POST-DOCTORAL POSITION IN EUKARYOTE GENOME EVOLUTION
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 Hanna.Johannesson@ebc.uu.se. 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.
The 2014 Neurospora conference at Asilomar conference grounds in Pacific Grove, CA will be held March 6-9, 2014. Registration is now open and a large proportion of the talks will be chosen from the abstracts. Deadline for registration is Dec 31, 2013 but sign up soon to get your preferred housing.
The Neurospora satellite meeting will be held just prior to the 2014 European Fungal Genetics conference in Seville, Spain. Additional the 11th International Aspergillus Meeting (Asperfest), and meetings for each of Fusarium, Dothideomycete, Colletotrichum and Mycorrhizal Genomics Initiative will be held just prior to or after the conference. Sign up soon (before 16-Decemeber) to receive reduced participation fees.
Postdoctoral research fellowship in evolutionary genomics at Uppsala University, Sweden
A postdoctoral fellowhip is available at the Department of Evolutionary Biology at Uppsala University. The postdoc is in the research-group of Dr. Hanna Johannesson, and will focus on testing general evolutionary paradigms in the filamentous ascomycete model system Neurospora. The fellowhip is for one year, with a high likelihood of extension another year.
This postdoc project can be developed after the interest of the applicant, but should fit in to the main interest of the reseach group (http://www.ebc.uu.se/Research/IEG/evbiol/research/Johannesson/publications/)
Research areas include sex chromosome evolution, mating system evolution, local adaptation, molecular evolution and speciation.
The Program in Evolutionary Biology
(http://www.egs.uu.se/evbiol/index.html) is situated in the Evolutionary Biology Centre in central Uppsala. The working atmosphere is international with English as working language. The Evolutionary Biology Centre constitutes an exciting arena for multidisciplinary research in evolutionary biology in a broad sense, with research programs including ecology, systematics, genetics, genomics, and developmental biology. Uppsala University is the oldest university in Scandinavia and the city of Uppsala is a vibrant student town with beautiful surroundings conveniently situated 40 minutes with train from Stockholm.
Required qualifications for applicants are 1) a PhD in Biology,
Genetics, Evolutionary Biology, Microbiology, or related field, 2) experience in one or several of the following areas: molecular biology, bioinformatics, comparative genomics, population genetics, experimental evolution, evolutionary biology, genetics, microbiology, mycology, and 3) demonstrated verbal and written communication skills in English.
To apply, send your CV, including contact information for two references, and a cover letter stating your research interest to: Dr Hanna Johannesson, firstname.lastname@example.org.
[From Kevin McCluskey at the FGSC]
I am pleased to send this invitation to the Neurospora Luncheon which will be held Wednesday at the Fungal Genetics Conference. It will take place in the Chapel and box lunches will be available. This luncheon is for everyone who works with Neurospora or who wants to work with Neurospora. Please come and hear what is going on and share your opinions. It is especially important that Post-docs and students come to these meetings.
Neurospora Business Meeting
26th FUNGAL GENETICS CONFERENCE
Wednesday, March 16, 12:15 pm – 2:00+ pm
12:15 pm Announcement of Perkins Award recipients for 2011 12:25 pm FGSC and Neurospora meeting update- Kevin McCluskey 12:30 pm Fungal Genetics Reports update- Matt Sachs 12:35 pm Neurospora e-news- Kathy Borkovich 12:40 pm Update on Neurospora gene set, James Galagan - discussion 1:00 pm Fungal Genome Database- Jason Stajich - discussion 1:15 pm Update on Systems Biology grant- Kathy Borkovich and Steve Osmani, James Galagan, Matt Sachs 1:30 pm Update on QTL grant- John Taylor and Louise Glass 1:40 pm Update on bioenergy grant- Louise Glass 1:50 pm Announcement for "Neurospora 2012" - March 8 - 11, 2012 Scientific Program Chairs: Stephan Seiler and Matt Sachs Further discussion - topics from the floor.
As an update to previous post, the N. crassa annotation has been updated to version 5 on the Broad Institute website. Previously the data was not yet available for this update, but as of 8-Mar-2011 it is. The assembly hasn’t changed but the annotation is updated and includes some fixes to improperly renamed locus names. On the N. crassa genome site you can see files with the history of loci through this to determine if a locus name was improperly changed in the past. This should be rectified in the currently released annotation, and definitely encourage you to take it for a spin and report back to the Broad Institute if you have any questions.
Here is a message from the Broad Institute about a gene annotation update that was made recently in response to an issue that was revealed in the June 2010 release. This new version is called V5 and should be on its way to GenBank.
