Category Archives: genome sequencing

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

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)

CSP: Letter of support time!

Several groups working on Fungi are submitting proposals to the JGI Community Sequencing Program.  Several proposals relating to the JGI’s interest in an encyclopedia of fungal genomes sequencing genomes of ascomycete and basidiomycete yeasts, filamentous ascomycetes, basidiomycetes,  and early diverging fungi are being put forward.  If you haven’t been contacted by these community members but would like to write a letter of support in these areas, please get in touch as the deadline for the proposals in early next week. There are also other proposals going in for Neurospora mutant strain resequencing, more Fusarium species, transcriptomes of mycorrhizal fungi, and other topics.  If you are are a user of data from any of the previous fungal projects that you know how important these resources are in both comparative genomics and molecular biology work, so support to get additional sequences generated will benefit many in the community.

I don’t know if it is appropriate for me to post the text of the solicitation for letters here, differing to the privacy of the groups submitting proposals, but if you want to help out the community by writing a letter showing that you would benefit from these resources, I can try to put you in touch.

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

a mushroom and a microsporidia walk into a bar

These papers got lost in my drafts of things to write about.  Grants and overdue manuscripts are keeping me away from the blog.

  • Published work from Gary Foster’s lab in Applied Env Micro show progress on genetic engineering tools to express introduced genes in the basidiomycete mushroom system Clitopilus passeckerianus. C. passeckarianus produces an antibiotic, pleuromutilin, an important antibiotic. Cover photo [Press] They also showed the  5′ intron is important for efficient expression, something that has been shown several times in fungi and provides more evidence for the role of introns in promoting or regulating an aspect of gene expression or translation. Perhaps by splicing-dependent export.
  • Corradi et al – the genome of the microsporidia parasite of Daphnia (water flea). It’s as big as a fungal genome at 24Mb (S.cerevisiae is about 12Mb, Neurospora crassa about 40Mb) but only has about 2,100 genes (S.cerevisiae has ~6,000, N.crassa ~ 10,000). DOI: 10.1186/gb-2009-10-10-r106

A cacophony of comparative genomics papers

A nice series of comparative genomics articles have been published in the last few weeks. The pace of genome sequencing has accelerated to the point that we have lots of sequencing projects coming from individual labs and small consortia not necessarily from genome centers. We are seeing a preview of what next (2nd) generation sequencing will enable and can start to imagine what happens when even cheaper 3rd generation sequencing technologies are applied. I’m behind in reviewing these papers for you, dear reader, but I hope you’ll click through and take a look at some of these papers if you are interested in the topics.

In the following set of papers we have some nice examples of comparative genomics of closely related species and among a clade of species. The papers mentioned below include our work on the human pathogens Coccidioides and Histoplasma (Sharpton et al) studied at several evolutionary distances, a study on Saccharomycetaceae (Souciet et al) clade of yeast species, and a comparison of two species of Candida (Jackson et al): the commensal and opportunistic fungal pathogen Candida albicans with a very closely related species Candida dubliensis.  There is also a nice comparison of strains of Saccharomyces cerevisiae looking at effects of domestication and examples of horizontal transfer.

There is also a report of de novo sequencing of a filamentous fungus using several approaches, traditional Sanger sequencing, 454, and Illumina/Solexa (DiGuistini et al).

Finally, a paper from a few months ago (Ma et al), gives a fantastic look at one of the early branches in the fungal tree – the Mucorales (formerly Zygomycota) – via the genome of Rhizopus oryzae.  This paper is a really excellent example of what we can learn about a group of species by contrasting genomic features in the early branches in the tree with the more well studied Ascomycete and Basidiomycete fungi.  More genome sequences will help us build on these findings and clarify if some of the observations are unique to the lineage or universal aspects of the earliest fungi.

I hope you enjoy!

Novo, M., Bigey, F., Beyne, E., Galeote, V., Gavory, F., Mallet, S., Cambon, B., Legras, J., Wincker, P., Casaregola, S., & Dequin, S. (2009). Eukaryote-to-eukaryote gene transfer events revealed by the genome sequence of the wine yeast Saccharomyces cerevisiae EC1118 Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.0904673106 (via J Heitman)

Jackson, A., Gamble, J., Yeomans, T., Moran, G., Saunders, D., Harris, D., Aslett, M., Barrell, J., Butler, G., Citiulo, F., Coleman, D., de Groot, P., Goodwin, T., Quail, M., McQuillan, J., Munro, C., Pain, A., Poulter, R., Rajandream, M., Renauld, H., Spiering, M., Tivey, A., Gow, N., Barrell, B., Sullivan, D., & Berriman, M. (2009). Comparative genomics of the fungal pathogens Candida dubliniensis and C. albicans Genome Research DOI: 10.1101/gr.097501.109

