies of plant genomes using nanopore long reads and optical maps. Nature Plants 4, 879–887. - PubMed
    1. Bolger AM, Poorter H, Dumschott K, et al. . 2019. Computational aspects underlying genome to phenome analysis in plants. The Plant Journal 97, 182–198. - PMC - PubMed
    1. Bolger ME, Weisshaar B, Scholz U, Stein N, Usadel B, Mayer KF. 2014. Plant genome sequencing—applications for crop improvement. Current Opinion in Biotechnology 26, 31–37. - PubMed
    1. Boykin LM, Ghalab A, De Marchi BR, et al. . 2018. Real time portable genome sequencing for global food security [version 1; peer review: 1 approved, 1 approved with reservations]. F1000Research 7, 1101.
    1. Campbell MS, Law M, Holt C, et al. . 2014. MAKER-P: a tool kit for the rapid creation, management, and quality control of plant genome annotations. Plant Physiology 164, 513–524. - PMC - PubMed

Publication types