Mucorales Genomes

Project Information

As part of the Fungal Genome Initiative at the Broad Institute, we have sequenced the genomes of two Mucorales: Rhizopus delemar and Mucor circinelloides f. sp. circinelloides. These species are the two most commonly isolated species causing mucormycosis in humans.

The Rhizopus delemar project released the genome assembly and annotation of Rhizopus delemar strain 99-880 (also termed RA 99-880). This strain was isolated in 1999 from a brain abscess of a diabetic patient who developed fatal rhinocerebral mucormycosis. The strain was collected by the San Antonio fungal testing group and was also deposited in the Fungal Genetic Stock Center (FGSC 9543) and the Agricultural Research Service Culture Collection (NRRL 43880). This primary collaborators for this project were 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. This work was supported by the National Human Genome Research Institute

More recently, we generated a genome assembly and annotation for a strain of Mucor circinelloides f. sp. circinelloides isolated from skin samples from a healthy human volunteer. This isolate was provided by Keisha Findley at the NIH, and Soo Chan Lee at Duke University confirmed the species typing by sequence analysis. This work was supported by the Human Microbiome Project.

Both Rhizopus and Mucor are classified under the family Mucoraceae in the order Mucorales.

What is Rhizopus?

 R. delemar and the related species R. oryzae are the most important and representative agents of mucormycosis. These species 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.

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.

Data access and citation

The genome assembly and annotation of Rhizopus delemar is available in Genbank.

For use of this data, please cite:  Ma LJ et al., "Genomic analysis of the basal lineage fungus Rhizopus oryzae reveals a whole-genome duplication.", PLoS Genet, 2009 Jul 3;5(7):e1000549

The genome assembly and annotation of Mucor circinelloides is also available in Genbank.

For use of this data, please cite: Lee SC et al. "Analysis of a food-borne fungal pathogen outbreak: virulence and genome of a Mucor circinelloides isolate from yogurt.". mBio 2014 Jul 8;5(4):e01390-14. doi: 10.1128/mBio.01390-14.

Data files formerly available on this website can be accessed on our fungal ftp site, and the R. delemar genome can also be accessed in the JGI MycoCosm site and FungiDb.

Photo credit

The micrographs images in the top banner depict several stages in the life cycle of Rhizopus oryzae. They were kindly provided by Chris Skory of the USDA Agricultural Research Service. In the top image, from left to right are:sporangia, immature sporangia, mature sporangia, (both from R. oryzae 99-880) and two images of zygospores from the crosses between R. oryzae stains NRRL 3133 x NRRL 13480.