From the very basic problems of how to break up different kinds of tissue in order to extract DNA, to working with the "pre-fragmented" DNA that is found in historic specimens, working in a Botanical Garden laboratory is full of challenges.
Developing best practises for field collection of plant material.
The quality and quantity of DNA recovered from stored plant material is becoming more important as DNA sequencing technologies change from the relatively simple Sanger sequencing to next generation sequencing (NGS) technologies. The gold standard for sample storage is cryopreservation. However, this is not a viable option for most field collections or small sized institutes. We are conducting a long-term experiment, assessing different methods of sample preservation to maximise DNA integrity.
Extracting the most from our collections.
Whether it is the need for large quantities of pure DNA from our living collections for Genome assembly projects, or minute amounts of degraded DNA from our historical collections for hyb-seq, a successful DNA extraction protocol is a crucial first step on the road to generating robust genetic data.
We are constantly developing DNA extraction protocols for the enormous diversity of taxa and tissue types we research at RBGE – from testing methods of tissue disruption on fungal spores to dealing with polysaccharides that co-extract with the DNA.
The successful application of advanced sequencing techniques to historical or processed plant material has revolutionised how we use our preserved collections in molecular research. We are currently investigating the effects of different specimen preservation techniques on the quantity and quality of DNA extracted from Begonia leaves. The different preservation treatments include being pampered by collection into silica gel to being dried with a hairdryer or pickled in alcohol – testing the saying of Garbage in, Garbage out to the max.
Capturing genes from Herbaria.
Herbaria contain a wealth of information about plant diversity and distributions; however, assessing the genetic component of this diversity is difficult due to the degraded quality of DNA after many years of herbarium storage. Focussing on our core research taxa, we are developing targeted enrichment, or “hybrid capture”, techniques to retrieve large scale genetic data from both our herbarium and silica gel preserved collections.
Natural history collections for the Genomic era
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