Congratulations Joyce Longcore!

Joyce Longcore

Congratulations to Chytrid biologist Joyce Longcore from the University of Maine who was elected as one of 701 of the 2012 fellows of the American Association for the Advancement of Science. This is a very high honor and I’m delighted to see Joyce recognized for her many years working in this field which is often overlooked because there are a small number of researchers.

Joyce has been a hugely influential researcher in studies of chytrid diversity and biology. She is probably most well known for first describing the amphibian pathogenic chytrid Batrachochytrium dendrobatidis. In addition her lab keeps the stocks of the hundreds of chytrid isolates including Bd strains from all over the world, and is one of the few places that maintains these. I’ll mention she does this on a very limited budget (so don’t be bashful about ordering strains from her and helping pay for this important service), yet it provides a hugely valuable resource to the community studying this disease as keeping the chytrids in culture can sometimes be a finicky process, and deep frozen specimens are required to be revived and grown up in regular intervals of ~6 months (see published protocol from her lab).

Joyce completed her MS training under Fred Sparrow in 1964 at the University of Michigan, one of the great mycologists of the 20th century who worked on Chytrids and aquatic fungi (see Aquatic Phycomycetes). She worked on her Ph.D. in the late 1980s after raising children and later obtained her current position at the University of Maine in the School of Biology & Ecology. She has trained many students and researchers in the field on how to isolate and identify chytrids, and I’ll mention is still actively out in the field collecting more isolates, characterizing them and discovering many new species and many new orders of Chytrids to study the diversity and origins of these fascinating organisms.  She continues to be an important person in Mycological community and her research has had important implications in studies of biodiversity, amphibian decline, and phylogenetics and taxonomic studies of the kingdom Fungi.

Congratulations again Joyce!

(No I didn’t write any letters for her AAAS nomination, but I did wanted to make sure this important accolade gets out to the community, so these are just my thoughts at the time – js)


Reference ITSdb for QIIME released

Good news!

An alpha version of the ITS reference database for use with QIIME was released this week as part of the QIIME team development. There are more details on the release and how to obtain it from the project’s post here.

Please note that this is an Alpha release and may not be completely consistent, but the team wants to make something available now to give people a starting DB for use of QIIME and ITS data.  Parameters will need to be modified from the defaults, so watch the QIIME space, and we are working on a best practices document in the lab here to help ease the training in this.

All the data are also in a github repository and this is built starting from the database provided and curated by the UNITE team. I love that the data are getting version controlled here so it is easy to look at versions and revisions.

Job: Senior Researcher in Mycology

Senior Researcher in Mycology

The Mycology Section at the Royal Botanic Gardens, Kew invites applications for an appointment as a Senior Researcher in the team. The successful candidate will conduct research on fungal systematics of Ascomycota or Basidiomycota. Candidates with research experience in molecular phylogenetics, molecular ecology, genomics, and areas related to fungal conservation are particularly encouraged to apply. The successful candidate will be expected to develop a strong, extramurally funded research programme investigating fungal systematics, contribute to curation of the collections, disseminate research findings in high impact scientific journals and at conferences, and provide expert taxonomic advice when needed.

Key Qualifications and experience

  • PhD in mycology or related discipline, and appropriate post-doctoral research experience
  • Strong publication record on topics relevant to the position
  • Excellent written & oral skills (communication and presentation of results of research, good publication record)
  • Demonstrable ability to raise external funding to support research

Benefits include 30 days holiday per year, a choice of defined benefit or stakeholder pension, a flexible benefits scheme, as well as a great working environment.

We are committed to equality of opportunity and welcome applications from all sections of the community. We guarantee to interview all disabled applicants who meet the essential criteria for the post. If you wish to be considered as a disabled applicant please make this clear in your application.

CLOSING DATE: 7 December 2012, 12 noon

INTERVIEW DATE: 17 December 2012

Announcing FungiDB 2.1 release

On behalf of the FungiDB development team I am pleased to announce the release of FungiDB 2.1 which includes 39 Fungal genomes from Ascomycota, Basidiomycota, and Mucormycotina (Zygomycota) and 6 genomes of Oomycetes.  This release builds on the 2.0 release from August to include 6 additional species, RNA-Seq from a population of Neurospora strains, growth time points in 3 fungi Coprinopsis, Neurospora, and Rhizopus, and Phytophthora species. The 6 new genomes include Batrachochytrium dendrobatidisCoprinopsis cinereusHistoplasma capsulatumCoccidioides posadasii, Rhizopus delemar (formerly oryzae), and Ustilago maydis.

While the Oomycetes are not true Fungi, as phylogenetically they are in a very distinctly different clade, however we have included them in the database as part of collaboration with Brett Tyler. It may be that some aspects of the convergent evolutionary patterns among these groups can be revealed by having the data in a common system and use of the same tools.

