I am a young scientist who is more or less completely inexperienced when it comes to conducting independent research projects. I have an idea for a research project, and I am planning on aplying to a short term fellowship program to pursue this project. I have a relatively fair idea of the project outline (data collecting time window, travel costs, etc) but I am unsure on how to go about figuring out the estimated cost of the DNA sequencing that will be one of the main components of the research project. Without going into too much detail on the project itself, I know that I will need to use DNA sequencing to identify fungal species and I will have very, very little morphological data to aid me in species identification. I expect at least some of the fungal samples to represent species that are unknown to science. Can anybody help me out in A) determining what DNA sequencing techniques will probably be useful (I plan on sequencing the ITS region, however I'm not quite sure what sequencing technique I should use) and B) How to go about estimating the costs of sequencing?
Thank you!
Hi Christopher,
It is pretty normal to find it very challenging to determine any project budget, specially when you targeting new subjects or topics where you have the least experience.
Now the international companies providing DNA sequencing services (e.g. Macrogen) can provide you a services related to fungal identification using several protocols including the traditional Sanger sequencing for ITS. Writing a project related to Mycology, make me assume that you are working in microbiology laboratory, thus, up to the isolation of your fungus is possible, afterwards you can send the isolate to the company to proceed with the DNA extraction, PCR of the desired region (I will detail on that later on), PCR purification and sequencing, even they can help you with the bioinformatic analysis. You can easily contact them for such services and make your order online or contact them personally by email. Based on my experience, they were the most cost-effective company (quality and price) when it comes to traditional Sanger sequencing. Therefore, no need to purchase related equipment if your budget is tight, or equipment purchase is not an option; you may redirect your budget toward the analysis and the company services for more samples to be processed.
In mycology, ITS (specially ITS2), LSU, SSU, 5S, mt-ITS, mt-12S, b-tubuline, RPB2 ...etc. are the most common DNA regions for fungal identification and genetic diversity studies. I usually use the following UNITE community website when it comes to the molecular identification and barcoding of fungal specimen.
Link:
https://unite.ut.ee/primers.php
Afterwards, many bioinformatic and phylogeny methods will help you out to precise-as-possible your identification, and to help you with the new, unknown species, at least to the genus level! UNITE community also has a training set include the most revised and updated fungal sequences of known species, which would help you out when the time comes.
Best wishes with your project!
Regards
Hi Christopher,
It is pretty normal to find it very challenging to determine any project budget, specially when you targeting new subjects or topics where you have the least experience.
Now the international companies providing DNA sequencing services (e.g. Macrogen) can provide you a services related to fungal identification using several protocols including the traditional Sanger sequencing for ITS. Writing a project related to Mycology, make me assume that you are working in microbiology laboratory, thus, up to the isolation of your fungus is possible, afterwards you can send the isolate to the company to proceed with the DNA extraction, PCR of the desired region (I will detail on that later on), PCR purification and sequencing, even they can help you with the bioinformatic analysis. You can easily contact them for such services and make your order online or contact them personally by email. Based on my experience, they were the most cost-effective company (quality and price) when it comes to traditional Sanger sequencing. Therefore, no need to purchase related equipment if your budget is tight, or equipment purchase is not an option; you may redirect your budget toward the analysis and the company services for more samples to be processed.
In mycology, ITS (specially ITS2), LSU, SSU, 5S, mt-ITS, mt-12S, b-tubuline, RPB2 ...etc. are the most common DNA regions for fungal identification and genetic diversity studies. I usually use the following UNITE community website when it comes to the molecular identification and barcoding of fungal specimen.
Link:
https://unite.ut.ee/primers.php
Afterwards, many bioinformatic and phylogeny methods will help you out to precise-as-possible your identification, and to help you with the new, unknown species, at least to the genus level! UNITE community also has a training set include the most revised and updated fungal sequences of known species, which would help you out when the time comes.
Best wishes with your project!
Regards
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