Tag Archives: news

Amphibian skin bacteria shown to fight off Batrachochytrium dendrobatidis.

A year ago researchers at James Madison University discovered that, Pedobacter cryoconitis, a bacteria first found on the skin of red backed salamanders, was found to prevent the growth of the chytrid B. dendrobatidis, which is currently decimating frog populations.

(Mountain Yellow-Legged Frog from wikipedia)

The newest research on the subject is being presented this year at ASM by Brianna Lam who worked with other biologists from both San Francisco State University and JMU.

Lam’s research indicates that adding pedobacter to the skin of mountain yellow-legged frogs would lessen the effects of Batrachochytrium dendrobatidis (Bd), a lethal skin pathogen that is threatening remaining populations of the frogs in their native Sierra Nevada habitats.

Lam first conducted petri dish experiments that clearly showed the skin bacteria repelling the deadly fungus. She then tested pedobacter on live infected frogs, bathing some of them in a pedobacter solution. The frogs bathed in pedobacter solution lost less weight than those in a control group of infected frogs that were not inoculated.

In addition to the lab experiments, the JMU and SFSU researchers have studied the yellow-legged frogs in their natural habitats and discovered that some populations with the lethal skin disease survive while others go extinct. The populations that survived had significantly higher proportions of individuals with anti-Bd bacteria. The results strongly suggest that a threshold frequency of individuals need to have anti-Bd bacteria to allow a population to persist with Bd. (from Eureka alert)

The research above is really interesting and I am curious as to how the bacteria is actually killing the chytrid. The only other research I can think of where chytrids were being killed was a BBC news article that wrote about scientists bathing frogs in chloramphenicol.

Server changes

LogoThe old site I setup during my PhD (fungal.genome.duke.edu) was shutdown by Duke. I have been able to migrate the domain name to the fungalgenome.org site that is funded by the TaylorLab, but have not had time to restore all functionality of the old data and site.

In the future I hope the community will consider what are important resources to utilizing these genomic data and how we want to fund and see these types of resources perpetuated.

(re)Annotating GenBank

NCBI LogoTom Bruns, Martin Bidartondo and 250 others sent a letter to Science describing the current problems with fixing annotation in GenBank. There is an entertaining accompanying news article that interviews several people about the problem of updating annotation and species assigned to sequences in the database. In particular the problem for mycologists that many fungi found from metagenomic approaches are only identified through molecular sequences and having the wrong species associated with a sequence can be difficult when studying community ecology composition.  This problem is not limited to fungi by any means, but recent reports find as many as 20% of fungal Intergenic Spacer (ITS) sequences are mis-attributed to the wrong species. 

There’s a nice quote in the news article from Steven Salzberg talking about the difficulties in getting sequences, especially from big centers, updated. I’m sure he is thinking of many examples, like reclassifying some Drosophila sequence traces.

Continue reading (re)Annotating GenBank

Ireland’s blight and Puccinia update

Hyphoid logic points out that it is appropriate to discuss about the oomycete Phytophthora infestans on St. Patrick’s Day and mentions a NYT article “The fungus that conquered Europe” that is worth a look.

It is also worth thinking about another blight, well rust, that is spreading through the middle east and could threaten wheat crops worldwide. New Scientist has excellent coverage of Puccinia graminis strain Ug99 which is spreading faster than expected due to a cyclone that spread the rust spores into Iran two years earlier than expected.

Related posts from last year. “Fungus could cause a food shortage”, “Puccinia black stem rust disease spreading”

B. dendrobatidis strain JAM81 released

B.dendrobatidis zoosporeThe following is an announcement to the B.dendrobatidis and fungal community at large from Alan Kuo at JGI. This is the JAM81 strain (Jess Morgan collected from a frog in the California Sierra Nevada). The JEL423 (Joyce Longcore, collected in Panama) strain genome sequence and annotation is available from the Broad Institute.

Please do contact me if you would like to contribute to assigning functions to the annotation. We’re in the last round of analyses for some of the genome work, but if there are particular questions you want to contribute to, we’re open to collaborators and can outline the basis of our work to see how other work can complement it.

