If there was any theme in the conference it was “Hey we are all using these genome sequences we’ve been talking about getting”. I only found the overview talks that solely describe the genome solely a little dry as compared to those more focused on particular questions. I guess my genome palate is becoming refined.

At some point my ability to take notes degraded so I may not have as detailed descriptions as others – I may have also totally mis-interpreted what the presenters were really saying… The conference proceedings are also made available on the FGSC page.

Tuesday

We arrived in the afternoon in time for a memorial service held for David & Dot Perkins and David Stadler who passed away in January and February. The service was a chance for some of us young scientists to appreciate the legacy and impact that these senior scientists have left for us.

The rest of the night was spent catching up with friends and trying to get enough sleep to make it through the rest of week.

Wednesday

The morning started with a presentation by Ken Wolfe who talked about the evolution of genomes after a whole genome duplication using the Kluyveromyces polysporus genome.

Bettina Tudzynski talked about gene clusters in Botrytis.

Michael Freitag spoke about their work on genome defense and RIP in Neurospora. They used some cool bioinformatics to screen for signals that relate to expectation of the mutational directional. A better explanation is definitely warranted here so I’ll have to read up a bit more on the Freitag and Selker work.

Laura Rusche now at my alma mater talked about chromatin silencing in Saccharomyces and Kluyveromyces. The work is looking at duplicated Sir genes involved in silencing in Saccharomyces and the role of the single copy ortholog in Kluyveromyces. I was really struck by the fact that the mechanism and molecular components of silencing in these hemiascomycete yeasts is very different from S. pombe and in the rest of eukaryotes.

I spent the afternoon after lunch at the Phycomyces genome project meeting. I am not necessarily directly involved with this project but was very interested to see how progress was being made. There were some clear reminders that we need to work hard to get a well annotated genome. The most surprising thing is the incredible duplication of several signaling pathways that also seems to be the case in the other zygomycete, Rhizopus oryzae.

The afternoon population genetics session was a nice series of population biology studies (some less population-y but oh well) in fungi.

• Ana Litvintseva from Duke talked about their work on C. neoformans serotype A and D population structure. Her MLST data is now up on the MLST.net site.
• Tatiana Giraud spoke about the structure of the anther smut Microbotryum populations.
• Patrick Brenner described two study systems including Mycosphaerella graminicola (wheat specific) and Rhynchosporium sealis (globally distributed) to contrast population structure of specialist and generalist plant pathogens. Because the fertile crescent is the origin of wheat, they could show migration of the pathogen alleles for the wheat specializier, but the other generalist pathogen was actually seen having migration out of Norway.  My unasked question was whether or not the Vikings are to blame…
• Rolf Hoekstra spoke about the facinating [HET-s] prion in Podospora anserina. This is the only other well studied prion system in fungi, [PSI+] being the other on that is found in yeast.
• Linda Kohn presented some of the work that Jeremy Dettman has been doing in collaboration with her lab and Jim Anderson’s group. Linda talked about four sets of independantly evolved experimental populations, the progeny of a high diversity interspecific cross (N. intermedia X N. crassa) and one low diversity cross (N. crassa X N. crassa) – these progeny were evolved in either high salt, or in cold temperature. They were able to show evidence for antagonistic eptistatis as a result of these divergent selection regime as predicted by ecological speciation theory.
• Hannah Johannesson talked about MAT gene evolution in Neurospora and some cool followup studies they are doing.
• Kathryn Bushley from Cornell presented some detailed analyses of NRPS genes in Cochliobolus and other fungi.
• Henk den Bakker from Cornell and Teresa Pawlowska’s lab present work on the basically clonal distribution of Glomus etunicatum, although the evidence was not totally convincing as Henk was happy to point out. There has been major difficulty in sequencing the Glomus genome because of the repeat structure.

Thursday

This was an exhausting day. The morning sessions flew by for me. There were several interesting talks. I found Joyce Longcore’s talk on Batrachochytrium dendrobatidis biology and pathogenesis very helpful. She made a point to explain the proper pronunciation of the species name as well since many people had been stumbling over it.

Barry Scott also talked about fungal endophytes in grasses. The part that stuck out the most in my mind was his description of ROS signaling in the fungus as a necessary part of multicellularity. He said there was a review paper submitted so I think this will be an interesting read.

We had a long meeting about Coprinus genome project to talk about what else we need to do to finish the so-called master paper on the sequence and comparisons.

Immediately afterwards I had the Zygomycete and Chytrid session where Erica was presenting our work in Batrachochytrium dendrobatidis.  Tim James and Scott Baker chaired the session which was apparently the first Chytrid/Zygomycete session ever.  The whole session was quite interesting as we had several good phylogenetics talks as well as genetics in these  systems.

• Erica was presenting our work in Batrachochytrium dendrobatidis strain JAM81 and her initial transcriptional array results in both frogs and fungi.
• Mary Berbee- focusing on cell wall evolution in chytrids and all fungi using phylogenetic methods and EST and genomic data.
• Franz Lang- focusing on placement of the most basal lineages in the fungal kingdo using mitochondrial and EST data.
• Christina Cuomo at the Broad Institute spoke about genome analyses on B. dendrobatidis for the JEL423 strain and gene family comparisons.
• Lena Lange (who is a 6th generation mycologist!) talked about a cool experimental project based on work she was doing at Novozymes (she is now professor at Univ Denmark I believe) to discover new enzymes. They have this clever screen for secreted proteins by inserting a marker into cDNA libraries and selecting for secretion of the marker.
• Catalina Sanz spoke about their work to clone white-collar genes involved in light response in Phycomyces.
• Russell Poulter described work to find intenins in the B. dendrobatidis genome as well as discovery of feasible markers for MLST studies and some preliminary work to actually cure frogs of this fungal infection.

