Postdoc: Population genomics and speciation in fungal pathogens

Post-doc position in genomics of introgressions in fungal pathogens

[from EvolDir]

We invite applications for a postdoctoral position in the Research Institute of Horticulture and Seeds. The position is for 1 year starting as soon as January 2016.

The Postdoc will conduct his research in the field of population genomics of secondary contacts and introgression in two fungal pathogens: Venturia inaequalis, an ascomycete responsible of the apple scab, and the Scedosporium apiospermum species complex which is responsible for pulmonary infections in children with cystic fibrosis.

The Postdoc will have to identify genomics regions involved in introgression between divergent populations of Venturia inaequalis and Scedosporium species. Indeed, secondary contacts between divergent genomics pools may favour the creation of new genetic combination of loci involved in pathogenicity. New hybrids should then exhibit hitherto unseen epidemiological properties. The Postdoc will work in a team involved in several projects of genetics or genomics, functional genomics, and evolutionary epidemiology (IRHS – ECOFUN team).

Using resequenced genomes (89 for V. inaequalis and 23 for the Scedosporium species complex), the Postdoc will be in charge of the assembling, genome aligning and SNP calling, prior to population genomics analyses. The Postdoc will have to infer evolutionary histories at the interspecies and species levels for both datasets, identify and characterise genomic regions involved in introgressions. He [or she] will possibly collaborate with all the researchers involved in this project : population geneticists, microbiologists, functional genomicists, phytopathologists.

We are looking for a candidate with a keen interest for population genomics and evolutionary history in structured populations. The candidate must hold a PhD in population genomics with strong skills in bioinformatics (manipulation of NGS data, assembling, demographic inferences). Good written communication skill and ability to work as part of a team are required.

How to apply:
Applicants should submit

  1.  a cover letter describing their research interests and background,
  2.  a detailed CV (including list of publications), and
  3. the contact details of three references to or The cover letter should also include possible starting dates.

Job: Assistant Professor of Microbiology, Clark University

Assistant Professor of Microbiology
Biology Department, Clark University
*Review of applications will begin November 1, 2015*

The Department of Biology at Clark University, Worcester MA ( invites applications for a tenure-track appointment at the rank of Assistant Professor to begin Fall 2016. The successful candidate will have research space in the LEED-certified Lasry Center for Biosciences and is expected to develop an externally-funded research program involving Ph.D., MS, and undergraduate students in Biology or in Biochemistry and Molecular Biology (BCMB). Postdoctoral experience and evidence of external funding success are desired. Promise of teaching excellence at undergraduate and graduate levels is expected. Any area of microbiology will be considered, although preference will be given to those incorporating genome-enabled approaches in their research. The successful candidate will teach microbiology and courses in their area of expertise.

Clark University is especially interested in qualified candidates who can contribute, through their research, teaching, and/or service, to the diversity and excellence of the academic community. We are an affirmative action/equal employment opportunity university and we strongly encourage women and members of minority groups to apply. Applicants should submit a curriculum vitae, statements of research and teaching interests, and three key publications in one electronic file.  Three letters of reference should be submitted electronically by the referees to the Microbiology Search Committee( Letters can also be mailed to the Chair of the Microbiology Search Committee, Department of Biology, Clark University, 950 Main St, Worcester, MA 01610-1477.  E-mail inquiries may be directed to Justin Thackeray (  Review of applications will begin November 1, 2015.



A two-year postdoctoral position is available in the research group of professor Hanna Johannesson, at the Evolutionary Biology Centre (EBC), Uppsala University.

State-of-the art sequencing technology has opened opportunities to comprehensively investigate structural variants (SVs: such as deletions, insertions, duplications, inversions and translocations) in genomes of natural populations. Such SVs are often associated with gene expression changes and may be of large phenotypic effects. The main goal of this postdoc project is to use sequencing data (e.g. PacBio long read sequence data) for the model system Neurospora, emerging from our most recent sequencing projects, to increase our understanding of the impact of SVs for the evolution of eukaryote genomes. In particular, we can use the well-established phylogenetic framework of Neurospora to study the accumulation of SVs over evolutionary time, and connect them to characters such as genome size expansion/retraction, mating-system transition and speciation. By combining comparative genomic, phylogenetic and population genetic analyses, the evolutionary significance of SVs in natural populations can be traced. The project will be developed after the interest of the applicant, but should encompass a perspective of genome evolution addressed by bioinformatic/genomic approaches.