Several human pathogenic and opportunistic fungi are now available in the system including 2 strains of Histoplasma capsulatum and 2 species of Coccidioides, Candida albicans, 2 Cryptococcus gattii strains, C. neoformans var grubii, and 2 C. neoformans var neoformans strains, Fusarium oxysporumAspergillus fumigatus and A. terreus. With the homolog tools available in the FungiDB system, one can map functional data from onto genes in these fungi from related models in the filamentous or yeast species.

Plant pathogens Magnaporthe grisea, Ustilago maydis, Puccinia graminis, and several Fusarium species, and the collection of 6 Oomycetes also provide a platform for comparative genomics among plant pathogens.

Functional annotation data have been imported from model system databases for Aspergillus nidulans, Saccharomyces cerevisiae, and C. albicans.  We also generate predicted GO annotations from InterPro based analyses.

The development team at UC Riverside including Raghu Ramamurthy, past member Daniel Borcherding, and new member Edward Liaw; our collaborators on Oomycete data at Oregon State Brett Tyler and Sucheta Tripathy; and the EuPathDB developers and systems teams that have been essential partners in everything from assisting in data development and software debugging to database administration and web and systems administration.

Future work

Work is likely to begin in the next quarter to curate and support further literature based annotation of gene function in the Cryptococcus species. In addition we plan to expand the supported phenotypic data for Neurospora to support work from the Program Project grant and the phenotyping of the systematic gene deletion collection.

Additional support will be rolled out for more functional and evolutionary genomics data including expanded RNA-Seq datasets, population genetic data sets for several species with cohorts of sequencing of strain populations. We plan to continue to add additional species, with priorities focused on pathogens and model systems, but are interested in the community feedback of specific species that are must include targets in future releases. Please email help[AT] with your suggestions or fill out feedback on the “Contact Us” link on the FungiDB page.

The work in this release was supported by grants from the Burroughs Wellcome Fund and the Alfred P. Sloan Foundation.The Oregon State team is supported by grants from the Agricultural and Food Research Initiative of the  USDA National Institute for Food and Agriculture.  The EuPathDB team is supported by grants from the NIH, Gates Foundation, and Wellcome Trust. Without the direct and indirect support of these funders none of this would have been possible.  All web and computational resources for FungiDB are currently housed at the Univ of Pennsylvania or the University of Georgia, thanks to the many system administrators who keep these services running that have allowed us to make this release.

Postdoc at Rutgers Univ of fungal population genetics of the Boxwood blight pathosystem

A Post-Doctoral Research Associate is sought to contribute to research of the boxwood blight pathosystem. The incumbent will: (1) Design and validate an isothermal molecular diagnostic assay for the boxwood blight fungus Calonectria pseudonaviculata; and (2) Utilize comparative RAD-Seq genome datasets to analyze genetic diversity across a global C. pseudonaviculata sample; and (3) Contribute to the training of student interns. The incumbent will be part of a multistate collaborative research initiative aimed at mitigating the effect of boxwood blight disease in the U.S.

The position will be physically located on the campus of the USDA-ARS Henry A. Wallace Beltsville Agricultural Research Complex in Beltsville, MD, the world’s largest and most diverse agricultural research center, located just 16 miles north of the U.S. capitol city of Washington, DC.

*Qualifications* Ph.D. in plant pathology, mycology, evolutionary biology or related field is required. Candidates must be willing to take a leading role in mentoring student interns, and interacting with other team members working on various components of boxwood blight research efforts. Demonstrated ability to conduct experiments independently, produce quality research output, a strong publication record and excellent verbal communication skills are required.

*Terms of Appointment* Salary is $50,000 per anuum, plus Rutgers University benefits. Funds are guaranteed for one year. An additional year is contigent on performance and funding. Position is available starting immediately, and review of applications will continue until a suitable candidate is found.

Email curriculum vitae, a brief description of research interests and career goals and contact information for three reference to:

Brad Hillman (hillman[AT] & Jo Anne Crouch (joanne.crouch[AT]

Rutgers University is an equal opportunity, affirmative action educator and employer. Applications from women and minorities are encouraged.

Assistant Professor – Bioinformaticist/Computational Biologist at Kansas State University

A tenure track job related to bioinformatics and plants or plant/pathogen interactions is available at Kansas State University. Review of applications will begin on November 23.

The successful candidate is expected to develop an independent, externally funded research program in bioinformatics and computational biology with an emphasis on the genomics of plants, microbes, and/or their interactions.  Kansas State University has faculty with dynamic research programs in the genomics of plants, microbes, their interactions, and related areas, many of whom are engaged with the Integrated Genomics Facility (IGF) and Bioinformatics Center.  The successful candidate is expected to develop a research program that complements these programs, and to collaborate with faculty, staff and students in the department and across campus in the design of experiments and the analysis of experimental data.