UCSC Fungal Herbarium Sequencing Project (by Henry Young)
"To expand through education, the understanding and appreciation of mycology and to assist the general public, related institutions or societies to further this goal as stated articles of incorporation."
2013 FFSC voted to allocate $15,000 to fund this project for DNA sequencing. And with the help of other contributors have reduced the FFSC amount. All FFSC funds and others for this project have been paid directly to the analytic lab that did the sequencing.
DNA sequencing is becoming the norm for species ID, the purpose of the sequencing project is to select ~500 species from the Santa Cruz area (with some outliers from other areas for comparison). These sequences will enable us to determine if we have “properly named” species or if ours are distinct. This has already happened with Entoloma medianox (formerly E. bloxami) and other names.
As of June, 2016, all 500 specimens have been processed, sent and sequenced. However, not all them were successful for a variety of issues completely normal to the process, but we had >90% success rate. The sequences are “raw” and need to be cleaned up, then compared with existing records in a public database to verify ID, or propose that the species is new to the database. We are using GenBank http://www.ncbi.nlm.nih.gov/ which is the recognized repository for DNA sequencing in the US. It can be cumbersome to use and time consuming to input data.
The results are also being entered into the UCSC Fungal Herbarium database, which is integrated with the rest of the specimens at the UCSC Herbarium (including all specimens, not just those that were sequenced). Then there is MycoPortal (http://mycoportal.org/portal/collections/list.php?usecookies=false&db[]=37&type=1&reset=1&taxa=) which is a repository that tracks fungal herbariums collections in North America. We are uploading and maintaining the UCSC Herbarium data there, including georeferencing. The herbarium work alone takes a ton of time.
Our UCSC student interns, Kristina Dinh, Mimi Fuchs, and Ali Coblentz made significant inroads on this task this winter and spring. Thanks to them! You can read more about them on our contributors page:
http://scmycoflora.org/contributors.php
Some people have access to the initial raw data, and we are happy to share the data with those who directly request it, but prefer to have all the data in good shape before we broadcast it. It is not fully public yet because we are still in an active period of working on it. Errors can be propagated if we don't take the time to release it only after a thorough check.
In the meantime, you can see the sequences as they are added to iNaturalist - http://www.inaturalist.org/projects/uc-santa-cruz-fungal-herbarium-sequencing-project
The SC Mycoflora website is getting a new projects page (http://scmycoflora.org/sequencing/sequencing.php) to present these specimens and associated data. This takes time to build as well. We are dealing with 500 entries that need pictures, locations, data, summaries, etc. added, and then presented in an 'easy to use' manner.
We are in phase I of a massive project. Everything is a work in progress - this is slow work. This is subtle work. The work is done by a few dedicated volunteers working on it in order to get this information out into the world.
We have done something excellent with this club - please take a moment to look through our results and enjoy the fact that as a club, we've achieved something unprecedented.