my team and I work with fungi at RBG Kew. Fungi can be incredibly different from each other: some are chunky mushrooms, some others look like leathery mats, others can come in tiny cup-like structures, stony-hard beads or could even have a powdery texture. We also culture many of the samples we receive in order to produce large quantities of mycelium, when possible (not all fungi can be cultured in the lab, though!). In addition, some fungi can produce chemical compounds that, if not eliminated, can inhibit downstream procedures, such as DNA extraction, PCR and sequencing. The preservation method is also crucial in ensuring the quality of the sample: fresh samples dipped in special preservative solutions are ideal for ensuring good DNA and good sequencing results. All these aspects represent a real challenge when trying to optimize a standard procedure in the lab, because it is really difficult to find a protocol that will work well for everything. And if we do not get good DNA, we will not get good sequencing results. To answer your question, we do encounter issues with the sequencing, and we generally tackle them by adjusting the lab protocols in order to extract good quality DNA, which is crucial for good quality sequencing. But do not get me wrong, fungal diversity is a treasure, not an issue: we just need to figure out the right protocol for the right group of fungi!