DNA Sequencing

There are as many protocols as there are species of Mycena and it is not always easy to find the best and most efficient methods for mycological research. We are working to compile useful resources and guidance but one of the best resources we have are our committee members who have extensive experience with different aspects of the process from making and submitting collections through advanced sequencing technologies and phylogenetics. We have identified the following subjects where we can provide guidance.

Protocols and Standardization

One shouldn’t have to reinvent the thermocycler to do DNA sequencing. With so many methods available, getting started can feel overwhelming. Through the troubleshooting of countless mycologists, a few methods have gained the most traction and are widely used with great success. We present to you here protocols that we find are the most reliable. . Please don’t hesitate to reach out if you have any questions about the protocols.

Data Hygiene and Traceability

After you have gone through all the hard work of DNA sequencing, we want to make sure that these results are findable and reusable according to FAIR data-management principles, not to mention accurate. One of the worst things that can happen is that all of these interesting sequences end up lost on an external harddrive in a club closet somewhere where other researchers cannot find them. It is important to provide raw data whenever possible to establish reproducibility and increase scientific value. If you have sequences that have not been made available on a public database like Genbank, let us know and we can help with this process as well as make sure the raw data is stored and made available.

Data Interpretation

Sometimes generating a DNA sequence is only half the battle. Interpreting and understanding your results can be difficult and confusing even with an advanced degree and years of experience. Sometimes exploring phylogenetics might help clarify the situation, identifying reputable reference material may be the most helpful, or asking an expert on the group in question might be your best bet. Feel free to ask about data interpretation and we will do our best to help you.

Software and Hardware

Investing in programs and equipment to perform your own DNA sequencing does not have to be expensive but not all are made equal. While there are several free software choices for data analysis and interpretation, the cost in terms of time may make purchasing worthwhile in the long run. We will provide general guidance on options, highlight some of the existing resources, and are available to help troubleshoot.

Specimen Archiving

Sequence data is less valuable without a vouchered, preserved specimen available for future research. We would love to help you find the best solutions to storage and archival, whether personally or, better yet, in an established fungarium.