FESIN MEETING - July 26, 2009
Tom Bruns: Report on FESIN activities for 2008
In 2008, FESIN sponsored a pre-ESA workshop for approximately 90 people. The PRE-MSA workshop in 2009 Attracted a similar number of students from both MSA and BSA.
A white paper concerning the need for 3rd party annotation of sequence data in GenBank was written and published as a letter to Science. The paper suggested a mechanism for annotation and is on the FESIN web site for comments. A white paper was also written concerning standards for annotation of sequences. This is posted on the FESIn web site for comments.
A proposal has been submitted to NESCent (National Evolutionary Synthesis Center). The goal of this proposal is to assemble a small working group to develop protocols and approaches for an automated classification system of fungal environmental DNA sequences. A stand-alone annotated database of sequences will be required. The proposal will be posted on the FESIN website.
Comment from Meredith Blackwell: A mechanism is needed for an automatic update of classifier so as new data are added, they are quickly available.
David Hibbett: Report on AFToL2 and JGI sequencing
AFToL2 is an NSF-sponsored program to further explore fungal phylogenies using an expanded range of genes. There are 10 labs organized into 6 working groups: Blackwell-insect biotrophs; Hibbett/Aime-basidiomycota and bioinformatics; Lutzoni-Lichen-forming fungi and Wasabi; McLaughlin – non-molecular characters and ontogenies for non-molecular characters; Spatafora – non-lichenized ascomycetes and pipelines from genomes; Vilgalys and Berbee - basal lineages.
Joint Genomics Institute Fungal Genomics Program
Projects are tied into the JGI mission which includes biofuels and bioproducts. Currently, emerging genomes are weighted more towards ascomycetes. Ultimately, they JGI plans an in-house Fungal Genome Index Project (FunGI) of about 20 genomes/year. This includes re-sequencing of industrial strains, feedstock health-related fungi, and biomass degrading fungi. An additional focus is the fungal tree of life. First 5 genomes are largely basal fungi: Coemansia reversa, Rhopalomyces, Gonapodya, Wallemia and Orbilia auricolor using 454 sequencing.
Anne Pringle: Report on the Encyclopedia of Life Activities
The Encyclopedia of Life is an attempt to create a webpage for every species on earth. It is funded by the McArthur and Sloan foundations. Dr. Pringle reports that the EoL is a good research tool for scientists. An association with the Biodiversity Heritage Library is making old inaccessible literature available. Literature that is out of copyright is being scanned and indexed on EoL.
EoL has a significant focus on Education and has developed a mechanism to involve undergraduate students in developing species pages. Experience has shown that undergraduates get involved in the process and are excited to have their material on line. The university species pages initiative available from mushroomobserver.org allows student to work on draft projects. A switch from draft to final submission occurs when the professor approves the submission. After approval final pages are swept to EoL.
Individuals can assume responsibility for groups by becoming a curator. Annotation is possible and may be regulated by the curator..
Taxonomy = Catalog of Life from Dictionary of Fungi (Paul Kirk)
Connections to GBIF to provide a map but maps are dependent on incomplete data.. Mushroom Observer.com uses the amateur community to post and develop distribution maps; eventually these may be useful for EoL.
For groups known only from sequence data, the group can be given a mycobank number and pages for the “species” created in EoL. This would be a good way to record ecological data for species known only from sequence data and is obviously of interest to FESIN participants.
Life Desks are a way to manage your individual projects, for example, if you want to create multiple species pages for a particular genus.
Andrea Porras-Alfaro: Identification of environmental sequences using a Markov Bayesian Classifier
Power Point File
A large scale microbial metagenomics project is being conducted at the FACE (Free-air carbon dioxide enrichment) experimental sites. The analyses include extensive titanium 454 and Sanger sequencing of soil and litter samples for fungi, bacteria ,and archaea. In order to handle the data, a program is being developed for automated classification of ribosomal sequences (LSU and ITS). Project coordinator: Cheryl Kuske at LANL funded by DOE.
The Markov classifier uses LSU and ITS DNA sequences. The code was based on RDP classifier and was developed by Gary Xie et al. at LANL. Classifier is based on Bayesian probability. It uses an 8-mer word in a sliding window and calculates a probability based on training data set. A training dataset for fungal sequences is under development, the first analyses were conducted with a training dataset of 500 sequences and work is in progress. When trained, the classifier will classify unknown sequences into higher order taxonomic categories. Alignments are not needed. The classifier also provides a confidence limits for the classification. This classifier will be made available to the scientific community using the RDP (Ribosomal Database Project). Negociations are in progress.
In order for the classifier to be of value in fungal metagenomics and fungal taxonomy, help is needed to developing a curated training database and automated updating will be needed. Representatives of all fungal group with taxonomy are needed. A mechanism is needed to name environmental sequences for use with the classifier. If you want to participate on this effort to develop the training dataset o If you have sequences that will like to share to develop the dataset please contact Andrea Porras-Alfaro (firstname.lastname@example.org, A-Porrasemail@example.com, Phone: (309 298 1267)
FESIN MEETING PLANS FOR 2010 – Tom Bruns
Fesin was scheduled to meet with the ESA in 2010 and the topic area was to be genomics. However, the
ESA meeting is in direct conflict with the International Mycological Congress in Scotland. FESIN will need to either have a stand-alone meeting or a pre-IMC satellite meeting. If we elect to meet in Europe, it would have the advantage of being able to meet with UNITE, the European equivalent of FESIN. A second advantage is that FESIN travel awards could fund travel to IMC.
The majority of people present at the meeting agreed to meet in Scotland.
What should be covered? A metagenomics workshop meeting has been suggested by Joey Spatafora. Focus would be how to manage, organize and analyze the massive numbers of sequences generated by 454 environmental sequencing.
A group was selected to put together preliminary plans with a deadline of 1-2 months maximum.
Fesin 2010 Working Group
Rasmus Kjoller (or someone from Unite)
Also mentioned as possible:
Suggested approach: Two-three day workshop featuring a practical, hands on approach using a common data set for teaching with time available for individual data sets. The goals include understanding input and output formats and data types.
Special FESIN-sponsored sessions at MSA or ESA are possible. Let MSA organizers know immediately if a special session is planned for next year.