From Alan Kuo at JGI:

The JGI Batrachochytrium annotation portal is now on the public JGI website. As it is public, no password is required.

For those of you who have not yet registered to be an annotator, go to this new link to register.As before, please choose a username that is personal, so that other annotators may be able to recognize it as yours. A derivative of your personal name would be best.

Those of you who are already registered, you do not need to do anything. Your old pre-release username and password are valid on the new public portal too.

As always, please direct all questions and problems to me. Use email or phone: Cheers, Alan.

Some information about the assembly and annotation:

The first annotation of the 127 scaffolds and 24 Mbp of JGI’s 8.74X assembly of the Batrachochytrim dendrobatidis JAM81 genome. We predict 8732 genes, with the following average properties:

Gene length 1825.16 nt
Transcript length 1407.29 nt
Protein length 450.56 aa
Exon frequency 4.29 exons/gene
Exon length 328.37 nt
Intron length 129.18 nt
Gene density 359.1 genes/Mbp scaffold

The genes were found by the following methods:
Total models 8732 (100%)
Jason’s models 3214 (37%)
cDNAs and ESTs 518 (6%)
Similarity to nr 1928 (22%)
ab initio 3072 (35%)

The genes were validated by the following evidence:
start+stop codons 7990 (92%)
EST support 2488 (28%)
nr hit 6787 (78%)
Pfam hit 4329 (50%)

Ectomycorrhizal fungus Laccaria bicolor genome

Today, I would like to share the news about the publication of the Laccaria bicolor genome. This is the first mycorrhizal symbiotic genome published in the Nature journal. The title is “The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis”.

The team consisteing of more than 60 researchers from 16 institutions have revealed the interaction between plant and fungi.

For complete publication and additional news.

Some links


I’ve been too busy to post much these last few days, but here are a few links to some papers I found interesting in my recent browsing.

Schmitt, I., Partida-Martinez, L.P., Winkler, R., Voigt, K., Einax, E., Dölz, F., Telle, S., Wöstemeyer, J., Hertweck, C. (2008). Evolution of host resistance in a toxin-producing bacterial–fungal alliance. The ISME Journal DOI: 10.1038/ismej.2008.19

LEVASSEUR, A. (2008). FOLy: an integrated database for the classification and functional annotation of fungal oxidoreductases potentially involved in the degradation of lignin and related aromatic compounds. Fungal Genetics and Biology DOI: 10.1016/j.fgb.2008.01.004

Shivaji, S., Bhadra, B., Rao, R.S., Pradhan, S. (2008). Rhodotorula himalayensis sp. nov., a novel psychrophilic yeast isolated from Roopkund Lake of the Himalayan mountain ranges, India. Extremophiles DOI: 10.1007/s00792-008-0144-z

New Saccharomyces resequencing assembly

SGRP LogoDavid Carter at the Sanger Centre emailed a message that new assemblies of Saccharomyces strain resequencing project have been posted including a new three-way alignment of S. bayanusS.paradoxusS.cerevisiae. This updates the Dec 2007 release.

Continue reading New Saccharomyces resequencing assembly

Next next-gen sequencing technology

I’m not at AGBT, but Jonathan and Anthony both have coverage of Pacific Biosciences’s new sequencing technology that uses detection of DNA polymerase activity to determine sequence.  I believe some of the details are in the paper “Selective aluminum passivation for targeted immobilization of single DNA polymerase molecules in zero-mode waveguide nanostructures“, but I’ve not had a chance to read it.

Stagonospora nodorum genome published

Blogging about Peer-Reviewed ResearchThe Stagonospra nodorum (teleomorph Phaeosphaeria nodorum) genome is now published in Plant Cell, “Sequencing and EST Analysis of the Wheat Pathogen Stagonospora nodorum”. The paper describes the sequencing and analysis of this Dothideomycete fungus. The analyses included identifying genes likely involved in pathogenecity such as PKS and NRPS genes and enabled the discovery of new genes like ToxA.

Continue reading Stagonospora nodorum genome published