Tag Archives: basidiomycota

New species of Cryptococcus found in seawater

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.

See also:

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

Little Coprinus mushroom pictures

Coprinus cinereus (renamed Coprinopsis cinerea) growing in the lab. The genome was sequenced, assembled into chromosomes, and annotated and we are working on the final analysis of it to describe some of the interesting biology about this little Coprophilic fungus. I’m excited to put up a few of my pictures of the tiny mushrooms growing in the lab (although others have better ones). A few more days and I might have better shots.

Coprinus cinereus Coprinus

Coprinus

Update: Chris Ellison in the Taylor Lab sent this post from Cornell Mushroom Blog which has a video of Coprinus comatus (shaggy mane) fungi deliquescing.

Genomes on the horizon at JGI

Several more fungi are on the docket for sequencing at JGI through their community sequencing program. This includes

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.

Genome of Postia placenta

The JGI has released the genome sequence and annotation of the Basidiomycete brown rot Postia placenta. Brown rotters can only break down cellulose but do not degrade lignin that white rotters (like Phanerochaete chrysosporium).

Using total genomic DNA from dikaryotic strain MAD-698, the JGI generated 571,000 reads that assembled into 1243 haplotype scaffolds, with 85 of these scaffolds covering half of the genome sequence.

v.1.0 (September 2006): Postia placenta genome assembly v1.0. The assembly release of whole genome shotgun reads was constructed with the JGI assembler, Jazz, using paired end sequencing reads at a coverage of 7.23X. After trimming for vector and quality, 574,631 reads assembled into 1243 scaffolds totaling 90.9 Mbp.

Since Postia placenta is known to be highly polymorphic with a polymorphism rate in the neighborhood of 3-4%, this particular assembly uses extra stringent parameters that should only assemble sections of the genome that are more than 99% identical.The current draft release, version 1.0, includes a total of 17,173 gene models predicted and functionally annotated using the JGI annotation pipeline.

The genome sequence is a whopping 90 Mb – big for a fungus – but I think this is not just the haploid genome since this was DNA from a dikaryon and only the highly identical haplotypes are assembled together (99% identity). So it means that the haploid genome is not likely to be quite this big. This is much like the Candida albicans diploid assembly. Presumably this means any analysis of gene duplicates needs to have at least two levels of classification to distinguish diploid copy from actual duplicated gene.

While nowhere near the density of sampling of genomes in the Ascomycota, the Basidiomycetes are starting to get their due. Kudos to the JGI for tackling this and the DOE and many of the researchers including Dan Cullen to work to get these genomic resources produced. This genome will be important in work to understand forest ecosystems, process of wood rotting, and maybe even in work to develop better fermentation systems for production of biofuels from cellulose.

The world’s largest organism

Take a guess: what’s the world’s largest organism? No, it’s not Yao Ming. While the Guiness Book of World Records hasn’t weighed in on this issue, scientists out of Oregon State University say that an Armillaria ostoyae individual residing in Oregon’s Blue Mountains is the largest living organism on the planet. Covering 2,200 acres, this tree killing fungus certainly is big. DNA fingerprinting and vegetative pairing confirm that a single individual spans this great distance. In addition to its great size, the fungus is quite old. By using growth rates to estimate age, this scientists estimate that this humongous fungus may be 8,000 years old.

While root rot, the tree killing phenomenon caused by A. ostoyae, slows the rate of tree harvest in a forest, the park service respects the organism’s vital role in the ecosystem. By clearing out old trees, fresh nutrients are resupplied to the soil and room is made for more resistant trees to grow. Besides, how do you kill something that is 1,600 football fields in size?

Fungal tree of life papers

Lots of papers in Mycologia (subscription required) this month of different groups analyzing the fine-scale relationships of many different fungal clades using the loads of sequences that were generated as part of the Fungal Tree of Life project.

Some highlights – there are just too many papers in the issue to cover them all. As usual with more detailed studies of clades with molecular sequences we find that morphologically defined groupings aren’t always truly monophyletic and some species even end up being reclassified. Not that molecular sequence approaches are infallable, but for many fungi the morphological characters are not always stable and can revert (See Hibbet 2004 for a nice treatment of this in mushrooms; subscription required).

  • Meredith Blackwell and others describe the Deep Hypha research coordination network that helped coordinate all the Fungal Tree of Life-rs.
  • John Taylor and Mary Berbee update their previous dating work with new divergence dates for the fungi using as much of the fossil evidence as we have.
  • The early diverging Chytridiomycota, Glomeromycota, and Zygomycota are each described. Tim James and others present updated Chytridiomycota relationships so of which were only briefly introducted in the kingdom-wide analysis paper published last year.
  • There is a nice overview paper of the major Agaricales clades (mushrooms for the non-initiated) from Brandon Matheny as well as as individual treatment of many of the sub-clades like the cantharelloid clade (mmm chanterelles…) .
  • Relationships of the Puccinia clade are also presented – we blogged about the wheat pathogen P. graminis before.
  • A new Saccharomycetales phylogeny is presented by Sung-Oui Suh and others.
  • The validity of the Archiascomycete group is also tested (containing the fission yeast Schizosaccharomyces pombe and the mammalian pathogen Pneumocystis) and they confirm that it is basal to the two sister clades the euascomycete (containing Neurospora) and hemiascomycete (containing Saccharomyces) clades. However it doesn’t appear there are enough sampled species/genes to confirm monophyly of the group. There are/will be soon three genome sequences of Schizosaccharomyces plus one or two Pneumocystis genomes – it will be interesting to see how this story turns out if more species can be identified.

This was a monster effort by a lot of people who it is really nice to see it all have come together in what looks like some really nice papers.

Fungus could cause a food shortage

A while back, Jason blogged briefly on a New Scientists article about the rise of a new Puccinia graminis strain, Ug99, that is spreading through West African wheat fields at an enormous rates. It looks like this story is growing in the scientific conciousness, as Science is now running an article on the spread of this wheat pandemic.

The article has a nice bit of background regarding the rise of the disease. It seems that it is spreading so quickly for due to its relatively broad host range compared to other strains. While scientists have been working to derive resistant wheat varieties, Puccinia has successfully foiled their recent attempts by mutating to acheive resistance to the plant expressed Sr24.

To boot, this strain has been found in Yemen, allowing its spores to hitch a ride along the winds that blow north along the Indian Ocean, putting much of the global bread basket at risk (I imagine that the last thing the middle east needs right now is a wheat shortage). The last time a rust spread through this area, it caused 1 billion dollars in damage. Given the extensive host range of this variety, experts predict that damages will exceede at least three times this amount.

The spread of the rust pandemic

Fortunately, researchers in Ethiopian have derived two wheat strains that may be resistant to Ug99. However, it can take several years to get these wheat strains in the ground and, ultimately, no one is certain that Ug99 won’t cleverly find a way to adapt resistance. We should keep our ears to the rail on this one: it could be a big problem.

Puccinia black stem rust disease spreading

The New Scientist has an article about the spread of black stem rust caused by Puccinia graminis. We briefly mentioned the 1st release of a Puccinia genome in January. Some more links about the spread of the Ug99 virulent strain.

Continue reading Puccinia black stem rust disease spreading

Fungi for bioremediation

Saprophytic fungi degrade organic matter to release carbon, nitrogen, and other elements locked up in complexes. There is interest in better degradation of recalictrant ligin and cellulose plant matter as part of a bioenergy program. Some fungi are able to break down these plant molecules that would otherwise remain behind when left to digestion by bacteria.

Continue reading Fungi for bioremediation