The Tremella mesenterica genome portal is now live at the JGI. The genome is ~28Mb and the JGI annotation group predicted 8,313 genes, a significantly larger number of peptides predicted for C. neoformans (~7000; 18Mb genome) which may represent new and interesting genes or aspects of gene loss in the Cryptococcus yeast lineage.
Tremella is a Basidiomycete jelly fungus and an interesting study system from the perspective of discovery of novel lignin degrading enzymes. It also occupies an interesting phylogenetic position being an outgroup to the human pathogenic yeast Cryptococcus neoformans and C. gattii. Comparative genomics on this system may also provide insight into the interesting evolution of the large mating-type locus that was formed through various rearrangements resulting in conversion from a tetrapolar to biopolar mating system.
Tremella may also be an important source of understanding wood degradation and how it differs in jelly fungi from the more distantly related Agaricomycotina (mushroom forming). The fungus is reasonably easy to grow in the laboratory and also to collect from nature. It can handle some desiccation to survive during a dry period only to swell up after moisture is available. It is also called Witch’s butter and Tom Volk has a summary of its features on his FOTM page. It can often be confused with a phylogenetically distinct jelly fungus named Dacyromyces, usually the differences can be best be determined microscopically. See what kinds of Tremella people have been finding at the Mushroom Observer.
An avid reader pointed out that I was not entirely thorough in describing that we don’t enough about the V8 agar media that is used to induce mating in Cryptococcus. In fact a great deal of work on mating in this fungus had focused on identifying what pathways are induced by V8 agar that induce mating. It was shown that inositol stimulates mating through use of defined media containing inositol (Xue et al, 2007). This paper interestingly explores plant-fungal interactions and Cryptococcus suggesting that mating may occur preferentially on plants in cases where inositol is abundant.
It is also worth noting that V8 media contains a high level of copper ions and it was also pointed out to me that Jef Edman’s lab showed that melanin mutants have mating defects, and both phenotypes are suppressed by copper. And more recently (Lin et al, PLOS Genetics 2006) found that alleles of the Mac1 copper regulated transcription factor are a QTL influencing hyphal growth and melanin production, and showed that copper can enhance hyphal growth.
So the role of copper and interplay with V8 agar media and how this induces mating is actually quite known.
C XUE, Y TADA, X DONG, J HEITMAN (2007). The Human Fungal Pathogen Cryptococcus Can Complete Its Sexual Cycle during a Pathogenic Association with Plants Cell Host & Microbe, 1 (4), 263-273 DOI: 10.1016/j.chom.2007.05.005
A paper in IJSEM describes a new species in the Cryptococcus basidiomycete yeast lineage. The name is proposed as Cryptococcus keelungensis sp. nov. for a strain isolated from the sea surface microlayer. Its identity as a Cryptococcus sp was determined by sequencing of 26S rDNA D1/D2 and ITS loci and molecular phylogenetics. This is quite diverged from the human pathogen Cryptococcus neoformans and C. gattii as the new species falls in the order Filobasidiales while C. neoformans is classified in the order Tremellales. Interestingly, based on the phylogeny in the paper it seems to be relatively close to newly discovered Cryptococcus himalayensis.
C.-F. Chang, C.-F. Lee, S.-M. Liu (2008). Cryptococcus keelungensis sp. nov., an anamorphic basidiomycetous yeast isolated from the sea-surface microlayer of the north-east coast of Taiwan INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 58 (12), 2973-2976 DOI: 10.1099/ijs.0.65773-0
A new and improved annotation of Cryptococcus neoformans var grubii strain H99 (serotype A) has been made available in GenBank and the Broad Institute website. This update is collaboration between several groups providing data and analyses and the genome annotation team at the Broad Institute.
Some changes noted by the Broad Institute include:
“This release of gene predictions for the serotype A isolate Cryptococcus neoformans var. grubii H99 is based on a new genomic assembly provided by Dr. Fred Dietrich at the Duke Center for Genome Technology. The new assembly consists of 14 nuclear chromosomes and a single 21 KB mitochondrial chromosome, and has resulted in a reduction of the estimated genome size from 19.5 to 18.9 Mb. Improvements in the assembly and in our annotation process have resulted in a set of 6,967 predicted protein products, 335 fewer than the previous release.”
NY Times article on how bark beetle are spreading fungi and causing a pine tree die-off in the West. There is also a recent article on how populations of the fungi from different latitudes are adapted to different temperatures (Rice et al, Forest Pathology, 2008).
A paper in Fungal Genetics and Biology on species definitions in Cryptococcus neoformans from multi-locus sequencing seeks to provide additional treatment of the observed diversity. A large study of 117 Cryptococcus isolates were examined through multi-locus sequencing (6 loci) and identified two monophyletic lineages within C. neoformans varieties that correspond to var. neoformans and var. grubii. However within the C. gattii samples they identified four monophyletic groups consistent with deep divergences observed from whole genome trees for two strains of C. gattii, MLST, and AFLP studies. By first defining species, we can now test whether any of the species groups have different traits including prevalence in clinical settings and in nature.
