Tag Archives: genome

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)

I’ll have the truffles and huitlacoche

Black TruffleA couple of papers should have captured your attention lately in the realm of fungal genomics.

One is the publication of the genome of the black truffle Tuber melanosporum. This appears as an advanced publication at Nature (OA by virtue of Nature’s agreement on genome papers) along with a NYT writeup and is a tasty exploration of the genome of an ascomycete ectomycorrhizal (ECM) fungus. There are several gems in there including the differences in transposable element content, content of gene families related to carbohydrate metabolism. This genome helps open the doorway for exploring the several independent origins of ECM in both ascomycete and basidiomycete fungi.

I’ll also point out there is some work on the analysis of mating type locus found in this genome has applied aspects suggesting that inoculation of roots with both mating types may increase truffle yields in truffle farms. Evidence for sexual reproduction is also discovered from this genome analysis based on the sexual cycle genes present and the structure of the MAT locus.  Much like what was revealed in the genome analysis of the previously ‘asexual’ species Aspergillus fumigatus (and later reconstitution of a sexual cycle), the Tuber genome has the potential for mating and is a heterothallic (outcrossing) fungus based on its mating type locus -just like many other filamentous Ascomycete species.

A second paper I encourage you take a look at (those with a Science subscription) is from Virginia Walbot’s lab on the formation of tumors by U. maydis in Maize. These tumors end up destroying the corn but can produce a delicious (to some) dish that is huitlacooche. The idea that the fungus is co-opting the host system by secreting proteins that acted in the same way as native proteins and that it has a tissue or organ specific repertoire was one that her lab has been pursuing. U. maydis can grow inside corn without detection and  the formation of tumors seems to be a manipulation of the plant as much as it is the pathogen directly taking resources from the plant.  It reminds me a bit of the production of secondary metabolites that can control plant growth like gibberellins produced by fungi.  This kind of manipulation and also ability to evade detection suggests a pretty specific set of controls that prevent the fungus from doing the wrong thing at the wrong time (to avoid detection). So they set out to see if there are a set of organ specific genes that the fungus uses during infection that would suggest a very host-specific strategy by this corn smut.

In this paper the authors evaluate the role of fungal genes specifically expressed in infection of different organs and also the role of secreted proteins in colonization of the organs.  In what is impressive and elegant work, the authors show through the use of microarrays and genetics that there is plant tissue specific gene expression of U. maydis – so infections in leaves express a different set of genes than those in seedlings.  Genetic and phenotypic evaluation of fungal strains with knockouts of sets of the predicted secreted proteins was able to confirm a role for specific secreted proteins that previously may have not had any discernible phenotype. They infect strains with knockouts of sets of genes that encode secreted proteins and compare the virulence when these strains infect individual organs of the maize host.  They showed there is significantly different virulence in the various tissues for a some of the mutants suggesting an organ-specific role for virulence of secreted proteins. They also go on to show that some of this organ specific infection requires organ-specific gene expression by evaluating maize mutants and the ability of the fungus to infect different organs.

Future work will hopefully followup to see what these secreted proteins are manipulating in the host and how they either enable virulence by protecting the pathogen, avoiding detection by turning of host responses, or co-opting host gene networks in some other way.

Martin F, Kohler A, Murat C, Balestrini R, Coutinho PM, Jaillon O, Montanini B, Morin E, Noel B, Percudani R, Porcel B, Rubini A, Amicucci A, Amselem J, Anthouard V, Arcioni S, Artiguenave F, Aury JM, Ballario P, Bolchi A, Brenna A, Brun A, Buée M, Cantarel B, Chevalier G, Couloux A, Da Silva C, Denoeud F, Duplessis S, Ghignone S, Hilselberger B, Iotti M, Marçais B, Mello A, Miranda M, Pacioni G, Quesneville H, Riccioni C, Ruotolo R, Splivallo R, Stocchi V, Tisserant E, Viscomi AR, Zambonelli A, Zampieri E, Henrissat B, Lebrun MH, Paolocci F, Bonfante P, Ottonello S, & Wincker P (2010). Périgord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis. Nature PMID: 20348908

Skibbe DS, Doehlemann G, Fernandes J, & Walbot V (2010). Maize tumors caused by Ustilago maydis require organ-specific genes in host and pathogen. Science (New York, N.Y.), 328 (5974), 89-92 PMID: 20360107

