Category Archives: fungi

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.

FungiDB 2.3 released with 52 genomes

The latest release of FungiDB (2.3) is now live and includes 52 genomes, 11 of which are new for this release. This was a longer than expected release cycle due to reintegration with the EuPathDB software team. Programmers Raghu Ramamurthy and Edward Liaw at UC Riverside did nearly all the Fungal specific work, collaborating closely with the EuPathDB team who provided many site-specific corrections and assistance in running the workflow. This is a joint collaborative project between the UCR,Oregon State (FungiDB) and U Penn, Univ of Georgia (EuPathDB) and the work in this release was funded through grants from the Burroughs Welcome Fund, the Alfred P. Sloan Foundation, and the USDA-NIFA.

An announcement for FungiDB 2.3 is here and included below.

New genomes included in this release include

Botrytis cinerea
Sclerotinia sclerotiorum
Aspergillus carbonarius
Neosartorya fischeri
Trichoderma reesei
Schizosaccharomyces japonicus
Schizosaccharomyces octosporus
Phanerochaete chrysosporium
Sporisorium reilianum
Malassezia globosum
Mucor circinelloides f. lusitanicus
Mitochondrial genomes were added for the following organisms

Aspergillus fumigatus
Neurospora crassa
Saccharomyces cerevisiae
Schizosaccharomyces japonicus
Schizosaccharomyces octosporus
New genomics data available in this release include additional RNA-Seq experiments for Coprinopsis cinerea. High Throughput SNP (HTS) discovery module have been addded for Aspergillus fumigatus and a population of 23 strains from JCVI.

Data fixes and update

Updated in this release include new versions of annotation for

Aspergillus fumigatus – s03-m02-r18 from AspGD
Aspergillus nidulans – s09-m05-r03 from AspGD
Fusarium oxysporum f. sp. lycopersici – correcting some annotation problems in Broad v2
Neurospora discreta – correcting some annotation problems from JGI
Saccharomyces cerevisiae version from 2012-11-20
The current annotation for N. crassa is still v10 release and does not reflect the V12 release made March 2013. The updated version will be available in the 3.0 release of FungiDB.

Corrections

The Coccidioides RNA-Seq data in the previous release had flipped the labels of the spherule and mycelium results, this has been corrected.

Errors in previous loading of gene product information for P. sojae had left many genes without sufficient product information and description. This has been corrected.

Synteny results between several species were not properly loaded in the previous release. This has been corrected.

Data summary tables of genomes and gene metrics have been updated to reflect the current state of the database.

Known errors

Alternative splicing and starting/ending non-coding exons may not be properly represented in GBrowse and in the GFF files available for download.

Basidiobolus! – genus of the month at ATCC

ATCC sent out this email with the Genus of the month as Basidiobolus. It is worth noting they call out B. ranarum as inhabitant of bat and rodent guts but it is mainly known (and named) for being associated with frogs (hence the ‘rana’). It has some quite cool biology, it grows dimorphically as a yeast or hyphae, and is reported to have a large genome (Henk and Fisher PLoS One 2012).
Note that the genome and transcriptome of B. meristosporus is being sequenced as part of the 1000 Fungal genomes project from samples Andrii Gryganski prepared. Don’t forget that YOU can propose genomes to this project by logging in here and submitting a proposed species in a family that is not sufficiently sampled (2 per Family).

The info below is from ATCC®. I couldn’t find a link to the on their site so I am copying the email text in.

There is nothing more fascinating than when a microbial species begins popping up in the literature as a true pathogen. Basidiobolus ranarum, which typically inhabits the guts of bats and small rodents, has been recently tagged as an emerging human pathogen that may have previously been unrecognized.1

       B. ranarum was first added to the CDC’s Morbidity and Mortality Weekly Report (MMWR)1 in 1999 after 6 immunocompetent individuals tested positive for gastrointestinal basidiobolomycosis over a 5-year period. The most interesting aspect of this study, however, was the fact that each patient was originally misdiagnosed with some other intestinal ailment, ranging from diverticulitis to cancer.

While many of the Zygomycetes, including Basidiobolus, have been implicated in subcutaneous human diseases, it is still relatively uncommon for Basidiobolus to colonize the human intestine. This new development piqued the interest of several researchers at the Mayo Clinic in Scottsdale, Arizona, a region of the U.S. where the majority of such cases have been reported.  Following an in-depth analysis of all known case records, they discovered a total of 44 cases of gastrointestinal basidiobolomycosis worldwide; 19 of which occurred in the southwestern U.S., 11 in Saudi Arabia, and 14 in other arid regions of the globe.2

Symptoms displayed in each case were similar, with complaints ranging from abdominal distention and pain to a palpable abdominal mass. Of particular interest was a patient originally treated for Clostridium difficile colitis. This patient underwent several surgeries and treatment with oral vancomycin before a stool fungal culture revealed the presence of B. ranarum. While this patient was successfully treated with a 3-month course of voriconazole, repeated at 1-year follow-up, the investigators cautioned that antifungal resistance may pose a problem in the future. Earlier work performed by the same group revealed uniform resistance to amphotericin B and flucytosine in four  B. ranarum isolates, as well as mixed resistance to several other azoles.2

The source of B. ranarum infection leading to gastrointestinal disease is still not understood, but the fecal-oral route has been suggested. Pathologists and clinicians should be aware of this potential new threat, and additional work to understand the pathogenesis and antifungal susceptibility/resistance of B. ranarum should be an on-going effort among the research and medical communities.

ATCC® Basidiobolus Strains
Want to learn more about ATCC Basidiobolus strains available from ATCC? View a list of Basidiobolus spp. online.

References

1. Centers for Disease Control and Prevention (CDC). MMWR: Gastrointestinal Basidiobolomycosis – Arizona, 1994-1999. August 20, 1999.

2. Vikram, et al. Emergence of Gastrointestinal Basidiobolomycosis in the United States, with a Review of Worldwide Cases. Clinical Infectious Diseases Advance Access published on March 22, 2012.

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.

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]fungidb.org with your suggestions or fill out feedback on the “Contact Us” link on the FungiDB page.

Support
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.

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).

Vote for some Fungi in Open Tree of Life project

Consider voting for for some Fungi in the Open Tree of Life project. Pathogens, model systems, and any charismatic (or non-charismatic if like) organisms can be proposed to be included in a tree that will serve as teaching and communicating the tree of life.

[From Laura Katz]
Dear Colleagues,

We need your help creating a list of exemplar species from across the tree of life!

As our team works to build an open tree of life for the systematics community, we are also working on an educational version of the tree for the public. Our goal is to depict about 200 better-known (i.e. phylogenetically or otherwise important in some way (pathogen,
food source, etc.)) species from all three domains of life. The intended audience of this effort includes educators, students, and the public in general.

Please follow the link below to vote for your 5 best exemplars… https://www.surveymonkey.com/s/favorite_species_for_tree_of_life

And please join the conversation through our website, email (opentreeoflife@googlegroups.com), or twitter (@opentreeoflife).

Thank you!

lkatz@smith.edu

Few fungi+host papers

Three papers on some cool fungi that interact with hosts and I recommend them for a good read.

One is coverage of by Ed Yong on rice blast (Magnaporthae orzyae) on paper from Nick Talbot and Gero Steinberg‘s lab on appressorium development in Science this week.

A paper from my lab on role of an expansion of copy number of a chitin-binding domain in the amphibian pathogen B. dendrobatidis.

New Scientist also provides a nice summary of tripartite symbiosis paper on Metarhizium, insects, and plants from Mike Bidochka’s lab.