Tag Archives: biology

Attend Fungal Genetics 2009!

If you are interested in fungal genetics and genomics, comparative biology, and of course dancing with fungal geneticists, plan to attend the 25th Fungal Genetics Meeting held at the beautiful Asilomar Conference Grounds in Pacific Grove, California. Below is info sent out from the Policy Committee and registration opens in a little over a month.  Budding (and conidiating) artists can also submit a Logo design so we have cool T-shirts to wear.

25th Fungal Genetics Conference Registration and Program

The Fungal Genetics Policy Committee invites you to attend the 25th Fungal Genetics Conference, sponsored by the Genetics Society of America.   The meeting will be held March  17-22, 2009 at the Asilomar Conference Center, Pacific Grove, California (near Monterey, California).

The FGSC is pleased to announce that the scientific program and registration information are available online at the FGSC website

Registration for the meeting will take place online at the FGSC and GSA websites from October 27th-December 12th.

Financial aid applications are due November 14th.

Abstract submission deadlines are the same as the registration deadlines, from October 27th to December 12.

LOGOS – Please Submit your artwork

We are also pleased to invite the submission of logos for the meeting. Past logos are available for review

The winner will receive a complimentary t-shirt.

Please send logos to the FGSC by October 17, 2008.

Basidiomycete genomes galore


Just finished attending Genetics and Cell Biology of Basidiomycetes in Cape Girardeau, MO which was an intimate gathering of basidiomycetaphiles.  I learned about systems that are used for studying fruiting body development, genetic mapping, pheromone and mating genes, kinesin dynamics, meoitic gene regulation, and a host of topics.  I’m happy I got a chance to meet more folks in the community and learned about where informatics and computational approaches are really needed to push along some of the interpretation of the more than a dozen basidiomycete genomes.  In particular it sounds like the PleurotusSchizophyllum, Agaricus bisporus, and Serpula genomes are all marching along to completion with some already in 4X assembly or further.  

GCBBVI Group Picture

So we’ll further have more samples from of key model and some less-model species to assist researchers working on many different mushroom-forming fungi that range from brown and white-rotting saprophyte fungi to mycorrhizal fungi that associate with plants.    I’m excited about the work to make transformation and knockouts more readily in these systems too to push the genetics and cellular biology of these systems even further.  The genome sequences will be another tool in these endeavors.

The last day ended with a discussion about genome annotation and future support for curating gene models.  Basically everyone is unhappy with computational predictions and want to be able to go in and fix things. (I think people remember the ones that are gotten wrong more readily than the ones that were right, but computational prediction definitely performs poorly in some situations).   In this Web 2.0-land we live in, this is still not something easily done with any of the freely available genome browsing tools. The JGI’s browser was lauded for its ability to handle these kinds of requests, but how do we proceed when genomes are not sequenced by that center or when (not too distant future) communities are able to sequence a genome themselves using 454/Illumina-Solexa/Helicos/Pacific Biosystems approaches in their own lab?  There is still a huge lag in what kinds of tools researchers can use to annotate genomes to fix gene models and add functions.  Hopefully projects like GMOD will continue to develop useful tools for solving these needs, but there is certainly a need for better support of distributed community annotation of genomes where this little direct money for supporting curators from a single place.

Podospora genome published

P.anserinaThe genome of Podospora anserina S mat+ strain was sequenced by Genoscope and CNRS and published recently in Genome Biology. The genome sequence data has been available for several years, but it is great to see a publication describing the findings.  The 10X genome assembly with ~10,000 genes provides an important dataset for comparisons among filamentous Sordariomycete fungi. The authors primarily focused on comparative genomics of Podospora to Neurospora crassa, the next closest model filamentous species.  Within the Sordariomycetes there are now a very interesting collection of closely related species which can be useful for applying synteny and phylogenomics approaches.

The analyses in the manuscript focused on these differences between Neurospora and Podospora identifying some key differences in carbon utilization contrasting the coprophillic (Podospora) and plant saprophyte (Neurospora).  There are several observations of gene family expansions in the Podospora genome which could be interpreted as additional enzyme capacity to break down carbon sources that are present in dung.