BOVERS, M., HAGEN, F., KURAMAE, E., BOEKHOUT, T. (2007). Six monophyletic lineages identified within Cryptococcus neoformans and Cryptococcus gattii by multi-locus sequence typing. Fungal Genetics and Biology DOI: 10.1016/j.fgb.2007.12.004
Eucalyptus is an utilitarian tree, so it’s no surprise that several organizations are interested in genetically engineering it. Indeed, its genome sequence is slated for release, which should facilitate a GE market for the species. One company in particular – ArborGen (they have a very interesting mission statement) – is using genetic engineering, cloning and classic hybridization techniques to make a cold tolerant variety. ArborGen’s grove of 355 hybrids is located in southern Alabama. While a cold tolerant genotype would enable harvest of the tree across North America, this project has been met with particular public resistance, given the species’ invasive abilities.
There may be another reason for the public to resist ArborGen’s new project: Cryptococcus gattii. Known to associate with eucalyptus, C. gattii is a yeast-like fungus that can infect and kill mammals, including humans, that inhale its spores. Recently, a rare C. gattii genotype was the subject of an outbreak in British Columbia. Scientists and environmentalists are concerned that standing groves of eucalyptus that may be inncoulated with C. gattii could result in a subsequent health hazard for anyone living nearby. This particular risk, it should be noted, is independent of genetic engineering, but rather results from increased reliance on Eucalyptus as an industrial wood (remember, it’s not native to North America). The concerned parties have raised the issue with the US Deptarment of Agriculture and the EPA, so hopefully Cryptococcus ecologists will be afforded the opportunity to determine if the pathogen lives in ArborGen’s grove.
Final note: a special thanks to Kabir Peay, a fungal ecologist, who brought this to my attention.
EST sequencing for Aspergillus terreus proposed by Scott Baker at PNNL
Scott is also helping lead a projects to sequence Piromyces and Orpinomyces both early branching Neocallimastigomycota fungi that live in the rumen (which I am probably a little too excited about). Apparently the high A-T content is causing problems in the sequencing phase.
Trichoderma actrovirdi (which doesn’t appear to have any sequence in GenBank) is reportedly in production (bottom of the page).
This complements an ever growing list of fungal genome sequences which is probably topping 80+ now not including the several dozen strains of Saccharomyces that are being sequenced at Sanger Centre and a separately funded NIH project to be sequenced at WashU.
As announced at the Fungal Genetics meeting, the FGI at the Broad Institute is focusing on clusters of genomes rather than single ones. Some of genome projects are already grouped.
Coccidioides has 3 strains already plus the outgroup Uncinocarpus and conceivable one could include Histoplasma in there. This resources will grow to 14 strains (which comprise two species) of Coccidioides contributed by FGI and one from TIGR.
Aspergillus currently has 8 species sequenced with several in pipeline at Broad and TIGR.
Fusarium group has 3 species including recently released F. oxysporium.
The Candida clade also have several different already sequenced genomes and of course there is the already well studied (and well utilized genome resources I’ll add) for the Saccharomyces clade.
There are 4 genomes (well 5 but JEC21 and B-3501 are nearly identical) of Cryptococcus.
All in all a very exciting time for comparative genomics and I’m particularly intrigued to see how people will begin to use the resources.
This work to consolidate the clusters of genomes will, I hope, be very powerful. However, I still feel we are not doing a good job translating and centralizing information from different related species into a more centralized resource. Lots of money is spent on sequencing but I don’t know that we have realized the dream of having the comparative techniques illuminate the new genomes to the point that we are learning huge new things.
It seems to me, initially there is the lure of gathering low-hanging fruit from a genome analysis (which drives the first genome(s) paper), but not always the financial support of the longer term needs of the community to feed the experimental and functional work back into the genome annotation and interpretation.Â The cycle works really well for Saccharomyces cerevisiae because the curators who work with the community to insure information is deposited and that literature is gleaned to link genomic and functional information. But this is expensive in terms of funding many curators for many different projects.
It seems as we add more genomes there isn’t a very centralized effort for this type of curatorial information and so we lack the gems of high-quality annotation that is only seen in a few “model” systems.Â At some point a better meta-database that builds bridges between resource and literature rich “model system” communities may help, but maybe something new will have to be created? I like thinking about this as a user-driven content via a wiki which also dynamic (and versioned!) content from automated intelligent systems to map the straight-forward things.Â Tools like SCI-PHY already exist that can do this and generate robust orthology groups (or Books as the PhyloFact database organizes them) for futher analysis. The SGD wiki for yeast is a start at this, but is mostly an import of SGD data into a mediawiki framework – I wonder how this can be built upon in a more explictly comparative environment.