Archive for February, 2011

Genomes of Skin Invaders

February 27th, 2011

hyphaecolonizinghairPathogenic fungi colonizing human skin, so-called dermatophytes, are a pleague for millions of humans. There are highly specialized filamentous fungi exclusively infecting keratinized animal structures causing mycoses.  Studies of dermatophyte pathogenic interactions have been hampered by a lack of full genome sequences. To provide broad insights into the molecular basis of the pathogenicity-associated traits, Burmester et al. published in the last issue of Genome Biology (2011/12/1/R7)  the first genome sequences of two closely phylogenetically related dermatophytes, Arthroderma benhamiae and Trichophyton verrucosum, both of which induce highly inflammatory infections in humans.

The genomes of A. benhamiae and T. verrucosum were sequenced by a whole-genome shotgun hybrid approach (Sanger, 454 FLX). These genomes are smaller than those of phylogenetically related ascomycetes. The assembly of A. benhamiae spans 22.3 Mb and that of T. verrucosum comprises 22.6 Mb. The genomes of A. benhamiae and T. verrucosum are compact and only contain 7,980 and 8,024 predicted protein-encoding genes, respectively. Most of these genes lie in collinear regions and are shared between the two fungi suggesting a very recent speciation.

As expected from their peculiar ecological niche, i.e. the animal skin, the two dermatophytes belong to the most protease-rich fungal species. They contain 235 protease-encoding genes, 87 of the predicted proteins having a secretion signal. A comprehensive analysis of the secretome during keratin degradation was carried out by combining 2D-PAGE and MALDI-TOF/TOF. RNA-Seq transcriptome profiling of A. benhamiae growing on human keratinocytes was performed to investigate the the entire process of infection. Subtilisin-like serine proteases, fungalysine-type metalloproteases, leucine aminopeptidases and dipeptidyl-peptidases are secreted during growth of A. benhamiae on keratin and keratinocytes. In addition, these dermatophytes can efficiently assimilate lipids, major constituents of the skin, thanks to the presence of 16 lipase genes. As discussed by the authors, the presence of large protease gene families in dermatophytes and their striking induction on keratin and human keratinocytes likely reflects selection during evolution and the ability of these fungi to adapt to different environmental conditions during infection and saprophytic growth. It appears that secondary metabolites also play a crucial role during keratinocyte infection.

Burmester et al. (2011) Comparative and functional genomics provide insights into the pathogenicity of dermatophytic fungi. Genome Biology 12:R7

Photo: A. benhamiae on human hair © Burmester et al.

New Phytologist Tansley Medal

February 23rd, 2011

The deadline for submission of abstracts for the prestigious Tansley Medal Award is 15 April 2011.

Full details at: www.newphytologist.org/tansleymedal.htm

Tansley Medal 2011

Bioenergy Trees – A New Phytologist Symposium

February 23rd, 2011

bioenergy-trees-Meeting-Image

You’ll be pleased to hear that we are getting lots of interest in the 26th New Phytologist symposium but, nevertheless, we do ask you to keep spreading the word to make sure we get the best possible attendance. The 26th NPS will provide a platform for brainstorming and discussions of the most recent systems biology applications aiming to deliver tailored sustainable tree lignocellulosic biomass for bioethanol.

The deadline for submitting poster abstracts for this meeting is Friday 11th March 2011. We would be grateful if you could forward this information to members of your research group who may be planning on attending the symposium. For more information about poster abstracts, please visit the symposium site.

Also, if you know of people who would like to attend the meeting, please encourage them to register using the following link: http://www.newphytologist.org/bioenergy/registration.htm.

The meeting is filling up quickly and the early bird registration fees will no longer be available from 14th March 2011.

Soil Biodiversity & Ecosystem Services

February 21st, 2011

ecofinders

MPMI 2011 in Kyoto

February 20th, 2011

mpmiThe XV International Congress on Molecular Plant-Microbe Interactions will take place in Kyoto (Japan) from August 2 to 6, 2011.

The MPMPI meeting is recognized as one of the most important international meetings for those working on plant-microbe interactions. Through plenary lectures, concurrent sessions, special workshops and various events, attendees experience innovative plant-microbe interactions research.

Plenary Sessions (speakers and topics) are now Online.

Abstract submission is open.

