Plant research

Offering ultra-long sequencing reads (>4 Mb), nanopore technology enables accurate assembly of large, highly repetitive plant genomes — resolving structural variants, transposons, and transgene insertions — to deliver new insights into plant biology, evolution, and breeding strategies. Base modifications (e.g. methylation) can be identified alongside nucleotide sequence with no additional protocol steps or expense, while the facility to sequence full-length transcripts supports enhanced gene annotation and gene expression studies.

…plant chromosomes can now be assembled in a single contig, gapless and from telomere to telomere…

Belser, C. et al. Communications Biology 4 (2021)

Technology comparison

Oxford Nanopore sequencing

Traditional short-read technologies

Unrestricted read length (>4 Mb achieved)

Read length typically 50–300 bp

Short reads do not typically span entire regions of interest, including repeats and structural variants, or full-length RNA transcripts, resulting in fragmented assemblies and ambiguous transcript isoform identification.

Direct, amplification-free protocols

  • Detect base modifications (e.g. methylation) as standard — no additional prep required
  • Eliminate amplification bias, GC-bias, and read length limitations
  • Expand the utility of targeted sequencing using real-time, on-device enrichment — adaptive sampling, or CRISPR/Cas9-based enrichment

Amplification required

Amplification can introduce bias — reducing uniformity of coverage with the potential for coverage gaps — and removes base modifications, necessitating additional sample prep, sequencing runs, and expense.

Flexible and on-demand

  • Scale to your throughput needs
  • Sequence in the lab or field with portable Flongle and MinION
  • Tackle large plant genome projects with flexible, high-throughput GridION and PromethION devices
  • No sample batching required

Limited flexibility

Platform costs and infrastructure requirements can limit global accessibility. Sample batching may also be required for optimal efficiency, potentially delaying results.

Streamlined workflows

Laborious workflows

Typically, lengthy sample preparation requirements and long sequencing run times, reducing workflow efficiency.

Real-time data streaming

  • Get immediate access to results for time critical applications such as plant pathogen identification
  • Enrich targeted regions based on real-time sequence composition using adaptive sampling
  • Stop sequencing when sufficient data generated — wash and reuse flow cell
  • Use simple EPI2ME workflows for real-time microbiome and plant pathogen analysis

Fixed run time with bulk data delivery

Increased time-to-result and inability to identify workflow errors until it’s too late, plus additional complexities of handing large volumes of bulk data.

White paper

Closing the gap in plant genomes

Discover how researchers are addressing the challenges of producing high-quality, highly contiguous plant genome assemblies through the use of nanopore sequencing technology — enabling new opportunities in plant conservation and breeding. Specific case studies cover the elucidation of centromere sequences, the role of structural variation in phenotypic traits, and the complete genomic characterisation of transgenic lines. Learn how long nanopore sequencing reads simplify the study of genome architecture and how the latest Oxford Nanopore Q20+ chemistry, combined with plant-trained basecalling models, is delivering even more accurate genomes.

Get more plant sequencing information, including case studies, getting started guides, and videos, in our Resource centre.

Case study

Conserving a threatened North American walnut

Juglans cinerea (a member of the walnut family) is currently listed as endangered. Genomic analysis can inform conservation efforts by monitoring population genetic diversity. The adoption of such techniques for threatened species has been limited by financial resources and, up until now, there has been no reference-quality assembly. Guzman-Torres et al. generated a highly-contiguous, chromosome-scale reference assembly for J. cinerea using only nanopore technology — saving both compute and financial resources.

Case study

Generating telomere-to-telomere assemblies using a single platform

At London Calling 2023, Sergey Koren (National Institutes of Health, USA) shared how they generated telomere-to-telomere assemblies using only the nanopore sequencing platform for two important crop species, Zea mays and Solanum lycopersicum. Highlighting that nanopore duplex data quality was similar to an alternative sequencing platform, Sergey also shared that nanopore sequencing reads were tens of kilobases longer. With an assembly base-accuracy exceeding 99.999%, Oxford Nanopore has the potential to provide a single-instrument solution for complete genome assembly.

Get started

Scalable sequencing for plant research

From powerful, portable Flongle and MinION devices to the high-throughput benchtop GridION and PromethION devices— scale your sequencing to match your specific research requirements.

Recommended for plant sequencing

PromethION 48

Our most powerful device, offering flexible, high-throughput sequencing using up to 48 independent, high-capacity flow cells. PromethION 48 delivers complete genomic and transcriptomic characterisation of large numbers of plant lines.


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