Friday

I missed some of the morning talks as we had an impromptu meeting about the Neurospora tetrasperma and Neurospora discrete genome projects that our lab is working on through the JGI community sequencing project.

I did make it back for Luis Corrochano’s talk on Phycomyces. We’ve posted about the genome project before. This was a great talk in terms of presentation: he had everyone laughing and interested in this incredible fungus. He also deftly laid out some of the big questions in the field (object avoidance, gravitropism, phototropism) and how he and others are addressing them using genomic and other techniques. One problem is the inability to transform the fungus. But as Alex Idnurum and Joe Heitman among others are thinking about how to make these techniques work, it seems hopeful as more people may return to work on this fungus that was championed earlier last century by Max Delbruck.

I attended the afternoon session on whole genome comparative analyses. Here are some highlights, leaving off some of the talks for brevity, I think the abstracts are mostly in the proceedings.

• Bill Nierman from TIGR talked about comparative analyses of Aspergillus fumigatus, Neosatria fisheri, and other Aspergillus species.
• Antonis Rokas gave an overview of processes like gene gain and loss among the large collection of Aspergillus genomes. He also introduced the new resources for comparative analyses of clusters of closely related genomes at the Broad Institute.
• Geraldine Butler described her lab’s work on MAT locus and mating evolution among the Candida species.
• Meeting organizer Barbara Howlett talked about her lab’s work on evolution of clusters of genes producting ETP (like gliotoxin).
• Igor Grigoriev from the JGI about tools and resources for fungal genomics. Igor pointed out there are more than 150 genomes sequenced or inprogress.

Saturday

The morning plenary sessions were a greatest hits of mostly medically relevant fungi. Leah Cowen talked about her work looking at how HSP90 buffers evolutionary through a series of experiments exploring evolution of drug resistance (Science 2005).

John Taylor talked about Coccidoidies and mine and Tom’s work on comparing the genomes. He made an interesting point with a graph relaying the inverse relationship between strength of hypothesis and the number of them – with genomics being the situation of many hypotheses of little strength. John argued that evolutionary biology can help us choose stronger hypotheses.

Deb Bell-Pedersen talked about the Neurospora circadian clock. I thought I was ready to understand more of this since she had come to Berkeley recently and given a presentation on similar material, but I still found myself lost in the multitude of ossilators that must exist some of which have unknown molecular elements.

Christina Hull talked about Cryptococcus neoformans sexual development. Her talk was started off with a bang as she showed a clip from House where they are investigating an infection of the fungus that lives in pigeon guano.

Arturo Casadevall gave a very provacative talk about his philosophy of pathogenic fungi – this had the punchline that there are not classes of opportunistic and primary pathogens, just microbes and hosts. Everyone else struggled to not make this distinction in the later talks. We were lucky enough here at Berkeley to have Arturo come and give a seminar and lunch meeting with some of the students so I was able to have a second chance to really absorb the work.

• Jeff Townsend talked about fungal microarrays and reviewed some of his published work on Saccharomyces expression differences in wild strains. He also emphasized design principles in array experiments to insure adequete power to detect patterns.
• Nora Khaldi spoke about her findings of horizontal gene transfer in Aspergillus oryzae. If there was a theme to the meeting in some of the genome analyses, it was that horizontal transfer is being described in a lot of taxa. Whether or not it is all real, still needs to be investigated, but Nora provided a pretty solid analysis and argument that it explains some of the differences in genome size between A. oryzae and its closest compared species. Not everyone has bought the argument so I suspect there will be considerable debate without some more analyses brought to bear.
• I talked about gene family expansions and contractions in Cocccidioides, the basidiomycetes C. cinereus and P. chyrsosporium, and very preliminary numbers in the Chytrid genome B. dendrobatidis.
• Dawn Thompson of Aviv Regev’s group at the Broad Institute described their work on the evolution of molecular networks in hemiascomycetes. They are gearing up to do some large scale phenotypic data, joined with comparative, and expression data to try and put together a nice story of how genes are connected and binding sites evolving.
• (At this point fatigue settled in, so I didn’t take notes, so from memory) JP Xu talked about mitochondrial and evolutionary genetics in Cryptococcus.
• Liz Turner from our lab spoke about her thesis project mapping reproductive isolation in Neurospora.
• Richard Oliver showed evidence for horizontal gene transfer among plant pathogens.
• Jeremy Dettman spoke about his other experimental evolution postdoc project by evolving yeast populations under different conditions.

Poor Jeremy had to be last so it was sort of inevitable that the dinner bell would ring during the talk, but someone had to be last and he handled it well.  The day ended with a banquet and the keynote speaker, June Kwon-Chung, one of the real founders of modern medical mycology who throughout her career championed studies in Aspergillus fumigatus, Histoplasma, Cryptococcus, and other medically relavant fungi. The talk was a bit too long for the audience as the restlessness started close to 9PM as everyone was ready to start dancing.

If you read all the way to bottom, well, wow!  I hope it was worth transcribing my notes so I’ll be able to remember all the interesting science I saw at the meeting.  Perhaps I’ll have to try harder to blog-as-I-go in the future to make this all in smaller bites.

A paper in PLOS ONE describes the Genesis of Fungal Non-Self Repertoire. This kind of work goes on down the hall from us as well in the Glass lab among others. This recent paper describes het genes, which contain WD40 repeats and different combinations of these help control specificity. There is of course a diverse literature on this subject especially in Neurospora, and I’m not reviewing it here, but it is an imporant process in understanding how fungi interact with their environment.