DiGuistini, S., Liao, N., Platt, D., Robertson, G., Seidel, M., Chan, S., Docking, T., Birol, I., Holt, R., Hirst, M., Mardis, E., Marra, M., Hamelin, R., Bohlmann, J., Breuil, C., & Jones, S. (2009). De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data. Genome Biology, 10 (9) DOI: 10.1186/gb-2009-10-9-r94 (open access)

Sharpton, T., Stajich, J., Rounsley, S., Gardner, M., Wortman, J., Jordar, V., Maiti, R., Kodira, C., Neafsey, D., Zeng, Q., Hung, C., McMahan, C., Muszewska, A., Grynberg, M., Mandel, M., Kellner, E., Barker, B., Galgiani, J., Orbach, M., Kirkland, T., Cole, G., Henn, M., Birren, B., & Taylor, J. (2009). Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives Genome Research DOI: 10.1101/gr.087551.108 (open access)

Souciet, J., Dujon, B., Gaillardin, C., Johnston, M., Baret, P., Cliften, P., Sherman, D., Weissenbach, J., Westhof, E., Wincker, P., Jubin, C., Poulain, J., Barbe, V., Segurens, B., Artiguenave, F., Anthouard, V., Vacherie, B., Val, M., Fulton, R., Minx, P., Wilson, R., Durrens, P., Jean, G., Marck, C., Martin, T., Nikolski, M., Rolland, T., Seret, M., Casaregola, S., Despons, L., Fairhead, C., Fischer, G., Lafontaine, I., Leh, V., Lemaire, M., de Montigny, J., Neuveglise, C., Thierry, A., Blanc-Lenfle, I., Bleykasten, C., Diffels, J., Fritsch, E., Frangeul, L., Goeffon, A., Jauniaux, N., Kachouri-Lafond, R., Payen, C., Potier, S., Pribylova, L., Ozanne, C., Richard, G., Sacerdot, C., Straub, M., & Talla, E. (2009). Comparative genomics of protoploid Saccharomycetaceae Genome Research DOI: 10.1101/gr.091546.109 (open access)

Ma, L., Ibrahim, A., Skory, C., Grabherr, M., Burger, G., Butler, M., Elias, M., Idnurm, A., Lang, B., Sone, T., Abe, A., Calvo, S., Corrochano, L., Engels, R., Fu, J., Hansberg, W., Kim, J., Kodira, C., Koehrsen, M., Liu, B., Miranda-Saavedra, D., O’Leary, S., Ortiz-Castellanos, L., Poulter, R., Rodriguez-Romero, J., Ruiz-Herrera, J., Shen, Y., Zeng, Q., Galagan, J., Birren, B., Cuomo, C., & Wickes, B. (2009). Genomic Analysis of the Basal Lineage Fungus Rhizopus oryzae Reveals a Whole-Genome Duplication PLoS Genetics, 5 (7) DOI: 10.1371/journal.pgen.1000549 (open access)

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.

Jelly fungus Tremella genome available at JGI

Tremella mesenterica (from K. Findley)
Tremella mesenterica (from K. Findley)

The Tremella mesenterica genome portal is now live at the JGI. The genome is ~28Mb and the JGI annotation group predicted 8,313 genes, a significantly larger number of peptides predicted for C. neoformans (~7000; 18Mb genome) which may represent new and interesting genes or aspects of gene loss in the Cryptococcus yeast lineage.

Tremella is a Basidiomycete jelly fungus and an interesting study system from the perspective of discovery of novel lignin degrading enzymes.  It also occupies an interesting phylogenetic position being an outgroup to the human pathogenic yeast Cryptococcus neoformans and C. gattii. Comparative genomics on this system may also provide insight into the interesting evolution of the large mating-type locus that was formed through various rearrangements resulting in conversion from a tetrapolar to biopolar mating system.

Tremella may also be an important source of understanding wood degradation and how it differs in jelly fungi from the more distantly related Agaricomycotina (mushroom forming). The fungus is reasonably easy to grow in the laboratory and also to collect from nature. It can handle some desiccation to survive during a dry period only to swell up after  moisture is available.  It is also called Witch’s butter and Tom Volk has a summary of its features on his FOTM page.  It can often be confused with a phylogenetically distinct jelly fungus named Dacyromyces, usually the differences can be best be determined microscopically.  See what kinds of Tremella people have been finding at the Mushroom Observer.

See also

    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).

    Schizophyllum genome portal live at JGI

    In preparation for Asilomar, JGI is releasing lots of the genome sequencing project portals. The Schizophyllum commune Genome Portal is now publicly available. Go get your white-rot gene investigation on! (Though please respect the community rules for 1st rights to publication of the genome-wide analyses).