Dear Neurospora scientists, Recently we discovered an issue with the way locus tags were assigned to our most recent Neurospora gene set, released publicly on the Broad website in June of 2010. Many genes in this gene set have mismatched locus numbers compared to the same genes released in February 2010. Adding to the confusion, both releases were labeled version 4. To remedy this we have recalled the June locus numbers and released a new, version 5 gene set. Genes in this set have been numbered to preserve historical locus numbers (back to the original genbank release) as much as possible. Folks who call their favorite genes by their v1, v2 or v3 numbers can search for them on our web page, which will map them to v5 automatically and accurately. The same will work for most v4 numbers. Unfortunately, 863 genes have different locus tags in the two v4 releases. If you search for one of them, you will get two hits - the v5 gene that the February edition mapped to, and the v5 gene that the June edition mapped to. Two examples to clarify: A. Suppose you search for NCU11713.4 on our web page. This query will retrieve two genes, NCU11688.5 and NCU11713.5. The gene which in the February release was called NCU11713.4 is the same as NCU11688.5, while the gene labeled NCU11713.4 in June is the same as NCU11713.5. B. Searching for NCU11324.4 yields but one hit because that gene, like most genes, was consistently numbered between the two releases labeled 4. If you are not sure when you downloaded your genes, the following may help. If you see any of these locus numbers in your gene set: NCU00129.4, NCU00457.4, NCU00499.4, NCU00556.4, NCU00627.4, NCU00685.4, NCU00768.4, NCU00856.4, NCU00986.4, NCU01064.4, NCU01065.4, NCU01282.4, NCU01299.4, NCU01300.4, NCU01483.4, NCU01559.4, NCU01560.4, NCU01610.4, NCU01611.4, NCU01664.4, NCU01665.4, NCU01871.4, NCU01903.4, NCU02200.4, NCU02259.4, NCU02666.4, NCU02758.4, NCU02837.4, NCU02998.4, NCU03047.4, NCU03206.4, NCU03773.4, NCU04239.4, NCU04240.4, NCU04518.4, NCU04519.4, NCU04710.4, NCU04711.4, NCU05275.4, NCU05512.4, NCU05776.4, NCU06013.4, NCU06370.4, NCU06732.4, NCU07107.4, NCU07259.4, NCU07260.4, NCU07301.4, NCU07405.4, NCU07856.4, NCU07857.4, NCU08090.4, NCU08182.4, NCU08323.4, NCU08332.4, NCU09085.4, NCU09256.4, NCU09257.4, NCU09998.4, NCU10166.4, NCU10574.4, NCU11040.4, NCU11240.4, NCU11253.4, NCU11376.4, NCU11390.4, NCU11393.4 then your genes are from the February 2010 gene set. However, if you see NCU00082.4, NCU00083.4, NCU00084.4, NCU00085.4, NCU00516.4, NCU01819.4, NCU04299.4, NCU04300.4, NCU04301.4, NCU04302.4, NCU04303.4, NCU04304.4, NCU04305.4, NCU05000.4, NCU05111.4, NCU05112.4, NCU05113.4, NCU05114.4, NCU05115.4, NCU05116.4, NCU05448.4, NCU05452.4, NCU06667.4, NCU07323.4, NCU09066.4, NCU10179.4, NCU10301.4, NCU10379.4, NCU10383.4, NCU10753.4, NCU10866.4, NCU10914.4, NCU11068.4, NCU11182.4, NCU12157.4, NCU12158.4, NCU12159.4, NCU12160.4, NCU12161.4, NCU12162.4, NCU12163.4, NCU12164.4, NCU12165.4, NCU12166.4, NCU12167.4, NCU12168.4, NCU12169.4, NCU12170.4, NCU12171.4, NCU12172.4, NCU12173.4, NCU12174.4, NCU12175.4, NCU12176.4, NCU12177.4, NCU12178.4, NCU12179.4, NCU12180.4, NCU12181.4, NCU12182.4, NCU12183.4, NCU12184.4, NCU12185.4, NCU12186.4, NCU12187.4, NCU12188.4 then your genes are from the June 2010 release. Attached please find five mapping tables which can be used to migrate locus numbers from any of the previous releases to the latest version 5 locus tags (linked below). We apologize for any confusion this may cause. Love, The Broad Institute
I’ve also uploaded the locus update files which maps between versions of the annotation.
I spy a picture of Neurospora growing on the cover of Genetics this month. The cover highlights the results from the work of the lab of Luis Corrochano who works on light regulation in a variety of systems like Neurospora and Phycomyces. This work describes their work on the fluffy gene which regulates conidiation (production of conidia or asexual spores). They show that an important interplay between an inducer of light response, the White Collar Complex (WCC), and the FLD protein on fluffy. The data from indicate hat FLD represses fluffy as a response to dark but that this repression is removed in response to light through the action of WCC.
Olmedo, M., Ruger-Herreros, C., & Corrochano, L. (2009). Regulation by Blue Light of the fluffy Gene Encoding a Major Regulator of Conidiation in Neurospora crassa Genetics, 184 (3), 651-658 DOI: 10.1534/genetics.109.109975