fbpx

Tissue 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. 

Notify us of the Shipment

Fill out a sequencing submission form to get the address of the facility that will be sequencing your specimens. Include your MO/iNat spreadsheet in this submission.

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.

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.

Paid Orders

 

See costs in Shop under
Paid Sequencing Service

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

Timeframes

We aim to get sequences back within 2 months from the date they are received by the facility. Sometimes difficult specimens need to be redone and can take longer.

Grant Orders

Grant Recipients

If you have applied for and received a grant from the North American Mycoflora project, please follow all protocols described on this website. When submitting your tissue samples to the sequencing lab, mention in the email that the specimens being submitted are to be paid for with funds from your grant.

Tissue collection tubes can be ordered here at no cost to grant recipients.

Sequencing Facility

The North American Mycoflora Project is using several sequencing labs. You will be assigned a location to send your specimens once you complete your order.

If specimens are being sent for sequencing, fill out the sequencing submission form to get the address of the facility that will be sequencing your specimens. Include your MO/iNat spreadsheet in this submission.

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.

Success Rates

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 more than 80% of gilled mushroom samples submitted.  Some groups like polypores are more difficult to sequence.

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 questions to info@mycoflora.org.

About North American Mycoflora Project

NAMP is a 501(c)(3) non-profit organization working to create a continent-wide community of volunteer citizen scientists and professional mycologists to document the biodiversity of North American fungi.

©2017-2019 North American Mycoflora Project. All Rights Reserved.

Search