Submit your samples

Paid & grant orders

What to expect

Submit your samples

Export your observations

Once you are ready to generate a shipment, export a spreadsheet of your observations.

From iNaturalist

• From your Project > Observations tab (on a desktop computer), click the “Export Observations” box (right side, midway down).
• On the Export screen, select these fields to export:
• Under 1. Create a Query, you can limit your export if desired.
• Under 3. Choose Columns:
  • Basic click None to clear, then one at a time select:
    • id, observed_on, user_login, description*
  • Geo click None, then select:
    • place_guess, latitude, longitude, place_county_name, place_state_name, place_country_name
  • Taxon click None, then select:
    • scientific name
  • Taxon Extras, click None, then select:
    • taxon_phylum_name, taxon_class_name, taxon_order_name, taxon_family_name taxon_genus_name, taxon_species_name
      • Bold requires these data!
  • Observation Fields, click None, then select if you have data:
    • field:collector's name
• Click 4. Create Export
  • The export will process; when it's finished click the “Download” link.
• Open the .zip file to access your .csv (comma separated values) spreadsheet. In the spreadsheet:
• You may change the name in the user_login field to your real name, e.g. john_doe to John Doe, or to a pseudonym e.g., mycofan212 to Jane Doe.
• WARNING: The ‘Description’ field cannot contain more than 800 characters including spaces in the Bold submission sheet. If you took extensive notes (a good thing!) you might want to edit it.
• Save this spreadsheet for uploading when you are ready to submit your samples through the Shop at Sequencing Submission - All Projects.

From Mushroom Observer

• From the Species List you created for this submission, click the “Download” option above your observations.
• On the new page, choose FunDiS format (formerly Mycoflora format) and UTF-8. Click the “Download” button. Save this spreadsheet.
• Manually add columns for each of these, replacing the Scientific Name column and fill in the data as far as you can:  phylum,   class,    order,    family,    genus,   species.   The higher lever taxa can be found by clicking the name of your observation (page top) and reading the Classification section in the middle of the  species page.
•  For more on MO Lists, see Post on Mushroom Observer.

Requirements for both iNaturalist and Mushroom Observer

Resubmitting a new sample from an observation

Prepare samples for shipment

Ensure all of your tubes are correctly labeled, in ascending order, and tightly sealed (see Collect Tissue for Sequencing).

• 30 or more tubes: secure the lid of your tube divider box for shipment with tape or a rubber band before placing in a mailing box.
• Under 30 tubes: place labeled tubes in a padded mailer. 
• Include a hardcopy of your CSV in your package

Fill Out the Sequencing Submission Form

• Go to the FunDiS Shop: Sequencing Submission - All Projects.
• Upload the CSV file you downloaded above, and fill in other information.
• NOTE: The filetype must be CSV and the title must be only letters or numbers with no punctuation, spaces or special characters.

Mail your package

Apply postage and mail to:

Allie Ludden

FunDiS Sequencing Coordinator 

1292 High St #323

Eugene, Oregon 97401

Review the Sequencing Submission Checklist

Paid & grant orders

Included services

• DNA extraction 
• DNA amplification (PCRl)
• DNA sequencing (two reads, forward and reverse)
• Sequence editing
• Updates communicated by our Sequence Coordinator.

Paid orders

• Cost: See Paid Sequencing Service in our Online Shop to order sequencing service. You can also order tubes and field data slips. All FunDiS projects include a 15% amount to cover overhead.

Grant orders

• Grant awardees receive free tubes and field data slips. See Apply for Sequencing Grant for details. 

Timeframe

• We aim to get sequences back within 2 months from the date they are received by the FunDiS Sequencing Coordinator.

What to expect from BOLD sequencing

The FunDiS Sequencing Coordinator will send project leaders an email informing them that their sequences are completed, what their processing numbers are, and a distance tree of the sequences within a 95-sample submission batch. The distance tree is helpful in spotting contaminated samples. 

• Project Leaders, depending on their comfort level, can request read-only access to the BOLD data files that contain theirs and other sequences produced from the same 96-well plate. 
• To request access, Project Leaders will need to create a profile in BOLD and inform the FunDis sequencing coordinator of their username.
• This pathway will give Project Leaders direct access to the ITS Barcode sequences, downloadable trace (chromatogram) files for the forward and reverse reads plus the computer generated stats and evaluation of each sequence. It also gives access to an identity search in the BOLD database, which often is not as complete as a BLAST search in GenBank or UNITE. 
• Links to iNaturalist or Mushroom Observer records are included for easy reference. 

If the Project Leader is not comfortable working directly in the BOLD database, they can request from the FunDis Sequencing Coordinator a file containing the consensus sequences for their samples and whether both the forward and reverse reads were successful. 

• Changes to the identification of the collection or edits to the ITS sequence will be made by the FunDis Sequencing coordinator at the request of the FunDis Project Leaders.
• Changes to IDs in MO, iNat or MycoPortal need to be made by the Project Leader or Collector. 

Success rates 

While genetically sequencing mushrooms is a process that is usually successful, not every specimen will be able to be successfully sequenced.

• Follow protocols for collection and drying your specimens to have the best chance for success. 

• Potential risks in DNA sequencing facility include:

• Unsuccessful PCR:  DNA amplification may be inhibited by proteins, sugars, or other types of molecules that mushrooms contain. 
• 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 either of these occur, due to the low cost of this service, we cannot offer a refund or another sequencing attempt without additional cost.
• We are not currently sequencing Chanterelles (Cantharellus & Craterellus);  Hard Ascomycetes (“carbonaceous”, e.g., Hypoxylon and Dead Man’s Fingers); Lichens; or slime molds. 
• For best results, please only send specimens that were collected in the last 5 years. 

Email FunDiS Sequencing Coordinator coordinator@fundis.org