Fungal marker selection

Question

[fatemehsanjar]

I am planning to sequence and analyze fungal populations from human samples. I understand that there are different fungal markers available and based on publications I have decided to use ITS primer for my studies. Originally I was planning to using the ITS1F and ITS4R primers which produced an amplicon covering ITS1, ITS2, and the 5S region but I see some suggesting to use smaller portions and only use ITS2.

I would appreciate feedback from folks who have more experience in this field and can tell me their experience with using any of the available ITS primers.

Thank you for your time!

Fatemeh

[lelle]

How will you sequence your amplified fragment? If you use ITS1+5.8S+ITS2 you will probably end up with a fragment to big for Illumina.

Answer 1

[5heikki]

AFAIK UNITE is the largest fungal ITS db, so, you should probably look into what region they cover..