Category Archives: ascomycota

Postdoc: Uppsala University on Meiotic Drive in Fungi

POST-DOCTORAL POSITION IN THE EVOLUTION OF MEIOTIC DRIVE

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

Conflicts arising from selfish genetic elements are important drivers for evolutionary change and innovation, and thus of crucial importance for genetic form and function.  The main goal of this project is to study the evolutionary dynamics of meiotic drive in fungi.  The study system is the Spore killers of Podospora anserina, a filamentous ascomycete. The ultimate aim of our research group is to combine large-scale genomic analyses with theoretical and experimental investigations to study the evolutionary dynamics of this meiotic drive system, both on a short and a long evolutionary timescale. This postdoc project will be developed after the interest of the applicant, but should preferably encompass a combination of experimental and genomic aspects. It will be a part of a collaborative effort within our research group.

Applicants should have a PhD in biology/evolutionary biology. Documented skills in molecular phylogenetics and/or population genetics, experimental and genomic work, especially using fungal model systems, is highly valued.

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

Please send your application materials by November 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.

Postdoc: Yeast evolutionary genomics, UW Madison

Chris Hittinger at UW Madison is seeking a highly motivated postdoctoral researcher with an exceptional background in bioinformatics, functional genomics, or evolutionary genomics. Experience analyzing Illumina sequence data, computer programming proficiency, and training in ecological or evolutionary genetics are highly desirable.

The lab has recently received generous funding for yeast
evolutionary genomics research from the National Science
Foundation¢s Dimensions of Biodiversity Program
(http://www.nsf.gov/news/news_summ.jsp?cntn_id=132506)
and the Pew Charitable Trusts
(http://www.pewtrusts.org/en/about/news-room/press-releases/2014/06/24/pew-grants-22-young-scientists-support-for-biomedical-research).

With Antonis Rokas (Vanderbilt) and Cletus P. Kurtzman (USDA), the Y1000+ Project (http://www.nsf.gov/awardsearch/showAward?AWD_ID=1442148&HistoricalAwards=false) seeks to sequence and analyze the to complete genomes of all ~1,000 known species of Saccharomycotina yeasts and determine the genetic basis of their metabolic, ecological, and functional diversification. Yeasts are genetically more diverse than vertebrates and have remarkable metabolic dexterity, but most remain minimally characterized. They compete vigorously for nutrients in every continent and biome and can produce everything from beer to oil. The history of yeasts is recorded in their genome sequences. Now is the time to read it and tell their story!

The Hittinger Lab has diverse funding for other basic and applied research from NSF, DOE, and USDA, but we are specifically expanding our basic research in ecological and evolutionary genomics.

The complete advertisement and application instructions can be found here: http://hittinger.genetics.wisc.edu/Research/Funding/PostDocAd2014.html.

The precise start date is flexible, but candidates should apply by November 30th to receive full consideration.

Sincerely,

Chris Todd Hittinger, Assistant Professor of Genetics
Genome Center of Wisconsin
J. F. Crow Institute for the Study of Evolution
University of Wisconsin-Madison
425-G Henry Mall, 2434 Genetics/Biotechnology Center
Madison, WI 53706-1580
cthittinger@wisc.edu, (608) 890-2586
http://hittinger.genetics.wisc.edu

Some recent fungal and oomycete genome papers

ResearchBlogging.org A few papers covering some published genomes you should definitely read if you have the chance.

