Which primer pair is better for amplifying endophytic fungal communities (metabarcoding with Illumina sequencing) in roots of trees while avoiding host amplification? I would greatly appreciate a suggestion of a suitable primer pair to identify endophytic fungal communities in tree roots using Illumina sequencing. Some sequencing facilities have the ITS1-1F-F / ITS1-1F-R available, while the ITS3mix / ITS4ngs is also suggested in the literature (Tedersoo et al 2015). Which is better? Is there any other option?
Any advice based on experience will be highly appreciated.