Category Archives: Agaricomycota

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.

Schizophyllum genome update

Robin Ohm at the JGI has announced the release of version 2 of the Schizophyllum commune genome. This is great news on the heels of the announcement that one of the funded 2012 CSPs will include detailed functional genomics experiments in this mushroom.

I am pleased to announce the public release of the JGI annotation and portal for the improved assembly of Schizophyllum commune.  Annotations of the assembly are now publicly visible at http://jgi.doe.gov/Scommune2 .  Annotation and editing privileges remain password-protected but all other tools are now available to the general public.

A detailed set of statistics on the assembly and annotation can be found on the Info page of that portal:  http://genome.jgi-psf.org/Schco2/Schco2.info.html

 

Genome sequence of mushroom Schizophyllum commune

Schizophyllum CommuneI am excited to announce the publication of another mushroom genome this week. The mushroom Schizophyllum commune is an important model system for mushroom biology, development of genome was sequenced as part of efforts at the Joint Genome Institute and a collection of international researchers.  The data and analyses from these efforts are presented in a publication appearing in Nature Biotechnology today.

Studies in mushrooms can have important impact on other research areas.  They can be useful in biotechnology as protein biosynthesis factories for producing compounds or even as an edible delivery mechanism for new drugs.  What we found in the analysis of this genome include clues to mechanisms of how white rotting fungi degrade lignin through analysis of enzyme families.  We also saw evidence for extensive antisense transcription during different developmental stages suggesting some important clues as to how some gene regulation could impact or control developmental progression.  Through gene expression comparison (by MPSS) a large number of transcription factors were shown to be differentially regulated during sexual development.  A knockout out two of these (fst3 and fst4) resulting in changes in ability to form mushrooms (fst4) or smaller mushrooms (fst3).

Several more interesting findings in this work that I hope to add back to this post when there is a little more time –

Ohm, R., de Jong, J., Lugones, L., Aerts, A., Kothe, E., Stajich, J., de Vries, R., Record, E., Levasseur, A., Baker, S., Bartholomew, K., Coutinho, P., Erdmann, S., Fowler, T., Gathman, A., Lombard, V., Henrissat, B., Knabe, N., Kües, U., Lilly, W., Lindquist, E., Lucas, S., Magnuson, J., Piumi, F., Raudaskoski, M., Salamov, A., Schmutz, J., Schwarze, F., vanKuyk, P., Horton, J., Grigoriev, I., & Wösten, H. (2010). Genome sequence of the model mushroom Schizophyllum commune Nature Biotechnology DOI: 10.1038/nbt.1643

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)

Underwater mushrooms?

ResearchBlogging.org The cover of the Jan/Feb Mycologia has a picture of a pretty weird place to find a mushroom growing – a new species of mushroom that was found fruiting underwater in the Rogue river in Oregon.  This was reported about two years ago for a discovery that was made in 2005, but this is a formal publication on the finding and species description of Psathyrella aquatica. It is quite cool to see discovery of a new habitat for mushrooms, but I expect some more work will be required to fully understand the mechanics and development dealing with the challenges of underwater growth.  I think it would be interesting to see what kind of dispersal mechanisms there are since the spores are probably forced to float downstream, if there is an animal or wind dispersal mechanism at some later stage too or whether one finds mycelium growing in the soil near and around the rivers.

The important part of identifying the species and sequencing identifying molecular marker like ITS is that when later metagenomics studies of soil are performed, the anonymous sequenced clones can be matched up to know species, and we can identify where else this fungus is found.

Frank, J., Coffan, R., & Southworth, D. (2009). Aquatic gilled mushrooms: Psathyrella fruiting in the Rogue River in southern Oregon Mycologia, 102 (1), 93-107 DOI: 10.3852/07-190

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

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).

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.