Gerry Fink wins Gruber Genetics prize

Congrats are in order to Gerry Fink on winning the 2010 Gruber Foundation award for his work on the genetics of yeast and Arabidopsis. He has been a pioneer in the field developing molecular biology approaches and leading the field in study of genetics.  See the press release announcement for more details on the award – I got word of this thanks to the Genetics Society of America email.

Gerry’s had profound impact on the field of genetics and biology it is wonderful to see this awarded to him. Personally, he’s subtly influenced several things that have benefited my career : helping get the fungal genome initiative started, as the mentor of my grad advisor, serving on advisory boards like the one for my postdoc fellowship, and his leadership and ingenuity producing new tools and approaches to understanding genetics and fungal biology.  Well deserved award and it is great to see recognition of a stellar geneticist.

A mushroom on the cover

I’ll indulge a bit here to happily to point to the cover of this week’s PNAS with an image of Coprinopsis cinerea mushrooms fruiting referring to our article on the genome sequence of this important model fungus.  You should also enjoy the commentary article from John Taylor and Chris Ellison that provides a summary of some of the high points in the paper.

Coprinopsis cover

Stajich, J., Wilke, S., Ahren, D., Au, C., Birren, B., Borodovsky, M., Burns, C., Canback, B., Casselton, L., Cheng, C., Deng, J., Dietrich, F., Fargo, D., Farman, M., Gathman, A., Goldberg, J., Guigo, R., Hoegger, P., Hooker, J., Huggins, A., James, T., Kamada, T., Kilaru, S., Kodira, C., Kues, U., Kupfer, D., Kwan, H., Lomsadze, A., Li, W., Lilly, W., Ma, L., Mackey, A., Manning, G., Martin, F., Muraguchi, H., Natvig, D., Palmerini, H., Ramesh, M., Rehmeyer, C., Roe, B., Shenoy, N., Stanke, M., Ter-Hovhannisyan, V., Tunlid, A., Velagapudi, R., Vision, T., Zeng, Q., Zolan, M., & Pukkila, P. (2010). Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus) Proceedings of the National Academy of Sciences, 107 (26), 11889-11894 DOI: 10.1073/pnas.1003391107

The roundup of twittered updates for 2010-06-28

  • SREB, a GATA TF directs disparate fates in B. dermatitidis including morphogenesis & siderophore biosynthesis http://bit.ly/bRwQcw #
  • All mold is not alike: the importance of intraspecific diversity in necrotrophic plant pathogens. http://bit.ly/czYxQL #
  • N-acetylglucosamine induces white to opaque switching, a mating prerequisite in Candida albicans. http://bit.ly/bWk05U #
  • Genomic analysis of two-component signal transduction proteins in basidiomycetes. http://bit.ly/9aYYEu #
  • Chitinase genes revealed & compared, DNA extracts & a metagenomic library from a phytopathogen-suppressive soil. http://bit.ly/cmkHaz #
  • Robustness from flexibility in the fungal circadian clock. http://bit.ly/chJ858 #
  • Spotlight on Aspergillus nidulans photosensory systems. http://bit.ly/azqzAh #
  • Assessment of soil fungal communities using pyrosequencing http://bit.ly/9yw7Cu #
  • Dueling in the lung: how Cryptococcus spores race the host for survival. http://bit.ly/bPSMts #
  • Dynamic linkage relationships to the mating-type locus in automictic fungi of the genus Microbotryum. http://bit.ly/ayH8uS #
  • Implications of hypoxic microenvironments during invasive aspergillosis. http://bit.ly/ad8oCH #

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Where can I get orthologs?

There are several databases that include orthology prediction for fungi. These all have pros and cons. Some are more comprehensive and have many more species. Some are curated orthologies and paralogy which should be pretty stable. Some are automated and groupings and ortholog group IDs change at each iteration.

  • A phylogenetic approach from a Saccharomyces perspective is at PhylomeDB.
  • Fungal Orthogroups is based on Synergy algorithm from I. Wapinski formerly of the Regev group at the Broad Institutue.
  • Yeast gene order browser (YGOB) for Saccharomyces spp and CGOB for Candida spp.
  • OrthoMCL database based on whole genomes, not a ton of fungi but useful starting set.
  • Ensembl Genomes provides ortholog prediction as part of the Compara pipeline though there is a limited phylogenetic diversity in the current Ensembl Fungal genomes.
  • TreeFam has Saccharomyces cerevisiae and Schizosaccharomyces pombe as the two fungi included in the curated ortholog assignments and phylogenies.
  • SIMAP provides pre-computed similarities among all proteins in UniProt.
  • InParanoid provides a pretty comprehensive of available 100 whole genomes and many fungal genomes which I tried to help select.
  • JGI’s Mycocosm attempts to provide a fungal focused paralog/gene family look at clusters of genes based on whole genomes
  • E-Fungi is also an attempt at automated clustering with some fancy webservices logic.
  • Fungal Transcription Factor database focused just on families of transcription factors.

