Oxford Nanopore sequencing : new opportunities for plant genomics?
| Autor: | Björn Usadel, Rod J. Snowdon, Kathryn Dumschott, Maximilian Schmidt, Harmeet Singh Chawla |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2020 |
| Předmět: |
0106 biological sciences
0301 basic medicine Expert View Basecalling Physiology Computer science Sequence assembly Plant Science Computational biology de novo assembly 01 natural sciences Genome DNA sequencing 03 medical and health sciences Plant science MinION flow cell Computational analysis Repeated sequence third-generation sequencing AcademicSubjects/SCI01210 fungi High-Throughput Nucleotide Sequencing food and beverages Genomics Sequence Analysis DNA gene annotation Nanopore Sequencing 030104 developmental biology ddc:580 Oxford Nanopore Nanopore sequencing Plant genomics Genome Plant 010606 plant biology & botany |
| Zdroj: | Journal of Experimental Botany The journal of experimental botany 71(18), 5313–5322 (2020). doi:10.1093/jxb/eraa263 The journal of experimental botany 71(18), 5313-5322 (2020). doi:10.1093/jxb/eraa263 |
| DOI: | 10.18154/rwth-2020-11209 |
| Popis: | The sequencing of plant genomes is challenging due to their large size and abundant repetitive DNA, but third-generation platforms such as Oxford Nanopore Technologies can now generate high-quality assemblies. 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. |
| Databáze: | OpenAIRE |
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