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 sequencing reads (up to 2 Mb) allow enhanced genome assembly with complete characterisation of complex genomic regions, delivering new insights into plant biology, evolution and breeding strategies. Identify base modifications alongside nucleotide sequence and explore the impact of epigenetics through direct sequencing of native DNA or RNA. 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
- Fully characterise and quantify plant transcript isoforms
- Scale to your needs using MinION, GridION or PromethION
How will you use nanopore technology?
Generate improved genome assemblies
Real-time pathogen characterisation
- Simplify plant genome assembly — create de novo reference genomes or correct and complete existing genome assemblies
- Resolve challenging regions, including repeats and transgene insertions
- Investigate gene linkage and haplotype phasing
- Directly detect epigenetic modifications alongside nucleotide sequence
- Rapid 10-minute library prep and low DNA input requirements
- High yields, on demand — 30 Gb MinION; 150 Gb GridION;
'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
- 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
- Unambiguous identification of splice variants with full-length transcripts
- Accurate transcript and isoform quantification
- Remove 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