Applicants should have a PhD in biology/evolutionary biology and have documented experience in bioinformatics. Documented skills in comparative genomics, molecular phylogenetics and/or population genetics is highly valued.

Start date is flexible, ideally January 1, 2016. The position can be extended for up to two more years.

Please send your application materials by September 25 to The application shall include:
1) a cover letter stating research interests,
2) a CV, including publication record,
3) a short (1-2 page) description of research accomplishments, and
4) name and contact information for three references.

Please feel free to contact me at the above listed e-mail with questions.

Remembering fungal genetics legends

The passing of two members of the fungal genetics community has saddened many of us but also brought smiles in remembering all the wonderful things they brought to the community. So sending this out to ask you to take some time to remember Rowland Davis  and Hans Van Etten who have passed away in the past month.

Rowland Davis, an eminent figure in the fungal genetics community, died on 18 July at his home in California. Rowland was 81 years old. He made many contributions to the community as a researcher, as an editor and reviewer, as a mentor, and as a valuable source of wise counsel, always delivered with intellect and humor. As a graduate student at Harvard University he developed an interest in microbial genetics and began to work with Neurospora. As a postdoc at Caltech with Herschel Mitchell he started his lifelong involvement in biochemical genetics. His early years as a Professor were at the University of Michigan (1960-1975). He subsequently moved to the Department of Molecular Biology and Biochemistry at the University of California, Irvine and became Emeritus in 2005. Rowland’s graduate research focused on heterokaryosis. As a young assistant professor he began to investigate the pyrimidine biosynthetic pathway, discovering that the pyr-3 gene encoded two catalytic activities – one of the first examples of “one gene, two enzymes.” He then went on to show that carbamyl phosphate, required for two different metabolic pathways, was synthesized by the enzyme products two different genes, each in a different organelle. This was a foundational discovery in understanding the role of compartmentation in the regulation of metabolism. He pursued this with seminal studies of arginine metabolism, showing that 99% of cellular arginine is sequestered in vacuoles, thereby avoiding wasteful catabolism by enzymes in the cytosol. In the latter half of Rowland’s career, he investigated the enzymes responsible for synthesizing polyamines. His lab group identified the genes that encoded these enzymes, discovered novel mechanisms by which polyamine levels are controlled, and described the systems by which polyamines were transported across the cell membrane. Rowland was a key player in the decision to open the Neurospora Information Conference to the larger Fungal Genetics Community. He served this community in many ways. He was a supportive presence on NSF and NIH review panels and a long-term Editor for Genetics. He wrote the definitive “methods guide” for Neurospora (Davis and De Serres, Methods in Enzymology, 1970). The breadth of his knowledge is illustrated by his book, Neurospora, Contributions of a Model Organism (Oxford, 2000). In his retirement Rowland pursued his life-long interest in writing by publishing two novels (co-authored with his wife Margot [Norris] Davis) and a collection of short stories. Rowland was always available to help people. Young and not-so-young investigators went to him to discuss research ideas, grant proposals, and manuscripts. He was a superb teacher at all levels, delivering flawless lectures to huge undergraduate classes and providing hands-on instruction to graduate students. He will be greatly missed. — Barry Bowman, Neurospora Policy Committee

Hans Van Etten finished his career at University of Arizona and trained so many scientists and students. I have heard some great stories from student who took his classes, or where he sat on their committee, those who trained in his lab, or collaborated with him on research all remark on what a positive and enthusiastic person for the science and for the people he worked with.  A longer remembrance from those who can tell even better stories will be circulated soon I am sure but I wanted to just post something now to note his passing.




