Primers for Fungal ID

Our next step for some of these fungal cultures is to be able to positively ID them by using DNA extraction methods along with PCR to amplify conserved regions of their genome. A couple of weeks ago, I was able to synthesize some common primers used for fungal barcoding. In general, some common regions that are highly conserved in fungal DNA are 15s, 5.8s, ITS1 and ITS4. We were able to come across a nice paper (Genomic DNA Extraction and Barcoding of Endophytic Fungi) that gave a solid procedure for DNA extraction, amplification and some commonly used primer sequences for fungal barcoding.

Specifically what we would like to do is culture a know fungal sample, such as Penicillium, extract its DNA, PCR a conserved region mentioned above and successfully ID it by sending the amplified region to be sequenced. If everything goes smoothly, we should be able to BLAST search the sequence we get back and confirm that we successfully isolated DNA from our sample and confirm that it is in fact Penicillium.

In doing this, we can assure that our protocol is robust enough to move on to unknown fungal samples. Hopefully from there we can move on to figuring out how to isolate secondary metabolites such as penicillin from the Penicillum culture and configure a procedure to use on unknown fugal samples.

 

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