Fungal diversity characterization using ITS

As Rachel has mentioned, there are some issues with using ITS primers for fungal characterization. One is that the ITS region does not provide phylogenetic information. As a result analyses need to use other approaches. Another problem is that the PCR products for different taxa differ dramatically in size and will not be sequenced uniformly. Does anyone have any thoughts about this?

From the little data I've seen recently on the size variation in ITS, I can't see how it can work to provide any information about relative abundance if using Illumina sequencing. Those taxa with small ITS regions will take over the entire flowcell and you'll never even see the taxa with large ITS regions. This should be fairly easy to confirm however, by size selecting pools of different ITS sizes (on say a Pippin) and then confirming the existence of taxa that don't appear in a pooled run.

Maybe other people aren't finding the same size variation in ITS amplicons?