Nanopore sequencing is now being used for the analysis of plant genomes, in the lab or in the field
How can nanopore sequencing support your plant research?
- de novo assembly of complex multi-gigabase plant genomes without the requirement for capital investment
- Resolution of repetitive sequences and transposons using long reads
- Insight into structural variants that can be used in plant breeding and selection studies
- Analysis of plant pathogens, with the option of using Direct RNA sequencing
- Use of MinION for analysis of samples at the source/outside the lab
Nanopore sequencing offers real-time, long read analysis of any genomes.
Reads can span long, repetitive regions; the longest read reported to date is ~850kb.
Offering high-throughput capability, or ultra-portable analysis the portable MinION has been used to sequence tomato and melon genomes, as well as sequencing Arapidopsis up a mountain. New approaches to assembly are being developed to significantly reduce the computational requirement and improve the speed of assembly of the complex genomes.
The portability of the MinION provides new opportunities to sequence samples in their local environment, avoiding transportation time. For projects which require higher throughput, GridION enables up to five MinION Flow Cells with integrated compute and PromethION is designed to deliver 280x the sequencing capacity of MinION.
Publications relevant to plant genomics:
What's in my pot (WIMP)
'What's in my pot' (WIMP) is a workflow that enables MinION users to identify pathogens, fungi, viruses or archaea in complex samples in real time.
Analysis begins as soon as sequence data starts being streamed (a few seconds after the experiment starts). Each read of streamed sequence data is compared against a database of microbial species, and an identification is made. At the same time, WIMP plots and updates a taxonomic tree of all microorganisms found in the sample
There are various workflows and techniques that have been developed by members of the nanopore community to perform or enhance assembly and species identification that can be explored in the publications area and within the nanopore community
How do I get started?
You can start using MinION straight away.
For a $1,000 fee you receive a MinION and starter pack of flow cells and kits. You also get access to a thriving online community of MinION users.