Applications Research areas
Offering ultra-long sequencing reads (up to 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
…plant chromosomes can now be assembled in a single contig, gapless and from telomere to telomere… Belser, C. et al. bioRxiv 440017 (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
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
- 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
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 complete characterisation of transgenic lines, assembling large plant genomes, elucidating the role of SV in phenotypic traits, and the value of full-length transcripts for enhanced genome annotation and gene expression studies.
Get more plant sequencing information, including case studies, getting started guides, and videos, in our Resource centre.
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. Researchers 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)
Scalable sequencing for plant research
From powerful, portable Flongle and MinION devices to the high-throughput benchtop GridION and PromethION platforms — scale your sequencing to match your specific research requirements.
Our most powerful platform, offering flexible, high-throughput sequencing using up to 48 independent, high-capacity flow cells — complete genomic and transcriptomic characterisation of large numbers of plant lines.View product
From genome assembly to gene expression, run multiple experiments on-demand using five independent MinION Flow Cells — perfect for busy labs running multiple projects.View product
Access the benefits of nanopore technology from just $1,000 — suitable for small plant genomes, targeted sequencing, and gene expression studies.View product
Integrated sequencing and analysis in a powerful handheld device — suitable for small plant genomes, targeted sequencing, and gene expression studies.View products
Adapting MinION and GridION for smaller, routine tests and analyses. Low plex targeted sequencing, RNA isoform analysis, and quality control applications.View product
Automated sample extraction and library preparation.View product