The genome of Neurospora has be shaped by the action of the genome defense mechanisms like RIP that has been on interpretation of the reduced number of large gene families and paucity of transposons. The authors report a surprising finding that in their analysis that despite sharing orthologs of genes that are involved in several genome defense, they in fact find fewer repetitive sequences in Podospora while it still fails to have good evidence of RIP.

Overall, these data suggest that P. anserina has experienced a fairly complex history of transposition and duplications, although it has not accumulated as many repeats as N. crassaP. anserina possesses all the orthologues of N. crassa factors necessary for gene silencing, including RIP, meiotic MSUD and also vegetative quelling, a post transcriptional gene silencing mechanism akin to RNA interference

I think this data and observations interleaves nicely with the work our group is exploring on evolution of genome of several Neurospora species which have different mating systems. The fact that the gene components that play a role in MSUD and a RIP are found in Podpospora but yet the degree of RIP and the lack of any observed meiotic silencing suggests some interesting occurrences on the Neurospora branch to be explored.  The potentially different degrees of RIP efficiency and types of mating systems (heterothallic and pseudohomothallic) among the Neurospora spp may also provide a link to understanding how RIP evolved and its role on N. crassa evolution.

Senescence in Podospora

Another aspect of Podopsora biology that isn’t touched on, is the use of the fungus as a model for senescence.  The fungus exhibits maternal senescence which involves targeted changes in the mitochondria that leads to cell death.  The evolutionary and molecular basis for this process has been of interest to many research groups and the genome sequence can provide an additional toolkit for identifying the factors involved in the apoptosis process in this filamentous fungi. Whether it will help find a real link for aging research in other eukaryotes remains to be seen, but it is a good model system for some aspects of how aging and damage to mtDNA are linked.

Espagne, E., Lespinet, O., Malagnac, F., Da Silva, C., Jaillon, O., Porcel, B.M., Couloux, A., Aury, J., et al (2008). The genome sequence of the model ascomycete fungus Podospora anserina. Genome Biology, 9(5), R77. DOI: 10.1186/gb-2008-9-5-r77

Summer 2008, Mycological Meetings

A few of the summer meetings that relate to fungal biology and evolution. 

Hope to see you at some of these.

More RIP without sex?

In followup to the Aspergillus RIP paper discussion, Jo Anne posted in the comments that her paper published in FGB about RIP in another asexual species of fungi also found that evidence for the meiosis-specific process of Repeat Induced Point-mutations (RIP).

Continue reading More RIP without sex?

Neurospora speciation through experimental evolution

ResearchBlogging.orgDettman, Anderson, and Kohn recently published a paper in BMC Evolutionary Biology on reproductive experimental evolution in two Neurospora crassa populations evolved under different selective conditions. This is a great study that complements work published last year in Nature on experimental evolution in Saccharomyces cerevisiae populations. Neurospora populations were evolved under high salt and low temperature and were started from either high diversity (interspecific crosses, N. crassa vs N. intermedia) or low diversity (intraspecific cross, two N. crassa isolates D143 (Louisiana, USA)and D69 (Ivory Coast)) as described in Figure 1. The experimentally evolved populations were then tested for asexual and sexual fitness (they were taken through complete meiotic cycle throughout the experiment to avoid insure there was selection on the sexual reproduction pathway.

Continue reading Neurospora speciation through experimental evolution

Fungal Genetics 2007 details

I’m including a recapping as many of the talks as I remember. There were 6 concurrent sessions each afternoon so you have to miss a lot of talks. The conference was bursting at the seams as it was- at least 140 people had to be turned away beyond the 750 who attended.

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.

Continue reading Fungal Genetics 2007 details

Wikis for genome (re)annotation

Steven Salzberg (who is nominated for the Franklin award at bioinformatics.org) has an opinion piece in Genome Biology proposing wiki technology to help solve the problem of genome annotations getting out of date.
Continue reading Wikis for genome (re)annotation