Category Archives: 1000 Fungal Genomes

Postdoc: Early diverging fungi in the James lab at U. Michigan

The James Lab at the University of Michigan is looking to hire a postdoctoral fellow in the area of single cell and comparative genomics. The research is centered on understanding the phylogeny, life cycles, and nutrition of early diverging fungi, including the Zygomycetes, Cryptomycetes, and Chytridiomycetes through genomic analyses. The ultimate goals of the project are to produce a well-resolved phylogeny of the basal branches of the fungal kingdom, to identify key evolutionary events associated with diversification and reproduction, and to use genomics to predict ecological roles of uncultured lineages. A major component of the work will be to develop or improve methods for sequencing genomes and transcriptomes using single or few cells or genome assembly using metagenomic approaches. This work will involve collaborations with the ZyGOLife research network (zygolife.org) and the Joint Genome Institute (JGI). The projects are supported by NSF and two JGI Community Sequencing Projects.

The ideal candidate will be skilled in bioinformatics, molecular biology, and cultivation/microscopy of fungi. Preference will be given to candidates with proficiency in both bioinformatics and molecular biology. Possible duties include environmental sampling, cell sorting (FACS, micromanipulation), microscopy, genome assembly and annotation, and comparative analyses of genome evolution. Opportunities for mentoring undergraduates or research associates will be provided. The initial appointment is for one year with a possibility of extension to a second year pending performance review.

Our lab (www.umich.edu/~mycology) pursues diverse projects in mycology, and the environment is conducive to development of a pathway to independence in academic research. The lab is in the Department of Ecology and Evolutionary Biology (http://www.eeb.lsa.umich.edu/eeb/index.html), which has strengths in phylogenetics, evolutionary genomics, and disease ecology.

Interested applicants should email Tim James (tyjames@umich.edu) with a CV, cover letter, and the names and contact information of three references.

An open letter to the fungal research community regarding genome database resources

An open letter to the fungal research community regarding genome database resources (from the Broad Institute & FungiDB/EuPathDB):

As many of you are already aware, fungal genome websites at the Broad Institute are undergoing a major transition. These resources were originally developed in support of sequencing projects, many of which have long-since been completed. While we have tried to keep such sites operational for as long as possible without funding, infrastructure changes now underway will make these websites nonfunctional over the coming weeks. We are therefore replacing formerly interactive websites with a static page providing information on fungal projects, along with links to the Broad FTP site where datasets can still be downloaded, and links to NCBI – the primary repository for all genomic data, where all genomes and annotation have been deposited and can be accessed, queried, and downloaded. We are also working to incorporate genomic data into other sites that support comparative analysis of fungal genomes, including FungiDB and MycoCosm.

The EuPathDB family of databases (funded by NIAID/NIH and the Wellcome Trust) supports a wide range of microbial eukaryotes; FungiDB includes many fungal (and oomycete) species, including non-pathogens. This resource has been designed to provide sustainable, cost-effective automated analysis of multiple genomes, integrating curated information (when available), with comments and supporting evidence from the user community (PubMed IDs, phenotypic information, images, datasets, etc). In addition to gene records, browser views, and data downloads, FungiDB offers sophisticated tools for integrating and mining diverse Omics datasets that fungal biologists will find quite useful. See the sidebar on the FungiDB web site for access to tutorials, videos, and exercises.

MycoCosm (supported by JGI/DOE) offers the largest available collection of fungal genomes, for comparative genomics across phylo- and eco-groups, along with interactive web-based tools for genome downloading, searching and browsing, and a form for nominating new species for sequencing to fill gaps in the Fungal Tree of Life.

For many years the Broad has been pleased to work closely with various fungal research communities, and we will continue to work with EuPathDB and MycoCosm to transition data valued by the community. Please direct any inquires or requests for help to help@FungiDB.org

NSF Poststdoc opportunity for Research using biological collections

Earlier this year the NSF released a postdoc opportunity for research to use Biological Collections. In particular these can be strain collections and stock collections. The US Culture Collection Network is a Research Coordination Network which brings together many collaborating culture collections. You can find many of the U.S. living collections there include fungal centers like the Phaff Yeast Collection and Fungal Genetics Stock Center. The Gilbertson Mycological Herbarium at U Arizona under Elizabeth Arnold‘s leadership has developed a rich collection of endophyte fungi which would be another excellent environment to work with these resources. Kyria Boundy-Mills who is the curator of the Phaff collection has also expressed interest in either hosting or helping working with a postdoc on this. There is tremendous biodiversity of the fungi available in these and other culture collections so seems like a great chance to tap into these.
This would be a great opportunity to link work in the 1000 Fungal genomes project and sampling from culture collections (not just sequencing, but growing and characterizing growth, carbon source utilization and integrating that with predictions made from genome comparisons). If this is something interesting to you – do get in touch with some of the curators at these collections, but also my lab and I expect many other labs would be interested hosting someone to work on these questions that take advantage of these living collections of fungi.
Proposals are to be submitted by potential post docs. Submitter must be a US citizen or US permanent resident. The next deadline is November 3, 2015Funding total for the program is $8 million, 40 awards anticipated, up to two years. Here’s some key text from the solicitation:

Competitive Area 2. Postdoctoral Research Fellowships Using Biological Collections.