Sequencing wine spoilage yeast

There is an article in Wine Spectator (Seen on the JGI feed) on sequencing the wine spoilage yeast bruxellensis (correct name is now Dekkera bruxellensis) which adds the not-so-excellent taste of “sweaty horse” to wines.  There is already some survey sequencing done by Ken Wolfe and Jurge Piskur’s groups so a full genome sequencing project will help work out how this yeast is able to out compete Saccharomyces and cause dramatic wine spoilage.  This is also relevant on the bio-fuel side since this yeast can also taint an ethanol bio-reactor.  It is an interesting ecology inside the wine bottle and this competition for resources can lead to bad tasting wine. The competition presumably originated in some form in the rotting fruit where these yeasts compete for space and use different approaches in their niche including the fermentation process which produces the revered ethanol by-product and helps establish a chemical-warfare driven landgrab.  The ethanol also helps prevent and of course this has implications for the Drosophila (Sophophora) flies that land there and eat yeast. They needed a good way to overcome the ethanol like the well studied Adh gene.

Early branching genomes available

Genome sequencing is underway on several early branches in the Opisthokont and some related linages as part of the “Origins of Multicellularity” project at the Broad Institute (BI) include some recently made available assemblies for:

  • Allomyces macrogynus (Blastocladiomycota “Chytrid”)
  • Capsaspora owczarzaki (Ichthyosporea)

Already available data from

Still in progress (BI)

Still in progress (Other centers)

For your reading pleasure

Too much on my plate as of late, so I’m woefully behind on posting much on interesting papers or news.  Here’s a short list of links and papers that are worth a look though.

  • “Evolution of pathogenicity and sexual reproduction in eight Candida genomes” published (Nature)
  • NYT Science article sort of summarizing the good, bad, and ugly of fungi and human interactions
  • Attempts to save amphibians from chytridiomycosis “Riders of a Modern-Day Ark” (PLoS Biology)
  • Looks like Scott Baker with the JGI are in the process of resequencing several classical mutant strains of Phycomyces, Neurospora and Cochliobolus, Cryphonectria for sequence-based mapping of mutants (i.e. here and here and here).

Aspergillus has a posse

aspergillusposse

Shepard Fairley has gotten alot of notice lately for his Obama art that has been replicated pretty much everywhere. I mocked up a homage to his earlier street art — here we’ll discuss the growing Aspergillus genome posse.

But the work from mainly the JCVI, Broad Institute, JGI, NITE, and Sanger centre has generated an excellent collection of genome sequences for the Eurotiales clade (feel free to get a login for the wiki and add other that are missing).  The Aspergillus community now has a AGD – Aspergillus Genome Database project that includes a curator of genome annotation (they are hiring) and presumably literature in the SGD and CGD model of curation.

I think a lot of other projects have a Posse too (or maybe just a loosely organized band) in terms of a community of people working on related species and willing to work together to coordinate.  As these sort of “clade” databases start to develop we will have better clusters of information that can be mapped among multiple species.

Eventually I hope this will spur efforts for more coordinated genome databases for comparative genomic and transfer of known gene and functional information between experimental systems.  The efforts really require coordination or centralization of the data so that gene models can be updated as well as orthologs and phylogenomic inference of function.

Brown rotting fungal genome published

ResearchBlogging.orgPostia placenta genome is now published in early edition of PNAS.   Brown rotting fungi are import part of the cellulose degrading ecology of the forest as well (hopefully) providing some enzymes that will help in the ligin to biofuels process. Brown rotters break down cellulose but cannot break down lignin or lignocellulose while white rotters (like the previously sequenced Phanerochaete chrysosporium) are able to break down the lignin.  This fungus was chosen for sequencing as it is another potentially helpful fungus in the war on sugars (turning them into fuels) including recently published Trichoderma reesei and 1st basidiomycete genome Phanerochaete (all incidentally with the Diego Martinez as first author – go Diego!). It is also helpful to contrast the white and brown rotters to understand how their enzyme capabilities have changed and how these different lifestyles evolved.  There had been some issues with the initial assembly of this genome which is basically twice as big as one would expect because the dikaryon genome was sequenced – this is where two nuclei with different genomes are present as the result of fusion between two parents of opposite mating types.  When genome sequenced is performed it is hard to assemble these into a single assembly since there are really two haplotypes present.  So these haplotypes have to be sorted out to obtain the gene ‘count’ for the organism for those who like simple numbers. This is a similar situation to the Candida albicans genome, although those haplotypes are much more similar.  The main problem is that one has to generate twice as much sequence to get the same coverage of each haplotype without playing some tricks to collapse them into a consensus and them afterwards separate the haplotypes back out.  At any rate, this sequenced provided a good summary of the gene content and thus metabolic and enzymatic capabilities to match up functional data collected from LC/MS and transcriptional profiling. 

