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.
Oxford Nanopore sequencing
Traditional short-read technologies
Unrestricted read length (>4 Mb achieved)
- Resolve complex and repetitive genomic regions such as structural variants and transposons
- Generate high-quality de novo plant genomes and correct reference genomes
- Analyse long-range haplotypes and phasing, and get greater insight into polyploid genomes
- Accurately annotate plant genomes using full-length transcripts
- Get isoform-level transcriptome characterisation and quantification
- End-to-end sequencing of structural variants
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
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
Platform costs and infrastructure requirements can limit global accessibility. Sample batching may also be required for optimal efficiency, potentially delaying results.
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.
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.
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.
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.
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.
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.
Offering two independently addressable PromethION Flow Cells for low-cost access to high-output sequencing, the PromethION 2 Integrated and PromethION 2 Solo are ideal smaller sample number plant genome sequencing projects.
Combining up to 24 independently addressable, high-capacity flow cells with powerful, integrated compute — ideal for cost-effective, high-throughput sequencing of large plant genomes and isoform-level transcriptome analyses.
From genome assembly to gene expression, run multiple experiments on-demand using five independent MinION Flow Cells — perfect for busy labs running multiple projects.
Access the benefits of nanopore technology from just $1,000 — suitable for small plant genomes, targeted sequencing, and gene expression studies.
Adapting MinION and GridION for smaller, routine tests and analyses. Low plex targeted sequencing, RNA isoform analysis, and quality control applications.
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