Early Registration is also open.

Human DNA Contamination

February 20th, 2011

Check your genome databases!!!

dna contamination

Read the related article in Le Figaro : ‘La contamination, bête noire de l’analyse ADN‘ and

the NCBI response: ‘While we understand that there is some contamination in sequences submitted to the public databases, we do not believe that the problem is as widespread as reported in the paper. Most of the examples provided by the authors were of preliminary data submitted to the archives under rapid data release policies. Database users must understand that preliminary data are just that, preliminary, because they have not been screened and vetted the way finished data have.’

Crunching Fungal Genomes at High Speed

February 19th, 2011

116-1660_IMG_2In October 2010, the US Department of Energy Joint Genome Institute (JGI) launched the Fungal Genomics Program (FGP), aimed at exploration of fungal diversity for energy and environmental sciences and applications through the scale-up of sequencing and analysis.

Within the framework of this JGI initiative, the project ‘Sequencing saprotrophic Agaricomycotina‘, lead by David Hibbett, has targeted 30 wood-decay fungi representing 12 orders. In the last few weeks, JGI has released 13 of these fungal genomes from saprotrophic white- and brown rots: Auricularia auricula-judae, Ceriporiopsis subvermisposa, Coniophora puteana, Dacryopinax spathularia, Dichomitus squalens, Fomitiporia mediterranea, Fomitopsis pinicola, Gloeophyllum trabeum, Phlebia brevispora, Punctularia strigosozonata, Stereum hirsutum, Trametes versicolor, and Wolfiporia cocos. These genome sequences are available through the JGI portal and their mining will keep us busy for months to go.

With the published genome of Schizophyllum commune and the annotated (and soon to be published) genomes of Agaricus bisporus, Heterobasidion annosum, Pleurotus ostreatus, Serpula lacrymans and Tremella mesenterica, we have now a unique opportunity to understand the biological lifestyles and lignocellulolytic strategies of the wood-decayers.

Photo: Laetiporus sulphureus © F Martin

Fungal Bioremediation

February 18th, 2011

large_cover201103Magic mushrooms‘ by Philip Patenall. I like this painting of fruiting bodies from the fly agaric (Amanita muscaria). It has been inspired by the review  ‘Untapped potential: exploiting fungi in bioremediation of hazardous chemicals‘ by Hauke Harms, Dietmar Schlosser & Lukas Wick in Nature Reviews Microbiology 9, 177-192 (March 2011).

[Fungi possess the biochemical and ecological capacity to degrade environmental organic chemicals and to decrease the risk associated with metals, metalloids and radionuclides, either by chemical modification or by influencing chemical bioavailability. Furthermore, the ability of these fungi to form extended mycelial networks, the low specificity of their catabolic enzymes and their independence from using pollutants as a growth substrate make these fungi well suited for bioremediation processes. However, despite dominating the living biomass in soil and being abundant in aqueous systems, fungi have not been exploited for the bioremediation of such environments.] To read more see Nature Reviews Microbiology.

Painting: © Philip Patenall.

Genomics of Energy & Environment

February 15th, 2011

6jgiJust a reminder…that the deadline for poster/abstract submission for the 6th Annual DOE Joint Genome Institute Genomics of Energy & Environment meeting (http://go.usa.gov/g4N) is rapidly approaching: February 21.

The meeting brings together, in JGI’s hometown of Walnut Creek, California, an international network of researchers interest in: Synthetic Biology, Ecogenomics and Ecoresilience of the Gulf Oil Spill, Hardware and Software Trends in Genomics Supercomputing, Computational Approaches to Massive Short Read Metagenomic Data Sets, Genomics of Biofuel Crops, Behavioral Genetics of Pollinating Bees, Microbiome Analyses from Humans to Shipworms, Metatranscriptomics of Marine Microbial Communities, Successful Transposable Elements Secrets, and Great Prairie Soil Metagenomics.

