Plant research with nanopore sequencing technology
Nanopore sequencing enables the accurate assembly of complex, multi-gigabase plant genomes and real-time detection of plant pathogens. Long DNA sequencing reads (up to 4 Mb) allow enhanced genome assembly with complete characterisation of complex genomic regions — including structural variants, transposons, and transgene insertions — delivering new insights into plant biology, evolution, and breeding strategies. Base modifications can be identified alongside the nucleotide sequence without any additional protocol steps or expense, providing even more comprehensive, cost-effective genomic characterisation. Sequence full-length RNA transcripts for enhanced gene annotation and gene expression studies. A range of nanopore sequencing devices are available — from the portable MinION to the high-throughput PromethION, capable of sequencing extremely large plant genomes or sample numbers, such as transgenic lines and seed collections.
- Simplify de novo genome assembly and correct reference genomes
- Resolve repetitive regions, structural variation, transposons, transgene insertions, and base modifications
- Identify plant pathogens rapidly and in the field
- Sequence full-length RNA transcripts for enhanced gene annotation and gene expression studies
- Streamlined, automatable workflows with low input requirements
- Scale to your needs using Flongle, MinION, GridION, or PromethION
Genome assembly & transgene mapping
Plant transcriptomics & gene annotation
Real-time pathogen characterisation
Plant genomes are typically large, highly repetitive, and exhibit a wide variety of ploidy, making them challenging to sequence and assemble using traditional sequencing technologies. Sequencing long and ultra-long DNA fragments — with read lengths up to 4 Mb — nanopore technology delivers enhanced plant genome assemblies, resolving complex repetitive regions, structural variants, transposons, and transgene insertions. Retain and detect modified bases, alongside nucleotide sequence, by direct, amplification-free sequencing of native DNA.
- Simplify plant genome assembly — create de novo reference genomes or correct and complete existing genome assemblies
- Resolve challenging regions, including repeats, structural variants, transposons, and transgene insertions
- Investigate gene linkage, haplotype phasing, and sub-genomes
- Directly detect epigenetic modifications alongside nucleotide sequence
- Rapid 10-minute library prep and low DNA input requirements
- High yields, on demand — up to 2.8 Gb Flongle; 50 Gb MinION; 250 Gb GridION; 14 Tb PromethION*
* Theoretical max output when system is run for 72 hours (or 16 hours for Flongle) at 420 bases / second. Outputs may vary according to library type, run conditions, etc.
‘The PromethION is a real game changer, combining ultra-long reads with high sequence output for the production of contiguous, high-quality reference genomes. Using this platform, we sequenced the 2.56 Gb lettuce genome at >100X coverage using just a few flow cells’
Alexander Wittenberg, KeyGene, PromethION service provider
Sequencing and assembling mega-genomes of mega-trees: the giant sequoia and coast redwood genomes
RNA sequencing is a powerful tool for gene discovery and transcript expression analysis in plants that can inform crop breeding and improvement programmes. With nanopore sequencing, read length is equal to RNA (or DNA) fragment length, allowing the unambiguous analysis of full-length transcripts — simplifying gene annotation and enabling accurate characterisation and quantification of gene expression at the isoform level. The facility for direct sequencing of native RNA removes potential sources of bias and allows the identification of base modifications alongside nucleotide sequence.
- Accurate transcript and isoform quantification
- Simplified gene annotation
- Unambiguous identification of splice variants with full-length transcripts
- Eliminate bias using direct cDNA and direct RNA sequencing
- Identify modified bases alongside nucleotide sequence using native RNA sequencing
- Access data in real-time
‘This [Arabidopsis] data reveals a wealth of new transcriptomic complexity that is not reflected in the established transcriptome annotations’
Nick Schurch, University of Dundee
Using full-length transcript sequencing to reveal the fate of mRNA in aging seeds
Rapid identification and characterisation of plant pathogens is essential for effective monitoring and control strategies. From just $1,000, the portable, real-time MinION device enables cost-effective detection of plant pathogens in the lab or field — without the requirement to ship samples to specialist sequencing facilities. In-field studies are also supported by VolTRAX and MinIT — providing rapid and portable solutions for sample preparation and data analysis. Long nanopore sequencing reads enable complete genomic characterisation, resolving repetitive regions and structural variation.
- Real-time metagenomic or targeted detection of plant pathogens
- Long reads enhance microbial identification and simplify genome assembly
- Scalable technology — sequence in the lab or field
- Rapid library preparation (DNA: 10 min; RNA: 105 min)
- A complete workflow — from library prep to pathogen identification
‘…the nanopore sequencing platform provides a rapid way for initial diagnosis of plant diseases caused by pathogenic viruses, bacteria and fungi’
Chalupowicz et al
Culture-free detection of boxwood blight to improve disease diagnosis and prevention