In the literature we can find different targets for each fungal species using different techniques like PCR-RFLP, PCR-sequencing, fingerprinting, etc.
How can we (young researchers) find the best and the most reliable target and method?
Hi Shahram
The most reliable molecular technique identify fungi to species level without doubts is DNA sequencing. The main molecular marker to sequence in order to identify species is the region of the nuclear ribosomal internal spacers commonly known as ITS.
In this paper you find the whole discussion of this topic:
http://www.pnas.org/content/109/16/6241.short
However, the molecular technique, and the DNA region will always depends on your objective, fungi of interest, the sate of your knowledge, and research questions.
For example, if you made an experiment of several known species from whose you already have their ITS sequences, the new samples can be identified by PCR or RFLP. In contrast, if you have several species of unknown identity you will have to sequence them.
good luck
Hi Shahram
The most reliable molecular technique identify fungi to species level without doubts is DNA sequencing. The main molecular marker to sequence in order to identify species is the region of the nuclear ribosomal internal spacers commonly known as ITS.
In this paper you find the whole discussion of this topic:
http://www.pnas.org/content/109/16/6241.short
However, the molecular technique, and the DNA region will always depends on your objective, fungi of interest, the sate of your knowledge, and research questions.
For example, if you made an experiment of several known species from whose you already have their ITS sequences, the new samples can be identified by PCR or RFLP. In contrast, if you have several species of unknown identity you will have to sequence them.
good luck
Dear Roberto Garibay-Orijel
thanks a lot for your answer.
In some cases, for example in dermatophytes, some authors used PCR-sequencing of beta-tubulin or tef1-alpha or calmodulin genes, instead to ITS. They reported higher resolution of these targets in comparison to ITS.
In such cases, which one is preferred? The old and common target, or the new reported one?
Shahram
It is genus specific, different genes haver better resolution for different genus. The way to procede is to look for the literature dealing with your target genus and look what region they are using. A common problem using new regions is that once you have sequenced them there are not data for comparison in genbank
my best
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