Archive for February, 2010

JGI Basidiomycete Genome Jamboree

February 24th, 2010

CoprinA Basidiomycete Genomes Jamboree will take place on March 24 – 26, 2010 at the Marriott in Walnut Creek, California, as a satellite meeting of the Annual JGI User Meeting. This jamboree will include brief updates on individual on-going basidiomycete genome projects (Agaricus, Ceriporiopsis, Coprinopsis, Heterobasidion, Melampsora, Pleurotus, Rhodosporidium, Serpula, Tremella) and discussion of comparative genomics of basidiomycete gene families (CAZy, transposable elements, secondary metabolism, pheromones, secretome, transporters).

Progress of the on-going Genome Encyclopedia of Fungi programme will also be discussed.

We will be there to discuss the progress of our own projects.

Photo: Coprinus comatus (the shaggy mane) (© F Martin).


February 23rd, 2010


PYFF4-logo2Research on the physiology of yeasts and filamentous fungi is booming and scientific interest in these ‘lower’ eukaryotes continues to grow. Key drivers include their relevance for industrial biotechnology, food and pharmaceutical industries and their role as highly accessible eukaryotic models for systems biology.

Three previous, highly successful editions of the Physiology of Yeasts and Filamentous Fungi (PYFF) conferences in Hindsgavl (2001), Anglet (2004) and Helsinki (2007) have brought together researchers active at the frontline of research on yeasts and filamentous fungi. Since the Helsinki meeting, the field has seen further spectacular developments, including the sequencing and analysis of important yeast and filamentous fungal genomes, the introduction of single-cell approaches in fungal research and breakthrough results in metabolic engineering. PYFF4 will celebrate these scientific developments and, once again, provide a platform for exchange of concepts between the yeast and fungal research communities.

PYFF4 will be organized in a dynamic environment: the harbour City of Rotterdam, the Netherlands. The conference venue, the Rotterdam World Trade Center, is located in the city centre, with excellent accessibility (plane, train) and many hotels in the immediate vicinity. The social event, an evening boat tour through the harbour area with an onboard dinner, will provide ample opportunity to take in more than fungal physiology.

The conference will be held from Tuesday June 1 (evening reception) – Friday June 4, 2010.
The scientific programme covers 3 full days.

The HiSeq 2000, new Illumina sequencer

February 20th, 2010

hiseq_2000Illumina announced their new, high-throughput sequencing instrument, the HiSeq 2000. The new HiSeq 2000 uses Sequencing By Synthesis (SBS), as the current Genome Analyzer (GA). The increase in sequence data generation rate (25 Gb/day versus 5 Gb/day for the GA IIx) comes from two major factors: increased data collection area and rate. The HiSeq 2000 has two 8-lane flow cells, as compared to the single flow cell on the GA, and images both the top and bottom surfaces of the flow cell. According to Illumina, the new sequencer will allow  ~30x coverage of two human genomes in a single run for under $10,000 per sample. David Dooling’s PolITiGenomics blog provides technical details on the new instrument for those inclined.

Gordon Research Conference on Cellular and Molecular Fungal Biology 

February 20th, 2010
800px-HoldernessSchool4The Cellular and Molecular Fungal Biology Conference (June 13-18, 2010 – Holderness School, Holderness, NH, USA) provides a forum for presentation of the latest advances in fungal research with an emphasis on filamentous fungi. This open-registration scientific meeting brings together the leading scientists from academia, government and industry to discuss current research results and future directions at Holderness School, an outstanding venue for scientific interaction. A key objective of the conference is to foster interaction among scientists working on model fungi such as Saccharomyces cerevisiae, Schizosaccharomyces pombe, Neurospora crassa and Aspergillus nidulans and scientists working on a variety of filamentous fungi whose laboratory tractability is often inversely proportional to their medical, industrial or ecological importance. Sessions will be devoted to Systems Biology, Fungi and Cellulosic Biomass, Small RNAs, Population Genomics, Symbioses, Pathogenesis, Membrane Trafficking and Polarity, and Cytoskeleton and Motors. A session will also be devoted to hot topics picked from abstracts. The CMFB conference provides a unique opportunity to examine the breadth of fungal biology in a small meeting format that encourages in-depth discussion among the attendees.

Emerging Fungal Diseases

February 17th, 2010

Roscoff-Port-ClocherConference – ‘New and Emerging Fungal Diseases of Animals and Plants: evolutionary aspects in the context of global changes? in Brittany, 17th – 21st April 2010.

