Batrachochytrium Genome Project

Project Information

Batrachochytrium is a pathogen of amphibians implicated as a primary causative agent of amphibian declines. This recently emerging pathogen was identified in 1998 as the cause of amphibian deaths in Australia and Central America. More recently, Batrachochytrium dendrobatidis has been implicated in population declines of frog species in North America, South America, Europe and Africa. This fungus invades the top layers of skin cells and causes thickening of the keratinized layer. As a representative of the Chytridiomycota (chytrids), the sequence of B. dendrobatidis is the first in this largely uncharacterized phylum of fungi.

The Batrachochytrium dendrobatidis sequencing project is part of the Broad Institute Fungal Genome Initiative. Its goal was to release an annotated assembly from 10X genome sequence coverage for Batrachochytrium dendrobatidis diploid strain JEL423, which was provided by Dr. Joyce Longcore at The University of Maine. This strain was isolated from a sick Phyllomedusa lemur frog in Panama. Genomic DNA from this strain was prepared by Tim James at Duke University.


Project Leadership

Christina Cuomo (Broad Institute)
Joyce Longcore (The University of Maine)
Tim James (Duke University)

What is Batrachochytrium dendrobatidis?

Batrachochytrium is a pathogen of amphibians implicated as a primary causative agent of amphibian declines (1,2). This recently emerging pathogen was identified in 1998 as the cause of amphibian deaths in Australia and Central America (3). More recently, Batrachochytrium dendrobatidis has been implicated in population declines of frog species in North America, South America, Europe and Africa. This fungus invades the top layers of skin cells and causes thickening of the keratinized layer (3,4). Because amphibians drink and breathe through their skin, the fungus may kill them by disrupting these mechanisms. Alternatively, the fungus may be secreting a toxin.

As a representative of the Chytridiomycota (chytrids), the sequence of B. dendrobatidis is the first in this largely uncharacterized phylum of fungi. Batrachochytrium is a non-filamentous (monocentric) chytrid firmly within the order Rhizophydiales, based on ultrastructural characteristics and molecular sequence data; the Rhizophydiales is a new order recently segregated from the polyphyletic Chytridiales (5).

As members of both aquatic and terrestrial microbial communities, chytrids are parasites and saprobes of many microscopic organisms (e.g. pollen, algae, and invertebrates) and play an important ecological role in the degradation of recalcitrant materials, such as chitin, keratin, and cellulose. Chytrids are unique among the true fungi in possessing zoospores, which move using flagella (6). Phylogenetic studies based on rDNA and on whole mitochondrial genome sequences indicate that the chytrids are basal in the fungal clade (3,7). This basal position increases the value of a whole genome sequence for comparative genomics within the fungal clade and also with the sister animal clade.

References

P. Daszak et al., Emerg Infect Dis 5, 735 (Nov-Dec, 1999).
J. A. Pounds et al., Nature 439, 161 (Jan 12, 2006).
L. Berger et al., Proc Natl Acad Sci U S A 95, 9031 (Jul 21, 1998).
A. P. Pessier, D. K. Nichols, J. E. Longcore, M. S. Fuller, J Vet Diagn Invest 11, 194 (Mar, 1999).
P. M. Letcher, M. J. Powell, P. F. Churchill, J. G. Chambers, Mycol Res 110, 898 (Aug, 2006).
J. E. Longcore, A. P. Pessier, D. K. Nichols, Mycologia 91, 219 (1999).
T. Y. James, D. Porter, C. A. Leander, R. Vilgalys, J. E. Longcore, Canadian Journal of Botany 78, 336 (2000).

Photo captions and credits

All photos are courtesy of Joyce Longcore, from The University of Maine.

Captions for the photos at the top (from left to right):

B. dendrobatidis begins its life cycle as a zoospore (shown), which grows into a thallus producing a single zoosporangium, which releases new zoospores.
A zoosporangium with zoospores exiting through discharge papilla.
Frog skin (smooth-sided toad: Bufo guttatus) infected with Batrachochytrium dendrobatidis; this frog died at the National Zoological Park.
Swabbing a Phylomedusa lemur for later molecular detection of B. dendrobatidis DNA by a PCR-based assay.
Phylomedusa lemur in native habitat (Panama). This individual was sick, as evidenced by its lack of righting response; it was the source of the sequenced strain JEL423.

Data access

The genome sequence of Batrachochytrium dendrobatidis is available in Genbank under bioproject PRJNA13653; the submitted sequence includes an RNA-Seq updated gene set, which was assigned new locus ids starting with BDEG_20000. Data files formerly available on this website including the first version of the gene set can be accessed on our fungal ftp site.