I would like to start a new plant phylogenomics project, but I am currently struggling with choosing the best-suited approach. My idea is to combine the latest genomic approaches (e.g., Oxford Nanopore Technology (ONT) Sequencing) with DNA extraction of herbarium specimens due to Covid-19 restrictions and thus restricted traveling possibilities.
- Do you have any experiences with DNA extractions from herbarium specimens and ONT genome sequencing?
- Assuming the availability of a reference genome, would you recommend using low-quality long ONT reads instead of high-quality short Illumina reads (also in terms of costs) from DNA herbarium specimens for reference-guided read assembly? Depending on the specimen age, DNA is already strongly fragmented and ONT won’t capture long fragments (> 1 kbp) anyway, or?…
- Are there software tools you would recommend for reference-guided ONT read assembly and generation of diverse output files for further downstream analysis (e.g., tree and structure software)?
The plant species I will use has a diploid genome size of 0.8 Gbp. The majority of samples are polyploid hybrids.
I hope one day there will be a simple scanner that tells us the species :)
The main problem here is that DNA from herbariu specimens is usually very fragmented. Therefore, you will lose the potential of nanopore for sequencing long reads. Under these circumstances, Illumina sequencing is in general preferable.
The question is, why do you what to use nanopore on herbarium vouchers?
I cannot remember of a study using nanopore on (old) herbarium specimens. But let's wait...maybe somebody else has more experience on that.
Greetings!
- Badges
- Science method