Saprolegnia genome Database
Data site retirement On 12/31/15 the Broad's Institute Saprolegnia parasitica database and web site will be retired due to expiration of funding. For many years we have been pleased to work closely with the Saprolegnia research community to create and support this resource.
The oomycete Saprolegnia parasitica and related pathogens are water molds in the class of Saprolegniomycetidae that attack a wide variety of fish, amphibians and crustaceans important to aquaculture and to aquatic ecosystems. They cause Saprolegniosis, a disease that is characterized by visible white or grey patches of filamentous mycelium on the body or fins of freshwater fish. Saprolegnia parasitica is economically one of the most important fish pathogens, especially on catfish, salmon and trout species. It causes millions of dollar losses to the aquaculture industry worldwide and has also been linked to declining wild fish stocks and amphibian populations around the world.
Funding for the Saprolegnia parasitica sequencing project was provided by the United States Department of Agriculture through the Microbial Genome Sequencing Program.
The Saprolegnia parasitica sequencing project is supported as part of the Microbial Genome Sequencing Program from United States Department of Agriculture - Agriculture and Food Research Initiative (USAD - AFRI), grant number 2008-35600-04646. Its goal is to release a high quality draft genome assembly and automated annotation for Saprolegnia parasitica isolate CBS223.65, together with polymorphims data from a highly-salmon-pathogenic isolate of Saprolegnia parasitica (N12) and an isolate of Saprolegnia diclina (It20). Genomic DNA from all strains was prepared from mycelia and mRNA was isolated from pre-infection and infection stages by the van West group at the University of Aberdeen, Scotland.
Our specific aims are as follows:
- Generate a whole genome shotgun assembly of Saprolegnia parasitica isolate CBS223.65 using an optimized combination of 454 and Sanger data
- Annotate the genome with respect to genes and other features, including the generation of paired-end Illumina EST sequences derived from several life stages of S. parasitica and fish infection models.
- Identify conserved and rapidly diversifying genes by generating Illumina data from a highly-salmon-pathogenic isolate of Saprolegnia parasitica (N12) and an isolate of Saprolegnia diclina (It20).
- Promptly release all reads, assemblies, annotation, discovered polymorphisms and EST alignments to the community. Integrate the annotated genome sequence into the centralized oomycete genomics resource at Virginia Tech.
We produced a whole genome shotgun assembly from data generated by Roche/454 (fragment and 3kb paired-end libraries) and Sanger (Fosmid library) sequencing technologies. The resulting 25x assembly was made public in December of 2009, and the results of automated genome annotation will be made public in future releases. Questions about the project should be directed to annotation webmaster.
Primary collaborators for the project are:
- Brett M. Tyler, Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University
- Carsten Russ and Chad Nusbaum, Broad Institute
- Pieter van West, University of Aberdeen, Scotland
- Javier Diéguez-Uribeondo, Real Jardin Botanico CSIC, Madrid, Spain
What is Saprolegnia parasitica?
The oomycete Saprolegnia parasitica, and related pathogens in the class Saprolegniomycetidae attack a wide variety of fish, amphibians and crustaceans important to aquaculture and to aquatic ecosystems (1). Saprolegnia parasitica is economically one of the most important fish pathogens, especially on catfish, salmon and trout species. It causes millions of dollar losses to the aquaculture business worldwide, notably in the USA, Scotland, Scandinavia, Chile, Japan, and Canada (2). Saprolegnia species have also been linked to declining wild fish stocks and amphibian populations around the world (3,4). Over the past ten years, aquaculture production has increased on average by 11% per year worldwide (FAO Fishery Information), and at this rate it will overtake beef as a protein source by 2010 (5). The high density of fish in aquaculture farms and the recent loss of the fungicide malachite green have exacerbated disease problems. Water molds (oomycetes) are destructive pathogens of aquatic animals and terrestrial plants. Members of the genus Saprolegnia (class Saprolegniomycetidae) cause Saprolegniosis, a disease that is characterized by visible white or grey patches of filamentous mycelium on the body or fins of freshwater fish. Besides mycelium, S. parasitica generates primary and secondary zoospores whereby the latter type is infectious on fish. Also fish eggs are infected by Saprolegnia spp, resulting in abundant mycelial growth and ultimately cell death. At present, oomycete genome sequencing projects have focused on plant pathogenic species from the order Peronosporomycetidae (Phytophthora and Hyaloperonospora), and have yielded dramatic insights into the pathology of these species. Saprolegnia parasitica is the first Saprolegniomycetidae and oomycetes animal pathogen to be sequenced.
- Phillips, A.J., Anderson, V.L., Robertson, E.J., Secombes, C.J. and van West, P. (2008) New insights into animal pathogenic oomycetes. Trends in Microbiology, 16, 13-19.
- Hussein, M.M.A. and Hatai, K. (2002) Pathogenicity of Saprolegnia species associated with outbreaks of salmonid saprolegniosis in Japan. Fisheries Science, 68, 1067-1072.
- Neitzel, D.A., Elston, R.A. and Aberneth, C.S. (2004). Department of Energy, pp. 1-B25.
- van West, P. (2006) Saprolegnia parasitica, an oomycete pathogen with a fishy appetite: new challenges for an old problem. Mycologist, 20, 99-104.
- Brown, L.R. (2000). Worldwatch Institute, Washington, D.C., Vol. 2008.