Some of these tools are better than others in terms of providing downloadable tables.  Another problem is what Identifiers are used. Many biologists are using gene names or Locus identifiers not UniProt/GenPept IDs to identify genes or proteins of interest.  So tools that just cluster UniProt data aren’t as useful as those which refer to the gene or locus names. Also, providing a way to download all the data from a comparison is important for further mining and grouping of the data or cross-referencing local datasets.  One-by-one plugging in geneids is not really a tool that respects the idea that your user wants to ask sophisticated queries.

Also – beware that some approaches are very much pairwise comparisons lists whereas others are finding orthologous groupings.  So if you want to fine the Rad59 ortholog from all fungi it may be easier or harder depending on the source.

[I may make this a static page in the future to allow for more detailed updating since I know the available resources wax and wane]

The roundup of twittered updates for 2010-06-21

  • Designing deep seq'n exp: structural variation, haplotype asmbly & transcript abundance (sw tools) http://bit.ly/abDAtW /via @nutrigenomics #
  • Insertional mutagenesis enables cleistothecial formation in a non-mating strain of Histoplasma capsulatum. http://bit.ly/9zVAbH #
  • Activation of the ustilagic acid biosynthesis gene cluster in U. maydis by the C2H2 zinc finger TF Rua1 http://bit.ly/dvVyMM #
  • Nucleotide sequences of four segments of chrysovirus in Korean Cryphonectria nitschkei BS122 strain, http://bit.ly/a4L9cW #
  • Insects harbor dsRNA viruses encoding a novel P-A rich protein and a polymerase distantly related to fungal viruses. http://bit.ly/a9buua #
  • Action and reaction of host and pathogen during Fusarium head blight disease. http://bit.ly/9W1aZn #
  • Molecular trait indicators: moving beyond phylogeny in arbuscular mycorrhizal ecology. http://bit.ly/aovjsl #
  • Transcriptional profiling reveals expr of novel genes in response to various stimuli in human dermatophyte T.rubrum. http://bit.ly/a2jrWm #
  • The host-infecting fungal transcriptome. http://bit.ly/dhzqeH #
  • QIP, a Protein That Converts Duplex siRNA Into Single Strands, is Required for Meiotic Silencing by Unpaired DNA. http://bit.ly/dysFaR #ncra #
  • Reinforced postmating reproductive isolation barriers in Neurospora, an Ascomycete microfungus. http://bit.ly/9mlRkz #ncra #
  • T6PP is required for cell wall integrity & fungal virulence – not trehalose biosynth in fungal pathogen A. fumigatus. http://bit.ly/9nlodi #
  • The high affinity iron permease is a key virulence factor required for Rhizopus oryzae (Zygomycete) pathogenesis. http://bit.ly/aXxkL6 #
  • 2 components of velvet-like cmplx control hyphal morphogenesis, conidiophore dev & penicillin biosyn in P.chrysogenum. http://bit.ly/biJK1g #
  • The {beta}(1-3)glucanosyltransferase Gel4p is essential for Aspergillus fumigatus. http://bit.ly/bz47ZZ #afum #
  • Distribution and abundance of the introduced ectomycorrhizal fungus Amanita phalloides in North America. http://bit.ly/at46rf #
  • Phylogenetic similarity and structure of Agaricomycotina communities across a forested landscape. http://bit.ly/afM5aN #

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Gordon Conference recap

Another excellent Cellular & Molecular Fungal Biology Gordon Research Conference held at Holderness School – I won’t blog about the details of the talks since they are intended to be off the record, but you can see the program here. Program chairs John Taylor and Michelle Momany did a great job setting the program slate and vice-chairs Judy Berman and Alex Andrianopoulos prepared the “hot topics” session and will be chairs for the 2012 conference.

I had a great time catching up with friends and meeting new folks – here’s a few pictures from the week including one of us catching up on our reading late night.

Late night reading assignment
Congrats to Jim Anderson and Jenny Lodge who were elected vice-chairs for 2012 and will be chairs in 2014.

Faculty jobs at UBC-MSL

University of British Columbia’s Michael Smith Laboratory and Center for High-throughput Biology are advertising 6 faculty positions some of which could be great match for candidates with fungal biology interests.  There is more information about the jobs and applying available here.

[note: I am more than happy to post mycology related job adverts on this site, so please feel free to be in touch]

An Inky-cap mushroom genome

Francis Martin has written up a delightful summary pointing to our publication of the genome of Coprinopsis cinereus which appears in the early edition of PNAS and will grace the cover at the end of the month.  I encourage you to take a look at Francis’s post and the paper, available as Open Access from PNAS.  I’ll do my best to post a summary of the paper when I get a free moment.

For now I’ll leave you with a picture of this cute little mushroom fruting in the lab and a link to many more at Flickr.

Mature Coprinus cinereus (Coprinopsis cinerea)