In my PhD, I want to analyse fungal communities in lake sediment cores from Siberia. One of the performed experiments will be a metabarcoding of the fungi. Therefore I am evaluating primers at the moment. In many publications, the ITS marker has been used. Now I evaluated various ITS marker combinations with ecoPCR to check which combinations are best suited for my purpose. In a recent discussion, also 18S as a possible target for metabarcoding popped up. So here my question:
Is someone experienced in analysing ancient fungal communities in soil samples? I am working with ancient DNA (so very small amounts of highly fragmented DNA). Which primers/markers do you use and why?
Thank you very much in advance!
We used ITS1-ITS4 to capture the entire ITS region. If you want to produce more amount of PCR product, you may do nested PCR as well. Here it is: Article A cost-effective and efficient strategy for Illumina sequenc...
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