Sample Submission Protocol

Collect the Tissue

Please review the protocols and videos on the best way to collect tissue.

Prepare Samples for Shipment

Ensure all of your tubes are properly sealed and secure the lid of your tube box in place for shipment with tape. Ensure your specimens are organized with the correct herbarium labels. 

Email your Specimen Spreadsheet

Download the specimen spreadsheet from your observational portal. Ensure it is properly filled out. Email it to submit@mycoflora.org.

Mail Packages & Await your Results

Mail your specimens to your project fungarium and mail your tissue samples to your project lab. DNA results will be emailed to you in 1-2 months from the time tissue samples are received.

Sample Submission Video Protocol

Please watch the video to the left to learn how to prepare your package for submission to the sequencing facility. 

Specimen Requirements

In order to get specimens sequenced as a part of this project, you must be a mushroom club or individual affiliated with the North American Mycoflora Project. All individual specimens must follow the NAMP protocol in terms of documentation, metadata, and sample preparation. Minimum metadata requirements for a collection include a proposed species (or genus) name, collection date, collection location, and images of the specimen in a fresh condition. All specimens must be appropriately dried and individually packaged with herbarium labels. A spreadsheet containing the metadata of all included specimens needs to be sent to the sequencing facility you have selected.

Cost

as low as $12 per specimen w/o tissue extracted*

as low as $10 per specimen with tissue extracted

          $8 for each additional locus (optional)

          *There will be an additional $10 charge per shipment if whole specimens are sent need to be forwarded onto a herbarium after tissue extraction.

Included Services

  1. DNA extraction (Specimen-dependent protocols)
  2. DNA amplification (PCR, with one additional repeat attempt)
  3. DNA sequencing (two reads - forward and reverse)
  4. Sequence editing
  5. GenBank submission

Timeframes

Expect sequences from specimens back in 1-2 months from the date they are received by the facility.

Grant Recipients

If you have applied for and received a grant from the North American Mycoflora project, simply follow the instructions outlined herein to prepare your specimens. When preparing your spreadsheet, mention in the email that the specimens being submitted are to be paid for with funds from your grant.

Tissue collection tubes will be made available at no cost for grant recipients. 

Final Shipment to Fungarium, and Sequencing

Create your Shipment

Be sure to include the following with the shipped package:

  1. The physical specimen with all of the labels with each specimen. Each specimen needs to be labeled with the reference number, location, collection date, and species name.
  2. A packing slip printed from your spreadsheet.

Email your fungarium about your upcoming shipment, along with the Symbiota spreadsheet of your collections. CC the Mycoflora Committee at submit@mycoflora.org.

Sequencing Facility Options

The North American Mycoflora Project will begin with two facilities as the primary locations for sequencing. You will be assigned a location to send your specimens once you complete your order. The locations include:

Osmundson Lab

℅ Todd Osmundson - Mycoflora Submission
University of Wisconsin Lacrosse
1725 State Street
3034 Cowley Hall
La Crosse, WI 54601  

Vilgalys Lab

℅ Alejandro Rojas - Mycoflora Submission
Duke University West Campus
130 Science Dr.
Rm 345, Biological Sciences Building
Durham, NC 27708-0338

What to Expect Back

You will get two ABI sequence (raw data) files back per submitted specimen. One file will be for a forward read and one for the reverse read. Secondarily, you will also receive the edited sequence files. This comes in the form of FASTA files (special format that can be opened with a text editor) containing the final edited sequences that has been formed from the two reads. This is known as a “contig.” A download link for a zipped folder of these individual files will be provided.

Finally, you will receive a link to a project that contains the metadata of all of your specimens, as well as BLAST results of your specimens. Here you will be able to review the names that have been applied to the collections and can view the metadata that is associated with the specimen. This metadata will be used to upload your specimens to GenBank (a public DNA sequence repository).


By participating in this sequencing service, you agree to allow the mycoflora project to make your DNA sequences public after one year. You also agree to release the metadata of your sequences to other project members immediately. The sequences will be placed in our local BLAST search. Other users will have access to the observational records that appear in the BLAST results, but not the actual sequences.

Potential Risks

While genetically sequencing mushrooms is a process that is usually successful, not every specimen will be able to be successfully sequenced. There are a number of reasons this process can be unsuccessful. Following the mycoflora project protocols for collection and drying your specimens will give you the best chance for success. Potential risks at the sequencing facility include:


Unsuccessful PCR

DNA amplification may be inhibited by proteins, sugars, or other types of molecules that mushrooms contain. Two attempts will be made to successfully amplify a given sample. If not successful after two attempts, no further attempts will be made, and you will be given a 50% credit on future sequencing.


Low Quality Sequence

Occasionally, DNA extraction and amplification appear to be successful, but the sequence comes out muddled. This can be due to low quality DNA (old or poorly dried specimens), contaminants, or a number of other factors. If this occurs, these are sunk costs, and due to the low costs of this service, we cannot offer a refund or another sequencing attempt without additional cost.

We generally have success with than 80% of all samples submitted.

For best results, please only send specimens that were collected in the last 5 years. Older specimens can still be submitted after consultation with the project staff. Additional costs may apply.

Check our FAQ page for additional questions.
Email any questions you have to info@mycoflora.org.

About North American Mycoflora Project

We are working towards a single goal - the development of the first comprehensive mycoflora of North America. This project is a consortium of citizen scientists and professional mycologists performing a biological survey of all the macrofungi that occur in North America.

Latest News

22 February 2018
16 October 2017
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