Confirmed speakers: Peer Bork, (European Molecular Biology Laboratory), Ed Buckler, Cornell University, Dan Distel, Ocean Genome Legacy, Dusko Ehrlich, French National Institute for Agricultural Research (INRA), Terry Hazen, Lawrence Berkeley National Laboratory (LBNL), Scott Hodges, University of California, Santa Barbara, Tom Juenger, University of Texas at Austin, Rob Knight, University of Colorado, Ruth Ley, Cornell University, Mary Ann Moran, University of Georgia, Magnus Nordborg, Gregor Mendel Institute, Gene Robinson, University of Illinois at Urbana-Champaign, Christopher Scholin, Monterey Bay Aquarium Research Institute (MBARI), Stephan Schuster, Penn State University, Pam Silver, Harvard, Jim Tiedje, Michigan State University, Mike Thomashow, Michigan State University, Jerry Tuskan, Oak Ridge National Laboratory/DOE JGI and Katherine Yelick, National Energy Research Scientific Computing Center (NERSC).

Workshops include:

  • Integrated Microbial Genomes (IMG)/Metagenomes data analysis systems http://img.jgi.doe.gov/
  • Mycocosm fungal genomics portal provides data access, visualization, and analysis tools for comparative genomics of fungi http://genome.jgi-psf.org/ programs/fungi/index.jsf
  • Phytozome provides data access and visualization tools for comparative plant genomics http://www.phytozome.net/
  • RNA Technologies & Analysis: a comprehensive suite for transcriptome interrogation, including RNA-Seq for expression profiling, etc.

Neurospora Population Genomics

February 13th, 2011

figure_1-neurosporaThanks to the dramatic decrease in DNA sequencing cost, genomics will soon be widely used to investigate population genetics of micro-organisms. Why bother sequencing the rDNA ITS or genotyping SSR when you could scan the whole genome. Population genomics, the large-scale comparison of DNA sequences, is now beginning to provide new insights in these areas. In fungi, large-scale population genomics has mainly been used for understanding yeast population structures and domestication of bread, beer and wine strains. e.g., the recent PLoS Genetics paper of Borneman et al. (2011). In the January 31 PNAS Early Edition, John Taylor and Louise Glass’s groups published one of the first population genomics study of a “wild” microbial eukaryote, the ascomycete Neurospora crassa (Ellison et al., 2010).

They performed Illumina whole-transcriptome sequencing of 48 individuals from different geographic origin to identify single nucleotide polymorphisms (SNP). They found two cryptic and recently diverged populations, one in the tropical Caribbean basin and the other endemic to subtropical Louisiana. They also carried out high-resolution scans for chromosomal regions of striking sequence divergence between these populations and found two genomic “islands”.  Several of the genes within these distinct genomic regions have functions related to the response to cold temperature as showed by growth assays. The whole-genome scan also identified a gene involved in environmental adaptation, i.e. the circadian oscillator frequency gene, suggesting that the 2.4°–10.6° difference in latitude between the populations may be another important environmental parameter. With the new Illumina HiSeq 2000 producing up 120M reads per lane and tagged cDNAs and/or gDNA, hundred of fungal accessions can now be surveyed for a nominal cost (<10,000$). Genes with functions related to ecologically-relevant traits will be much easier to identify by examining patterns of genetic diversity within and between populations. We are developing a similar approach for identifying ecologically-relevant traits in the ectomycorrhizal symbionts Laccaria bicolor (through a JGI CSP project) and Tuber melanosporum.

Christopher E. Ellison, Charles Hall, David Kowbel, Juliet Welch, Rachel B. Brem, N. L. Glass, and John W. Taylor (2011) Population genomics and local adaptation in wild isolates of a model microbial eukaryote. Proc Ntl Acad Sci USA doi: 10.1073/pnas.1014971108.

Borneman AR, Desany BA, Riches D, Affourtit JP, Forgan AH, et al. (2011) Whole-Genome Comparison Reveals Novel Genetic Elements That Characterize the Genome of Industrial Strains of Saccharomyces cerevisiae. PLoS Genet 7(2): e1001287. doi:10.1371/journal.pgen.1001287

Recommended Reading: ‘Population Genomics’ By Patrick Nosil

Photo: Neurospora crassa asci © Namboori Raju (Stanford University).