  • Youssef NH, Couger MB, Struchtemeyer CG, Liggenstoffer AS, Prade RA, Najar FZ, Atiyeh HK, Wilkins MR, & Elshahed MS (2013). The Genome of the Anaerobic Fungus Orpinomyces sp. Strain C1A Reveals the Unique Evolutionary History of a Remarkable Plant Biomass Degrader. Applied and environmental microbiology, 79 (15), 4620-34 PMID: 23709508
    Describes first published genome of a Neocallimastigomycota fungus that resides within the rumen gut. Cool findings related to lignocellulolytic degradation pathways and basic biology about early diverging fungi which have intact flagellar apparatus.
  • Bushley KE, Raja R, Jaiswal P, Cumbie JS, Nonogaki M, Boyd AE, Owensby CA, Knaus BJ, Elser J, Miller D, Di Y, McPhail KL, & Spatafora JW (2013). The Genome of Tolypocladium inflatum: Evolution, Organization, and Expression of the Cyclosporin Biosynthetic Gene Cluster. PLoS Genetics, 9 (6) PMID: 23818858Describes the genome of a pathogen of beetle larvae (and related to Cordyceps). This fungus is important as it produces the immunosuppresive drug cyclosporin as a secondary metabolite. Analysis of the complete secondary metabolite pathways in the genome help shed light on the origin of this and other secondary metabolite gene clusters.
  • Schardl CL, Young CA, Hesse U, Amyotte SG, Andreeva K, Calie PJ, Fleetwood DJ, Haws DC, Moore N, Oeser B, Panaccione DG, Schweri KK, Voisey CR, Farman ML, Jaromczyk JW, Roe BA, O’Sullivan DM, Scott B, Tudzynski P, An Z, Arnaoudova EG, Bullock CT, Charlton ND, Chen L, Cox M, Dinkins RD, Florea S, Glenn AE, Gordon A, Güldener U, Harris DR, Hollin W, Jaromczyk J, Johnson RD, Khan AK, Leistner E, Leuchtmann A, Li C, Liu J, Liu J, Liu M, Mace W, Machado C, Nagabhyru P, Pan J, Schmid J, Sugawara K, Steiner U, Takach JE, Tanaka E, Webb JS, Wilson EV, Wiseman JL, Yoshida R, & Zeng Z (2013). Plant-symbiotic fungi as chemical engineers: multi-genome analysis of the clavicipitaceae reveals dynamics of alkaloid loci. PLoS Genetics, 9 (2) PMID: 23468653 

    A very rich and detailed paper, this presents a gold mine of complete genome data of 15 species and secondary metabolite profiling. The data include genomes of 10 epichloae fungi that are endophytes of grasses, three Claviceps species (ergot fungi), a morning-glory symbiont and a bamboo pathogen. The analyses of the genes from pathway analyses of the genomes along with profiling alkaloid productions the authors were able to link clusters to products in many cases. This is a rich and useful paper for anyone working in this field of secondary metabolites and sets the standard for a how a biological question can be answered by genome sequencing of a clade of related species.

  • Wicker T, Oberhaensli S, Parlange F, Buchmann JP, Shatalina M, Roffler S, Ben-David R, Doležel J, Simková H, Schulze-Lefert P, Spanu PD, Bruggmann R, Amselem J, Quesneville H, van Themaat EV, Paape T, Shimizu KK, & Keller B (2013). The wheat powdery mildew genome shows the unique evolution of an obligate biotroph. Nature Genetics PMID: 23852167

    Genome of wheat pathogen Blumeria graminis f.sp. tritici.This paper includes an identification and analysis of effector genes and dating the emergence of the pathogen relative the domestication and diversification of wheat.
  • Jiang RH, de Bruijn I, Haas BJ, Belmonte R, Löbach L, Christie J, van den Ackerveken G, Bottin A, Bulone V, Díaz-Moreno SM, Dumas B, Fan L, Gaulin E, Govers F, Grenville-Briggs LJ, Horner NR, Levin JZ, Mammella M, Meijer HJ, Morris P, Nusbaum C, Oome S, Phillips AJ, van Rooyen D, Rzeszutek E, Saraiva M, Secombes CJ, Seidl MF, Snel B, Stassen JH, Sykes S, Tripathy S, van den Berg H, Vega-Arreguin JC, Wawra S, Young SK, Zeng Q, Dieguez-Uribeondo J, Russ C, Tyler BM, & van West P (2013). Distinctive Expansion of Potential Virulence Genes in the Genome of the Oomycete Fish Pathogen Saprolegnia parasitica. PLoS Genetics, 9 (6) PMID: 23785293

