Tag Archives: chytridomycota

Fungus Finds Frogs, Frogs Croak

Frogs have been having a tough time of it lately. While there are likely many contributing factors to the global frog decline, one known cause of frog dieoff is a fungal pathogen: Batrachochytrium dendrobatidis. Unfortunately, little is known about how this aquatic fungus kills frogs or how the disease was originated and spread.

However, Dr. Jess Morgan and colleagues published in PNAS (open access article) this week a study aimed at answering the latter questions. Specifically, the authors investigated Batrachochytrium populations in the Sierra Nevada Mountains and sampled the genetic diversity. A clonal population structure with few genotypes indicates that the fungus is new to the region as it hasn’t had time to accumulate mutations. Conversely, should the disease be endemic, there should be many distinct genotypes. Without giving too much of the punchline away, the authors find evidence for an epidemic spread, though certain locations have populations that are recombining.  Any migration of the fungus may even be human assisted.  It will be interesting to see how the disease is controlled and the authors raise a good point here: distribution of resistant sporangia may make it easy for the organism to spread and remain dormant.  As a result, this may be a particularly tough disease to control.

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.

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.

FGI Chytrid annotations available

The public release of the Batrachochytrium dendrobatidis automated annotation from the Broad/FGI has been made available.

“This project is part of the Fungal Genome Initiative at the Broad Institute and was funded by NHGRI. This release contains a set of 8,794 predicted genes, BLAST databases, precomputed BlastX and HMMer analyses, alternative gene predictions, tRNA predictions, and RFAM features.

The annotation can be accessed through the project website:
http://www.broad.mit.edu/annotation/genome/batrachochytrium_dendrobatidis

We would like to thank Franz Lang and Mary Berbee for sharing their B. dendrobatidis EST sequences and contributing a cDNA library for end-sequencing.”