Nominate genomes for F1000 project

I posted over in the 1000 Fungal genomes blog, as well as a post by Francis Martin, about details for nominating your fungus for the F1000 project. You have to be able to supply DNA and RNA and justify the project under DOE/JGI mission, but we are looking for contributors to help fill in all the gaps in the diversity of sampled fungal genomes.

There might even be a way to use these projects to support mycology or genomics classes. For example one part of a class could work on isolation and growth of the fungi, obtaining RNA and DNA and sending this off to to the sequencing center. The rest of the class would be spent analyzing existing fungal genomes. In the subsequent year the nominated genome would likely be completed and the next year’s class could work on processing it.

2012 Fungal Genomes: a review of mycological genomic accomplishments

2012 was certainly a banner year in genome sequence production and publications. The cost of generating the data keeps dropping and the automation for assembly and annotation continues to improve making it possible for a range of groups to publish genomes.

I made a NCBI PubMed Collection of these here Fungal Genomes 2012

Some notable fungal genome publications include

There were also several new insights into the evolution of wood decay fungi derived from new genomes of basidiomycete fungi. This includes

(Now I might have missed a few in my attempt to get this done before holidays overtake me – if so, please post comments or tweets and I’ll be sure to amend the list on pubmed and here.)

A new trend for fungal genome papers can be seen now in the Genome Announcements of Eukaryotic Cell which aim to get the genome data out quickly with a citateable reference. These are short descriptions which I expect will become more popular ways to insure data made public can also be cited. I only counted about 5 published in 2012 but I expect to see a lot more of these in the 2013 either at EC or other journals. I’m sure there will still be some tension between providers making data public as soon as possible and the sponsoring authors’ desire to have first crack at analyzing and publish interpretations and comparison of the genome(s). The bacterial community has been doing this for Genome Reports in the SIGS journal and the Journal of Bacteriology so will see what happens as these small eukaryotic genomes become even easier to produce.

I look forward to exciting year with more of the 1000 Fungal genomes and other JGI  projects start to roll out more genomes.  I also predict there will be many more resequencing datasets published as functional and population genomics. It will also probably be a countdown for what are the last Sanger sequenced genomes and how the many flavors of next generation sequencing will be optimized for generation.  I am hopeful work on automation of annotation and comparisons will be even easier for more people to use and that we start to provide a shared repository of gene predictions.  I’ve just launched the latter and look forward to engaging more people to contribute to this.

Abstract deadlines for Fungal genetics and satellite meetings

Don’t be late! – December 12 is the abstract submission deadline for the Fungal Genetics meeting in Asilomar from March 12-17, 2013.  Submit your abstract so we can hear about your awesome fungal genetics research.

Dec 12 is also the deadline for satellite meetings including organism specific focus meetings. The 10th Aspergillus meeting, 6th Ustilago meeting, and the Fusarium workshop will take place on the days before the FGC meeting. There are opportunities to present talks and posters at this meeting and many openings for more abstract submissions, so if you’d like the chance to give a talk on your work in one of these species, this is a great opportunity.  You need to register separately for the satellite meetings – go here to register and submit abstracts.

The Oomycete Molecular Genetics Annual meeting will also take place in the days before FGC (March 10-12) but the registration deadline isn’t until end of January.

Junior Professorship for Biochemistry and Biotechnology of Fungi

Goethe-University Frankfurt, Department of Biosciences,

Institute of Molecular Biosciences invites applications for the following position: JUnior Professorship (W1) for Biochemistry and Biotechnology of Fungi 

We are seeking a scientist with research activities complementary to the activities in the LOEWE priority program “Integrated Fungal Research”. The newly established priority program brings together scientists from four hessian universities and a Leibnitz Institute, all working in different areas of mycology ranging from fungal biodiversity, molecular biology and genomics to applied aspects of fungal biotechnology and biochemistry.  Possible areas of research could be biochemistry and biotechnology of ribosomal peptides, alkaloids, unusual amino acids, or sugars in fungi, the production of biotechnologically relevant products in fungal model organisms (like Aspergillus, Penicillium, Yarrowia or Rhodotorula), or fungal cultivation technologies.  Candidates must have an excellent publication track record. The successful applicant is expected to engage in crossdisciplinary research activities, as well as to compete for research funding actively. Willingness to participate in the LOEWE priority program “Integrated Fungal Research” is expected.