Biological research collections represent the documented scientific history of life on Earth, and the U.S. museum community alone curates over a billion specimens ranging from bacteria to plants, insects and vertebrates, as well as fossils. Across the globe, collections represent critical infrastructure and support essential research activities in biology and its related fields. Scientists, government agencies, industry and citizens utilize collections to document and understand evolution and biodiversity, study global change, formulate advice on conservation planning, educate the general public, improve interactions between sciences, and devise new practical applications from science to every day life. New technologies supported by NSF in digitization, such as the Advancing Digitization of Biodiversity Collections (ADBC) program, are making collections and their associated data, whether they are physical specimens, text, images, sounds, or data tables, searchable in online databases. Despite this clear progress in improving access to physical specimens and their associated metadata, collections remain under-utilized for answering contemporary questions about fundamental aspects of biological processes. Thus, collections are poised to become a critical resource for developing transformative approaches to address key questions in biology and potentially develop applications that extend biology to physical, mathematical, engineering and social sciences. This postdoctoral track seeks transformative approaches that use biological collections in highly innovative ways to address grand challenges in biology. Priority may be given to applicants who integrate biological collections and associated resources with other types of data in an effort to forge new insight into areas traditionally funded by BIO. Examples of key questions in biology of interest include, but are not limited to, links between genotype and phenotype, evolutionary developmental biology, comparative approaches in functional and developmental neurobiology, and the biophysics of nanostructures. Using collections as a resource for grand challenge questions in biology is expected to present new opportunities to advance understanding of biological processes and systems, inspiring new discoveries in areas with relevance to other disciplines with overlapping interests in biological systems. Applicants must document access to the selected collection(s) in the research and training plan.

Basidiobolus! – genus of the month at ATCC

ATCC sent out this email with the Genus of the month as Basidiobolus. It is worth noting they call out B. ranarum as inhabitant of bat and rodent guts but it is mainly known (and named) for being associated with frogs (hence the ‘rana’). It has some quite cool biology, it grows dimorphically as a yeast or hyphae, and is reported to have a large genome (Henk and Fisher PLoS One 2012).
Note that the genome and transcriptome of B. meristosporus is being sequenced as part of the 1000 Fungal genomes project from samples Andrii Gryganski prepared. Don’t forget that YOU can propose genomes to this project by logging in here and submitting a proposed species in a family that is not sufficiently sampled (2 per Family).

The info below is from ATCC®. I couldn’t find a link to the on their site so I am copying the email text in.

There is nothing more fascinating than when a microbial species begins popping up in the literature as a true pathogen. Basidiobolus ranarum, which typically inhabits the guts of bats and small rodents, has been recently tagged as an emerging human pathogen that may have previously been unrecognized.1

       B. ranarum was first added to the CDC’s Morbidity and Mortality Weekly Report (MMWR)1 in 1999 after 6 immunocompetent individuals tested positive for gastrointestinal basidiobolomycosis over a 5-year period. The most interesting aspect of this study, however, was the fact that each patient was originally misdiagnosed with some other intestinal ailment, ranging from diverticulitis to cancer.

While many of the Zygomycetes, including Basidiobolus, have been implicated in subcutaneous human diseases, it is still relatively uncommon for Basidiobolus to colonize the human intestine. This new development piqued the interest of several researchers at the Mayo Clinic in Scottsdale, Arizona, a region of the U.S. where the majority of such cases have been reported.  Following an in-depth analysis of all known case records, they discovered a total of 44 cases of gastrointestinal basidiobolomycosis worldwide; 19 of which occurred in the southwestern U.S., 11 in Saudi Arabia, and 14 in other arid regions of the globe.2

Symptoms displayed in each case were similar, with complaints ranging from abdominal distention and pain to a palpable abdominal mass. Of particular interest was a patient originally treated for Clostridium difficile colitis. This patient underwent several surgeries and treatment with oral vancomycin before a stool fungal culture revealed the presence of B. ranarum. While this patient was successfully treated with a 3-month course of voriconazole, repeated at 1-year follow-up, the investigators cautioned that antifungal resistance may pose a problem in the future. Earlier work performed by the same group revealed uniform resistance to amphotericin B and flucytosine in four  B. ranarum isolates, as well as mixed resistance to several other azoles.2

The source of B. ranarum infection leading to gastrointestinal disease is still not understood, but the fecal-oral route has been suggested. Pathologists and clinicians should be aware of this potential new threat, and additional work to understand the pathogenesis and antifungal susceptibility/resistance of B. ranarum should be an on-going effort among the research and medical communities.

ATCC® Basidiobolus Strains
Want to learn more about ATCC Basidiobolus strains available from ATCC? View a list of Basidiobolus spp. online.

References

1. Centers for Disease Control and Prevention (CDC). MMWR: Gastrointestinal Basidiobolomycosis – Arizona, 1994-1999. August 20, 1999.

2. Vikram, et al. Emergence of Gastrointestinal Basidiobolomycosis in the United States, with a Review of Worldwide Cases. Clinical Infectious Diseases Advance Access published on March 22, 2012.