    Genome of the fish pathogen and Oomycete Saprolegnia provide additional perspective on this diverse group organisms, evolution of metabolism and host-associated lifestyles.
  • Aylward FO, Burnum-Johnson KE, Tringe SG, Teiling C, Tremmel DM, Moeller JA, Scott JJ, Barry KW, Piehowski PD, Nicora CD, Malfatti SA, Monroe ME, Purvine SO, Goodwin LA, Smith RD, Weinstock GM, Gerardo NM, Suen G, Lipton MS, & Currie CR (2013). Leucoagaricus gongylophorus produces diverse enzymes for the degradation of recalcitrant plant polymers in leaf-cutter ant fungus gardens. Applied and environmental microbiology, 79 (12), 3770-8 PMID: 23584789Genome of the ant farmed fungus Leucoagaricus. This paper presents a draft genome assembly a useful step in understanding the fascinating symbiosis between ants and their cultivated fungi.

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.

Recent animal-associated fungal genome papers

The genomes of five dermatophyte fungi were sequenced and the analyses of their lifestyles presented in a new paper out in mBio in Martinez et al. 2012. The authors were able to identify gene family changes that associate with lifestyle changes including proteases that can degrade keratin suggesting how these species have adapted to obtaining nutrients from an animal host. The continued finding of fungal-specific kinase families in these fungi, extending the observations from previous studies in Coprinopsis and Paracoccidioides on the FunK1 kinase family, makes me hope we will some day get some molecular information on the specificity of these families in addition to these copy number observations.
Another paper published in Genome Research this summer from Emily Troemel‘s lab and the Broad Institute describes the sequencing of two microsporidia species that are natural parasites of Caenorhabditis.The paper reveals some suprising things about Microsporidia evolution including the presence of a clade-specific nucleoside H+ symporter which is only found in bacteria and some eukaryotes and not in any Fungi. The phyletic distribution suggested it was acquired more recently and couple from lateral gene transfer. This acquisition likely helps the microsporidia cells obtain nucleosides from the host since the parasite cannot synthesize these. There is also evidence of evolution of microsporidia-specific secretion signals in the hexokinases which may be a mechanism for delivery of these enzymes into host cells to catalyze rapid growth once inside the host. Many more gems in this paper including phylogenetic placement of the microsporidia from phylogenomic approaches (also see related recent work from Toni Gabaldon‘s lab).

Cordyceps on the brain

Cordyceps militaris (Ryan Kepler)I gave a lecture on animal-fungal symbionts and parasites this week so was doing more reading of recent literature on insect-fungi associations. A couple of quick notes worth sharing.

Ophiocordyceps unilateralis was the parasite of the day last week and includes a description of an interesting recent paper looking at the consistency of the symptoms of zombie ants. The article also mentions Carl Zimmer’s post on the same paper in more detail.

You of course have seen the very cool electronic/online Cordyceps monograph at cordyceps.us from Joey Spatafora’s lab?

The genome of Cordyceps militaris was sequenced by researchers at the Chinese Academy of Sciences. They find a reduced copy numbers of many gene families suggesting to the authors that the specialized ecology of the fungus may have limited the need for expanded gene families. The do find expanded copy numbers of metalloproteases – a finding we have also seen in human and amphibian associated pathogens as well as by the authors who looked at the insect associated fungus Metarhizium. There is also a reduction in cutinases and genes related to degrading plant cell walls similar to findings in the human associated pathogens Coccidioides suggesting similar genomic routes to specializing on an animal host from a generalist. They also found that this fungus is heterothallic based on genomic identification of the MAT1-1 locus. There are several more interesting findings in the paper including expression profiling of fruiting body via RNA-Seq.
Zheng, P., Xia, Y., Xiao, G., Xiong, C., Hu, X., Zhang, S., Zheng, H., Huang, Y., Zhou, Y., Wang, S., Zhao, G., Liu, X., St Leger, R., & Wang, C. (2011). Genome sequence of the insect pathogenic fungus Cordyceps militaris, a valued traditional Chinese medicine Genome Biology, 12 (11) DOI: 10.1186/gb-2011-12-11-r116