There are several other rotting fungi that are nearly done at JGI (but the task of writing and coordinating the analyses for the papers are ongoing!) include Schizophyllum commune and Pleurotus ostreatus. There are also several more mycorrhizal and plant pathogenic basidiomycete fungi as well as some classic model systems that have finished genomes and are in the process of finalizing papers.  It is an exciting time that is just beginning as these genome and transcriptional data are integrated and compared for their different ecological, morphological, and metabolic capabilities.

The article is unfortunately not Open Access so I haven’t even read it from home yet, but pass along this news to you, dear reader. Will get a chance to read through more than the abstract to see what glistening gems have been extracted from this genomic endeavor.
D. Martinez, J. Challacombe, I. Morgenstern, D. Hibbett, M. Schmoll, C. P. Kubicek, P. Ferreira, F. J. Ruiz-Duenas, A. T. Martinez, P. Kersten, K. E. Hammel, A. V. Wymelenberg, J. Gaskell, E. Lindquist, G. Sabat, S. S. BonDurant, L. F. Larrondo, P. Canessa, R. Vicuna, J. Yadav, H. Doddapaneni, V. Subramanian, A. G. Pisabarro, J. L. Lavin, J. A. Oguiza, E. Master, B. Henrissat, P. M. Coutinho, P. Harris, J. K. Magnuson, S. E. Baker, K. Bruno, W. Kenealy, P. J. Hoegger, U. Kues, P. Ramaiya, S. Lucas, A. Salamov, H. Shapiro, H. Tu, C. L. Chee, M. Misra, G. Xie, S. Teter, D. Yaver, T. James, M. Mokrejs, M. Pospisek, I. V. Grigoriev, T. Brettin, D. Rokhsar, R. Berka, D. Cullen (2009). Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.0809575106

Coprinopsis cinereus genome annotation updated

Coprinus cinereus genome projectThe Broad Institute in collaboration with many of the Coprinopsis cinereus (Coprinus cinerea) community of researchers have updated the genome annotation for C. cinereus with additional gene calls based on ESTs and improved gene callers. The annotation was made on the 13 chromosome assembly produced by work by SEMO fungal biology group and collaborators across the globe including a BAC map from H. Muraguchi.  Thanks to Jonathan Goldberg and colleagues at the Broad Institute for getting this updated annotation out the door.

 

This updated annotation is able to join and split several sets of genes and the gene count sits at just under 14k genes in this 36Mb genome. There are a couple of hiccups in the GTF and Genome contig/supercontig file naming that I am told will be fixed by early next week.  Additional work to annotate the “Kinome” by the Broad team provides some promising new insight to this genome annotation as well.

We’re using this updated genome assembly address questions about evolution of genome structure by studying syntenic conservation and aspects of crossing over points during meiosis.  The C. cinereus system has long been used as model for fungal development and morphogensis of mushrooms as it is straightforward to induce mushroom fruiting in the laboratory.  It also a model for studying meiosis due to the synchronized meiosis occurring in the cells in the cap of the mushroom.

Happy genome shrooming.

Genome survey sequencing of Witches’ Broom

Genome survey sequencing (1.9X coverage) was generated for Moniliophthora perniciosa, the cause of witches’ broom disease on cacao plants. The sequence for this basidiomycete plant pathogen was published in BMC Genomics this week. The authors report a higher number of ROS metabolism and P450 genes. Evaluating whether these copy number differences are significantly different from other basidiomycete fungi and are lineage specific expansions will help determine if these families played a role in the adaptation of this plant pathogen.

This work provides an important stepping stone in understanding and eventually controlling this pathogen which is devastating cacao plantations. An associated review describes what we have and can learn about Witches’ broom disease.

See related:

Jorge MC Mondego, Marcelo F Carazzolle, Gustavo GL Costa, Eduardo F Formighieri, Lucas P Parizzi, Johana Rincones, Carolina Cotomacci, Dirce M Carraro, Anderson F Cunha, Helaine Carrer, Ramon O Vidal, Raissa C Estrela, Odalys Garcia, Daniela PT Thomazella, Bruno V de Oliveira, Acassia BL Pires, Maria Carolina S Rio, Marcos Renato R Araujo, Marcos H de Moraes, Luis AB Castro, Karina P Gramacho, Marilda S Goncalves, Jose P Moura Neto, Aristoteles Goes Neto, Luciana V Barbosa, Mark J Guiltinan, Bryan A Bailey, Lyndel W Meinhardt, Julio CM Cascardo, Goncalo AG Pereira (2008). A genome survey of Moniliophthora perniciosa gives new insights into Witches’ Broom Disease of cacao BMC Genomics, 9 (1) DOI: 10.1186/1471-2164-9-548