Applications Research areas
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.
Telomere-to-telomere gapless banana chromosomes
Read the paper…plant chromosomes can now be assembled in a single contig, gapless and from telomere to telomere… Belser, C. et al. Communications Biology 4 (2021)
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
- 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 with long, amplification-free reads using the Cas9 Sequencing Kit or real-time, on-device adaptive sampling
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
- Prepare DNA samples for sequencing in as little as 10 minutes, including multiplexing
- Use whole genome, metagenomic, targeted, and RNA sequencing approaches
- Automate sample prep using the portable VolTRAX device
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
This review outlines 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
The importance of structural variation in crop breeding
Brassica napus (oilseed rape) is a major oil crop worldwide, with widespread application in cooking, biofuel, and animal feed. The 1.2 Gb allotetraploid B. napus genome displays extensive gene and chromosome-level structural variation (SV), which underlies important phenotypic traits, such as flowering time, disease resistance, and seed quality. Precise resolution of these SVs could support improvement of this economically important crop. Harmeet Singh Chawla and colleagues at the Justus Liebig University in Germany, utilised long nanopore sequencing reads to fully characterise and compare SVs across four diverse B. napus lines. Initial analysis allowed correlation of average SV length with specific flowering phenotypes, while SV diversity provided further insights into the breeding history of the crop.
'Our results suggest that simple reference-based resequencing and alignment with long reads can uncover a new dimension of genetic and genomic diversity associated with important traits in crop plants'
Chawla, H.S. et al. Biotechnol J. 19:2 (2021)
From enhanced plant genome assembly to support conservation and crop breeding, through to the analysis of gene expression, base modifications, and plant pathogens, get comprehensive information in our Investigations pages.
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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.
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