Mining Short Reads from Trace Archive

February 13th, 2011

For those wanting to get a large dataset from NCBI SRA trace archive: Must read! Must use Jason’s script! –

A HyphalTip: Get a bunch of SRA data

Fungal Genomes … on the Beach

February 10th, 2011

embo

For those interested by comparative genomics of micro-organisms, don’t miss the forthcoming EMBO meeting: COMPARATIVE GENOMICS OF EUKARYOTIC MICROORGANISMS: UNDERSTANDING THE COMPLEXITY OF DIVERSITY

to be held in San Feliu de Guixols, Spain, 15-22 October 2011 (see Website: http://events.embo.org/11-comparative-genomics/).

This conference will address the big evolutionary questions of what makes a eukaryote, how multicellularity arose, the evolution of reproduction, pathogenesis, and so on. Lineages of the Eukaryotic Tree of Life (TOL) that until now received only moderate attention, such as the Excavates, Archaeoplastids, Amoebozoa and Choanozoa, will be discussed, together with the better studied Chromalveolates and Fungi.

There will be opportunities for participants to present both short talks and posters, which will be conducted interactively with plenty of time reserved for questions and discussions. In addition there will be interactive workshops on ‘Do It Yourself’ genomics, databases and bioinformatics.

This is the 4th time the meeting will be held at this very nice venue on the Costa Brava, on the Mediterranean near Barcelona. The weather is still generally nice at this time of year and the food is great. There will be free shuttle buses from the Barcelona airport.

There are still spaces available and room for more short talks as well as poster presentations. We hope to see you at what will be an exciting and informative meeting. Please contact Heather Barnett at heather.barnett@nottingham.ac.uk +44-(0)115-823 0354 for details.

Teun Boekhout, Amparo Querol and Ed Louis, conference organisers

t.boekhout@cbs.knaw.nl

Unearthing the truffle genome

February 5th, 2011

np‘The ‘black diamond’, the ‘mysterious product of the earth’, the ‘ultimate fungus’ and ‘la grande mystique’ are some of the common names describing the delectable Périgord black truffle (Tuber melanosporum Vitt.). The culture, harvesting and marketing of this highly prized ectomycorrhizal fungus is a world that retains some of the secrets and intrigue of the past. Truffle cultivation is notoriously difficult, in part because of its cryptic life cycle as an underground symbiont, in which the fungus trades nutrients with oak-tree roots. By the end of the 1960s, there had been some success in devising new methods for producing truffle-infected seedlings under controlled conditions in glasshouses by inoculating plants with truffle cultures and spores. After successful plantation in orchards, reliable information on truffle yields and production is very difficult to obtain as a result of under-reporting of harvests, under-the-table marketing practices and a lack of administration records. It appears, however, that the production of truffles, as with other mushrooms, is erratic from year to year (depending on the weather conditions) and tends to decline as a result of global climate change. Decreasing supply and rising market prices have provided a strong incentive for research on truffle cultivation.’ (from my edito)

The February issue of New Phytologist (189: 3) includes a Special Feature dedicated to the Perigord Truffle genome with 7 papers discussing the transcriptome, the repertoire of transcriptional factors, the carbohydrate metabolism, the aroma biosynthesis and the molecular ecology  of sex of this ultimate fungus. Another raft of companion papers have been published in Fungal, Genetics & Biology.

To date, genomes of two mutualistic fungal symbionts, the basidiomycete L. bicolor and the ascomycete Tuber melanosporum, have been sequenced.  Based on their symbiosis-induced gene networks, evolution of the ectomycorrhizal lifestyle appears to be quite divergent (Plett & Martin, 2011).  To better understand the differences between symbiotic lineages and types of symbiosis, our JGI project is aiming to sequence 25 mycorrhizal fungi from different orders.  As of today, genomic DNA from Amanita muscaria, Cenococcum geophilum, Hebeloma cylindrosporum, Laccaria amethystina, Oidiodendron maius, Piloderma croceum, Paxillus involutus, Pisolithus microcarpus and P. tinctorius is currently being sequenced using next generation sequencing platforms. Sequencing of Boletus edulis, Cantharellus cibarius, Coltricia cinnamomea, Cortinarius glaucopus, Gymnomyces xanthosporus, Lactarius quietus, Meliniomyces bicolor, Paxillus rubicundulus, Ramaria formosa, Rhizoscyphus ericeae, Scleroderma citrinum, Suillus luteus, Sebacina vermifera, Tomentella sublilacina, Tricholoma matsutake, Tulasnella calospora and Terfezia boudieri will follow in 2011.