Oxford Nanopore sequencing: new opportunities for plant genomics?
Open Access
- 27 May 2020
- journal article
- review article
- Published by Oxford University Press (OUP) in Journal of Experimental Botany
- Vol. 71 (18), 5313-5322
- https://doi.org/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, 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
Funding Information
- German Ministry of Education and Research (FKZ 031B0293A, FKZ 031A536C, 031B0187)
This publication has 76 references indexed in Scilit:
- Plant genome sequencing — applications for crop improvementCurrent Opinion in Biotechnology, 2014
- MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome AnnotationsPlant Physiology, 2013
- The MaSuRCA genome assemblerBioinformatics, 2013
- Detection and Quantification of Methylation in DNA using Solid-State NanoporesScientific Reports, 2013
- TRAPID: an efficient online tool for the functional and comparative analysis of de novo RNA-Seq transcriptomesGenome Biology, 2013
- MIPS PlantsDB: a database framework for comparative plant genome researchNucleic Acids Research, 2012
- Establishing, maintaining and modifying DNA methylation patterns in plants and animalsNature Reviews Genetics, 2010
- High-throughput functional annotation and data mining with the Blast2GO suiteNucleic Acids Research, 2008
- Finishing the euchromatic sequence of the human genomeNature, 2004
- Nucleotide sequence of bacteriophage φX174 DNANature, 1977