Dear MycoBlitz participants,
Hello from the 2019 Mycoblitz! I hope everyone is safe and well and enjoying the summer.
I know a lot of you are wondering what’s happened to the project during COVID-19—Purdue, like so many Universities, shut down in March and we were unable to return to the lab until mid-June. So now that we’re back, I thought this would be a good time to give you all an update on where we are with the project and when we hope to finish.
Thanks to all of you who participated, the forays were a success. We received more than 1250 specimens at Purdue that were selected for sequencing and accessioning. All of these were in various stages of processing at the time of the shut-down. Our processing steps include: Initial quality control of submissions and logging receipt; DNA extraction; DNA amplification of the fungal barcode (ITS) region; barcode sequencing; sequence editing and validation; tentative IDs based on sequence and specimen data; specimen accessioning and databasing into the Kriebel Herbarium (PUL); and final conservation, boxing, and storing of specimens in perpetuity. At each step along the way, we provide feedback in iNat on the observation page for each specimen as it passes through each step.
Our original funded timeline was to complete this work by the end of July 2020. And then COVID came. I just want you to know that during the shutdown we have been doing as much of this work as possible from home – this includes a lot of back-end stuff you wouldn’t normally see, things like conserving, boxing, and accessioning specimens, taking tissue samples for DNA extraction, and updating iNat. But the bench work (i.e., the actual DNA extractions and barcode sequencing) and work that requires specialized lab software (sequence editing and herbarium databasing) have not been possible as we have not been able to work in the lab.
The good news is that our lab was granted permission to begin restricted operations at the end of June, and, the herbaria were just granted permission. However, we still have limited access (for instance only two people can work at one time in the lab, and I have 15 other people with projects trying to work this summer!), and so progress is still likely to be slower than it would have been. Altogether we are now projecting a completion timeline of the end of November 2020.
What does this mean for you, if you submitted samples? Keep checking and tracking your sample information on iNat—this is the official repository for all MycoBlitz data and is constantly and conscientiously updated by our project manager, Sarah Verhaeghen and myself. Sequence data that have been pasted in iNat are verified to the best of our ability and free for you to use in any downstream applications that you wish. All we ask is, if you publish these in another data repository such as GenBank, that you drop us a note to that effect so that we don’t end out duplicating efforts when we make our final grant report. If you need additional information for deposition, such as who to credit for sequence generation, editing, identification or how to credit the funding source, just ask. I will do my best to respond within 24 hours. Otherwise I will upload all sequences to GenBank at the end of the project and note the accession numbers for you in iNAT.
At the end of the project we will also be uploading all of your PUL accession data into MycoPortal (https://mycoportal.org/portal/index.php).
For easy access, here’s the link to the MycoBlitz on iNat for tracking progress and data for your specimens. We are in the process of changing some of the observation fields for easier use, so be on the lookout to changes in the way your data are returned. And I am constantly updating IDs (under MycoBlitz ID) to the best of my ability as I examine sequences and specimens:
Several people have emailed me to ask if they can still send in specimens. The answer is yes! If you have specimens collected during the two one-week forays (August 12–19, 2019 and October 20–27, 2019) that you haven’t had time to submit yet, go ahead and send them to me at the address below, and shoot me an email when you’ve done so so I can keep a lookout for them (we still don’t have regular departmental mail service). This has been a very strange and hectic time in academia; I hope you and your families have all been doing well and still logging some time for fungi! And I hope you will continue to bear with us as we strive to get all the rest of your data back to you as quickly as possible. Finally, I would like to thank each and every one of you who participated, advertised, or promoted this project.
Stay well everyone and feel free to reach out to me if you have any questions.
Professor of Mycology
Director of the Arthur and Kriebel Herbaria
Purdue University Faculty Scholar
Department of Botany and Plant Pathology, Purdue University
915 W. State Street
West Lafayette, IN 47901 USA