I want to look at diversity of fungal endophytes in trees using MiSeq. I tried a couple of primer pairs targeting either ITS1 or ITS2 e.g., ITS1F/ITS2, ITS3_KYO2/ITS4, ITS3_KYO2/ITS4_KYO3 (Toju et al., 2012) and BITSf/B58S3R (Bokulich and Mills, 2013), but none of them returned a satisfied result. All of the primers amplified a relatively large portion of trees ITS1/2.
Do you have any suggestions which primer pair I should try on, or any method I can try to reduce amplification of trees ITS?
Thank you in advance and have a great day!