Project Info
Project Information
The Rhizopus oryzae sequence project is part of the Fungal Genome Initiative at the Broad Institute of Harvard and MIT. The goal of this project is to release 10X sequence coverage for Rhizopus oryzae strain 99-880 (it also have been called RA 99-880). The strain was isolated in 1999 from a brain abscess of a diabetic patient who developed fatal rhinocerebral mucormycosis. The strain was collected by San Antonio fungal testing group and it is also deposited in the Fungal Genetic Stock Center as FGSC 9543 and Agricultural Research Service Culture Collection as NRRL 43880. Additional Fosmid reads were generated to improve the assembly quality. It was accomplished through collaborations with Ashraf Ibrahim at UCLA School of Medicine, Christopher Skory at USDA National Center for Agricultural Utilization Research, Brian Wickes at the University of Texas Health Science Center at San Antonio, and Franz Lang at University of Montréal, Canada.
Our specific aims are as follows:- Generate and assemble sequence reads yielding 10X coverage of the R. oryzae genome through whole genome shotgun sequencing.
- Perform automated annotation of the sequence assembly.
- Release the sequence assembly and results of our annotation and analysis to public
Data Releases
November, 2005 - Release of the results of automated annotation.
August 2005 - The initial release of assembly version 3 of the Rhizopus oryzae (RO3). This assembly (12X) included additional Fosmid sequence reads which greatly improved the assembly quality.
December 2004 - Release 1 of assembly version 1 consisted of a 10X whole-genome shotgun assembly generated at the Broad
Questions about the project should be directed to annotation-webmaster@broad.mit.edu.
What is Rhizopus oryzae?
The genus Rhizopus is classified under the family Mucoraceae in the order Mucorales of the phylum Zygomycota. R. oryzae is the most important and representative agent of mucormycosis. R. oryzae and the other members of Mucorales are recovered in profusion from decaying vegetables, fruits and their seeds, grains, compost piles, soil, animal excreta, and molding bread. Since it is ubiquitous in nature, mucormycosis cases are reported worldwide. The majority of mucormycosis patients have a serious underlying condition, such as diabetes mellitus, immunosuppression, starvation, burns, or other major trauma. Pathologically, mucormycosis is characterized by vascular invasion with hyphae, infarction and necrosis of tissue, and by an acute or subacute course of infection. Of the many forms of clinical manifestation, the most common form caused by Rhizopus species is the rhinocerebral and craniofacial mucormycosis. This originates in the paranasal sinus but presents in contiguous structures of orbit, palate, face, nose, or brain. Ordinarily death occurs in untreated cases within 4 weeks of onset.
The most prominent predisposing factor for the facial cranial mucormycosis is diabetes mellitus, and the diabetic population is on the rise worldwide. The second most common form of mucormycosis is pneumonia, which occurs most frequently among patients with hematologic disorders, lymphoma, severe nutropenia, or history of deferoxamine therapy. Infection in these patients has been observed to be fatal in a very short period of time in all cases reported to date. Although the number of cases has been small, children appear overrepresented among the mucormycosis patients without a known underlying disease. Rhizopus species also can cause skin and soft tissue infection in the setting of local trauma or by the hematogenous route.
The zygomycetes are evolutionarily divergent from ascomycetes. R. oryzae, like other members of Mucorales, is a rapidly growing mold that propagates by hydrophobic sporangiospores that readily disperse after maturation. It is one of the common laboratory contaminants due to its ubiquity in soil and decomposing organic material. It is different from ascomycetes or basidiomycetes in that its hyphae are tube-like, without septation, and the cell wall contains chitosan and chitin instead of glucans, mannans, and chitin. Asexual spores are produced within sporangia and are released upon maturation. The fungus can also undergo sexual reproduction and produce zygospores upon mating between the positive and negative strain on an appropriate mycological medium.
R. oryzae occurs as a haploid. Although R. oryzae has a defined sexual cycle involving mating between the positive and the negative strains, classical genetic approaches have rarely been applied to study this organism. That is because germination of zygospores takes months and the rate of germination is erratic. Molecular biological approaches have been developed, including transformation systems and gene disruption by homologous integration. In addition, episomal plasmids, cDNA expression libraries, and animal models are available. It is now possible to identify the genes of interest and study their impact on pathobiology.