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

Meeting: Exploring the genomic complexity and diversity of eukaryotes

Registration for the 2015 EMBO meetingExploring the genomic complexity and diversity of eukaryotes is open. The meeting is held from 17 – 22  of October 2015 in Sant Feliu de Guixols, Spain. This is a beautiful venue and a It should be an excellent opportunity to discuss and hear about work on genome evolution, pathogenesis, and complexity in fungi and protists.

Unicellular eukaryotes comprise the overwhelming majority of eukaryotic diversity, pervading all branches of the eukaryotic tree of life. Recent sequencing efforts have significantly increased the number and diversity of unicellular eukaryotes for which genomic/cellular/proteomic data is available. Metagenomics, transcriptomics, single- cell genomics, and other ‘omics’ approaches are being applied to unravel the ecology, physiology, diversity and evolution of microbial eukaryotes and are shedding light on fundamental questions such as the origin of the eukaryotic cell, endosymbiosis, the origin of multicellularity and the evolution of major cellular processes in eukaryotes.

Job: Montana State University Assist/Assoc/Full Environmental Microbiology

The Department of Microbiology & Immunology at Montana State University- Bozeman ( invites candidates with a PhD in Microbiology or related area to apply for a full-time, nine-month tenure-track position in Environmental Microbiology (Assistant/Associate/Full Professor) beginning January 2016. The successful candidate will have postdoctoral and/or Assistant Professor experience and will be responsible for developing/growing an extramurally funded, nationally recognized research program within the broad field of environmental microbiology. Scientists that use interdisciplinary approaches that include biochemical, cellular, physiological, ecological, genomic, and/or molecular tools to investigate areas including microbe-environment interactions, microbe biology/ecology, and/or microbial engineering are encouraged to apply. We are seeking an individual with a research program to complement and expand expertise in the Department. The Department, which is nationally recognized for its strengths in both environmental and human-related microbiology, includes state-of-the-art core facilities both in the department and campus research centers. The Department strives to maintain a diverse faculty group, and women and underrepresented minorities are encouraged to apply. The position includes a competitive institutional salary (9-months) and generous start- up package. While a funded research program is preferred, it is not required. Full details about the position and application procedure are available at

Potential candidates are encouraged to contact the Search Committee Chairperson, Dr. Matthew Fields, ( for more details. Screening will begin September 9th, 2015 and will continue until a suitable applicant is hired. ADA/EO/AA/Veterans Preference.

PDF of the advertisement: Faculty Position in Microbiology at MSU

Research Microbiologist at USDA-ARS (UC Davis)


Research Microbiologist, USDA-ARS

A new Research Microbiologist position is available with the USDA-ARS located on the campus of the University of California, Davis.  The successful candidate will conduct independent research to discover and develop novel fumigation independent approaches to control soil-borne pathogens.  This work will focus on developing an understanding of the ecological, structural and functional aspects of the soil-borne microbial communities shown to suppress target pathogens.  Applicants with a strong computational biology/metagenomics background are encouraged to apply.  We would greatly appreciate it if you would forward this announcement to prospective candidate(s) for their consideration.  The position announcement can be found at

This is a competitive, permanent appointment and U.S. citizenship is required.  For further details about this position and how to apply, go to the vacancy on-line at:  vacancy announcement number ARS-D15W-0129 (all US citizens) or ARS-M15W-0128 (Current federal employees).  For questions contact: Dr. Daniel Kluepfel, Research Leader at

AAAS and NSF looking for female US faculty researchers in STEM to attend Gender Summit 6

[Deadline is in 3 weeks, via Victoria McGovern]

The American Association for the Advancement of Science (AAAS), with support and funding from the National Science Foundation, is currently seeking U.S. female faculty researchers in Science, Technology, Engineering and Mathematics ( STEM) who are interested in attending the Gender Summit 6 (GS6), in Seoul, South Korea, on August 24-31, 2015.

AAAS is releasing travel awards to US female faculty researchers to attend GS6, with the goal of creating new international networks and initiating plans for future collaborations with foreign counterparts in STEM research.

If you are interested in creating and sustaining an International Research Collaboration network, submit your application today at the following link:

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.