The position comes with adequate administrative and teaching obligations within the Institute of Molecular Biosciences.  The junior professor will be hired for a period of three years.  An extension for another three years can be granted subject to a successful evaluation. The designated salary for the position is based on “W1” on the German university scale. For further information regarding the general conditions for professorship appointments, please see: http://www.uni-frankfurt.de/aktuelles/ausschreibung/professuren/index.html.  Qualified scientists are invited to submit their applications accompanied by the usual information, such as CV, degrees and certificates, list of publications, details about teaching and international experience, information on grant applications and a concept for future research and teaching within three weeks of publication of this announcement. Please send applications preferentially by E-Mail in a single PDF file to the Dean of the Faculty of Biosciences,

Prof. Dr. Anna Starzinski-Powitz, Johann Wolfgang Goethe-University Frankfurt, Maxvon- Laue-Straße 9, 60438 Frankfurt/M. Germany, E-Mail dekanat1[AT]@bio.uni-frankfurt.de.

Details regarding the LOEWE priority program “Integrative Fungal Research” can be obtained from Prof. Dr. Helge B. Bode (h.bode[AT]bio.uni-frankfurt.de) or Prof. Dr. Marco Thines (thines[AT]bio.uni-frankfurt.de).

Postdoctoral Researcher, Boxwood Blight

We are seeking applications for a Post-Doctoral Research Associate to study the interaction between boxwood plants and the boxwood blight fungus Calonectria pseudonaviculata (syn. Cylindrocladium buxicola) using microscopic bio-imaging and transcriptomic investigations.

The incumbent will generate strains of fluorescent protein-labeled C. pseudonaviculata and inoculate susceptible and non-susceptible boxwood plants to evaluate the infection process and fungal development in planta. Available bio-imaging platforms will include digital light microscopy, fluorescence microscopy, confocal laser scanning microscopy, variable pressure and low temperature scanning electron microscopy (SEM), and the Oxford X-ray Diffraction System for qualitative and quantitative identification of chemical elements. The incumbent will simultaneously generate RNA-Seq data from the host/pathogen interaction to develop hypotheses related to the colonization of hosts by this pathogen.

The position is based 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, D.C. The incumbent will work under the guidance of Dr. Jo Anne Crouch at the Systematic Mycology & Microbiology Laboratories and in collaboration with Dr. Gary Bauchan at the on-site core Electron & Confocal Microscopy Unit. The Crouch lab is part of a multidisciplinary, multi-state collaboration between the USDA-ARS, the U.S. National Arboretum, the IR-4 Project, and eleven university and experiment station research groups, working in cooperation with the nursery industry in an integrated, coordinated effort toward the common goal of understanding and mitigating boxwood blight disease.
* Qualifications *
This position requires a recent (within 4 years) Ph.D. in plant pathology, microbiology, mycology, molecular biology or a closely related field that has equipped the applicant with the necessary knowledge, skills and abilities to perform the duties and responsibilities of the position. Knowledge of fungal transformation, advanced microscopy techniques, biostatistics and transcriptome analysis are desirable. Demonstrated ability to conduct experiments independently, produce quality research output and a strong publication record are required.

* Terms of Appointment and Application Instructions *
This is a two-year appointment, at the GS-11 level (starting salary $62,467).

Citizenship restrictions apply. Eligible Foreign Nationals must meet both Appropriations Law and Immigration Law requirements found under “Foreign Nationals Eligible for Federal Employment” at http://www.afm.ars.usda.gov/hrd/EmployForeignNationals/index.htm.

Visit the following website for instructions on how to apply for the position: https://www.usajobs.gov/GetJob/ViewDetails/331850000.

Informal inquiries are welcome: Dr. Jo Anne Crouch, joanne.crouch[AT]ars.usda.gov
ARS is an equal opportunity provider and employer. Women and minorities are encouraged to apply.

Review of applications will begin immediately, and continue until a suitable candidate is found.