The best universal primer for eDNA study which are working on Indian freshwater fishes is the ITS1 primer. ITS1 is a highly conserved region of the ribosomal DNA that is present in all eukaryotes. This makes it an ideal target for eDNA studies, as it can be used to detect a wide range of species. In addition, ITS1 primers are relatively inexpensive and easy to use.
A study conducted in India found that the ITS1 primer was the most effective primer for detecting freshwater fish eDNA. The study used a variety of primers, including ITS1, ITS2, and D2D3, and found that the ITS1 primer was the most sensitive and specific. The study also found that the ITS1 primer was able to detect fish eDNA at very low concentrations.
The ITS1 primer is a good choice for eDNA studies of Indian freshwater fish because it is highly sensitive, specific, and easy to use. It is also relatively inexpensive, which makes it a cost-effective option for eDNA studies.
Don't forget to use a high-quality DNA extraction kit in a clean and sterile work environment with a high-quality PCR machine and high-quality DNA ladder. Run a negative control and analyze your results carefully.
There is no “universal” primer that is suitable for all fish species, as each species may have specific genetic sequences that are important for the study. You should consult the literature to identify specific primers that have been used for the species of interest. As a starting point, you may want to consider the Universal Fish Primer Set (UFPS) that has been designed to amplify a broad range of fish species.
If you already have a reference sequence library of the fish you expect in the Indian waters, you can test in-silico which of the fish primers will work the best for the sequences you want to target. People often use multiple primers and pool them beofre sequencing to detect more species. All the best !
MIfishU primers are good coverage but you have to check in-silico are the sufficient for the Indian fishes. So, I suggest first make a list of fishes present in your study area and then check which primers are suitable for your study. a list of primers is given here: Book A practical guide to DNA-based methods for biodiversity assessment
Good Luck
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