Nuclear Pore Complex studied in thermophilic fungus

ResearchBlogging.orgSometimes choosing a hot lover can make all the difference. In this case, choosing a thermophilic fungus was the right eukaryote for the job to purify stable proteins from the nuclear pore complex and test their interactions. Since high temperatures (60C as compared to what its relative Chaetomium globosum prefers, 24C) will denature proteins, this fungus has evolved the ability to still fold up proteins nicely at those high temperatures. Thus at more standard laboratory room temperature or below, these proteins should be really stable and easier to work with.  This manuscript (not OpenAccess sadly) includes the genome sequence of Chaetomium thermophilum sequenced with 454 FLX and XLR at 24X and assembled into 20 scaffolds – (8 chromosomes expected so they say – and I agree – this is quite good).The used the Celera assembler to make this final assembly for those of you taking notes at home on how to assemble your fungal genomes. The genome is available for download at the authors’s site or at GenBank. Their assembly is quite a bit smaller (28.3 Mb) than the related C. globosum (34.9) or Neurospora crassa genome (41Mb – though the authors use the old version and report 39.2; they also say “*based on the published genome (Galagan et al., 2003), although there is a newer assembly of N. crassa available from Broad, the newer assembly is not annotated for protein coding genes yet.” which is kind of weird because there is an annotated version here). I do wonder if the tendency of repeated elements to be collapsed in the assembly process resulted in a smaller assembly or if this really does have a smaller genome and less genes (~7k genes while Neurospora has ~10k).  Also worth noting that several other thermophilic fungi have been public for a while at the JGI too – Thielavia terrestris and Sporotrichum thermophile and our lab and others are investigating the genome content and how some genome properties like transposons have evolved in these lineages.

The thermophilic adaptation of this fungus has lead to stable proteins which can be studied more easily than mesophilic fungi. They have been able to determine how the nucleoporins (Nups) interact because of the biochemical and structural assays that are possible with the more stable protein complexes. This highlights the value of targeting an experimental system that has the properties needed and the simple and straightforward tactics needed to generate and use the genome sequence (the genome is but a minor note in the findings of this paper).  I can only wonder why none of my de novo genome assemblies go together as nicely as this one, but I’m excited to see this work present new insights into the biology of nuclear pore complexes.

Amlacher, S., Sarges, P., Flemming, D., van Noort, V., Kunze, R., Devos, D., Arumugam, M., Bork, P., & Hurt, E. (2011). Insight into Structure and Assembly of the Nuclear Pore Complex by Utilizing the Genome of a Eukaryotic Thermophile Cell, 146 (2), 277-289 DOI: 10.1016/j.cell.2011.06.039

Ncrassa v5 annotation released

The Missing PieceAs 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.

Neurospora annotation update (v5)

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.

FGSC – a key partner in fungal biology research

FGSC logoAn article about the Fungal Genetics Stock Center written by the curators provides some insight into the 50 year history of this resource. It is a great summary of how the stock center has grown over the years and demonstrates how it is an essential aspect of how research on filamentous fungi is possible. The FGSC staff also provide important infrastructure in organization of meetings like the Neurospora and Fungal Genetics meetings and are also active pursuing their own research.  So don’t forget to cite FGSC in  your talks and (very importantly) papers.

McCluskey K, Wiest A, & Plamann M (2010). The Fungal Genetics Stock Center: a repository for 50 years of fungal genetics research. Journal of Biosciences, 35 (1), 119-26 PMID: 20413916