Herbarium collections are increasingly becoming enormous resource for DNA studies; but for many species in certain families, there is difficulty in obtaining amplifiable DNA. I would like to know, so far, which is the best commercially available DNA extraction protocol and its performance in terms of DNA purity and yield, and PCR amplification successes.
Hi,
As you said, the herbarium collections are usually old and sometimes contaminated with insectisides and/or other pesticides. Almost all of the commercial DNA extraction kits are fine for fresh tissues. But for the herbarium specimens, especially not conserved in good conditions, the commercial kits are insufficient since ther are not optimizable. Older samples accumulates some secondary metabolites and other inhibitors that decrease extraction performance. Manual methods such as CTAB uses PVP and Mercaptoethanol removes those kind of substances.
So I strongly reccommend manual methods instead of kits.
Cheers
https://www.thermofisher.com/order/catalog/product/K0792#/K0792
https://www.researchgate.net/post/What_is_the_best_DNA_extraction_kit_for_herbarium_specimens
Hope both the links will be help for you.
Thank you
Hi, i think sometimes it depends on the species. Some species will have no challenge depending on the compounds present. However, CTAB (some modifications required based on species) has worked for me in degraded samples and also some studies recommended it. First, is to identify whether the main challenge is DNA quantity or quality. If quantity is the challenge, then CTAB will give more yield. If quality is the challenge, then the CTAB- extracted DNA can be purified. Incase the yield is very low, you can extract two tubes parallel for one leaf material and combine later (just non-official but worked for me).
This paper can also help maybe.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3429509/
I’ve had success using qiagen pland and fungi dna extraction kit. I’ve used it on root samples that came from the sewer and its worked just fine.
Qiagen extraction kit can be used.
For manual extraction CTAB or Miniprep method can be used.
In case of high level of alkaloids which leads to sticky solution. I found used of polyvinylpyrrolidone,
Many thanks to all of you; for your very helpful suggestions -- I will come back to you on the outcome.
I prefer the use of CTAB which uses PVP and Mercaptoethanol to remove those kinds of substances, mostly for the species which are difficult to preserve in the herbarium and the ones which are brittle in nature.
for herbarium species EZNA plant kit (Omega Biotech) is best and you can follow this paper. Article How to Open the Treasure Chest? Optimising DNA Extraction fr...
CTAB ( I have modify methods; I will send you on messenger ),and FAVCRGEN DNA extraction kit will be best
Niroj Paudel can you share that with me as well?? I am also kind of stuck with DNA extraction of Berberis
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