From the site: “The world is changing rapidly as environments are modified by human activity. Superimposed upon this background of environmental change are signatures of ‘Globalisation’ as species are introduced into non-native, ecosystems. Many of these species are invasive, often pathogenic, organisms, and this conference Jacques Monod focuses on a Kingdom that is increasingly being recognised as having a widening impact on ecosystem, agricultural and human health, the Fungi.”

Soil Science in a Changing World

February 15th, 2010


Climate change. Food security. Water resources. Biodiversity. Not issues that provoke vivid images of soil scientists contributing to solutions to mitigate these problems. These solutions are addressed, however, by many scientists participating in multidisciplinary think tanks. In the first Wageningen Conference on Applied Soil Science, titled “Soil Science in a Changing World”, we will discuss the importance of soils and soil science for combating the problems we are facing around the globe.

On behalf of the Soil Science Centre of Wageningen University we would like to invite you to this conference. The first edition of the Wageningen soil meetings will address the importance of soil scientific knowledge for global issues. We want to address these topics in a dynamic way, by top key-note speeches, challenging debates, inspiring workshops and master classes as well as oral and poster presentations by participants.

Waking the Dead

February 14th, 2010

InukIt’s not a plant genome …  It’s not a fungal genome … But this paper is so exciting. For the first time, the nuclear genome of an extinct human being — a Palaeo-Eskimo – has been reconstructed and this spectacular findings are published in the February 10th, 2010 issue of Nature.

Morten Rasmussen and Eske Willerslev, from the Centre of Excellence in GeoGenetics, The Natural History Museum at the University of Copenhagen, Denmark, led the international team of scientists responsible for the sequencing of a male individual, Inuk*, who lived in Greenland 4,000 years ago and belonged to the first culture to settle in the New World Arctic, the Saqqaq. Genomic DNA was extracted from permafrost-preserved hair, found in Qeqertasussuk, an archaeological site in southwest Greenland. The sequencing was performed by using Illumina GAII and yielded a total of 3.5 billion reads, from a total of 242 lanes.

The genome-wide SNP analysis suggested that Inuk was genetically adapted to cold temperatures (according to its p53 gene sequence) and has a tendency to baldness, dry earwax, brown eyes, dark skin, the blood type A+, and shovel-shaped front teeth .

Analysis of 350,000 SNPs revealed that populations closest to the Saqqaq are the contemporary Koryaks and Chukchis inhabiting Chukotka and northern Kamchatka of the Siberian far east. This provides evidence for a migration from Siberia into the New World some 5,500 years ago, independent of that giving rise to the modern Native Americans and Inuit. Inuk’s ancestors separated from their Chukchis relatives and almost immediately crossed the Bering land bridge connecting Siberia and the New World.

Rasmussenn et al. (2010) Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature 463, 757-762.

* “Inuk” means “man” or “human” in Greenlandic.

Image: Nuka Godfredsen/Nature. Artist’s impression of Inuk.

The first legume species with a complete genome sequence

February 14th, 2010

soybeanThe face of Legume genetics has changed in early 2008  with the release of the complete draft assembly of the soybean [Glycine max (L.) Merr.] genome delivered by a triogency group [National Science Foundation (NSF), United States Department of Energy (US DOE), and United States Department of Agriculture (USDA)]. The genome project was initiated by by a consortium led by Gary Stacey, Randy Shoemaker, Scott Jackson, Jeremy Schmutz, and Dan Rokhsar. DOE JGI’s interest in sequencing the soybean genome stems from its role as a major source of biodiesel, a renewable, alternative fuel with the highest energy content of any alternative fuel. The genome data can be accessed at the Phytozome genome portal and the main features of this crop genome are discussed in the 14th January issue of Nature. The 1.1-gigabase genome containing 46,430 protein-coding genes has been sequenced by a whole-genome shotgun approach and integrated with physical and high-density genetic maps to create a chromosome-scale draft sequence assembly. Repeated elements make up ~59% of the assembled genome.

Soybean’s set of chromosomes has been duplicated at least twice, approximately 59 million years ago the first time and then again about 13 million years ago and, as consequence, soybean plants still have multiple copies of almost three-quarters of their genes. Mining this coding space allowed the identification of genes involved in the nitrogen-fixing symbiosis. Interestingly, the number of genes involved in lipid signalling, degradation of storage lipids, and membrane lipid synthesis were two- to threefold higher in soybean than Arabidopsis, indicating that these areas of acyl lipid synthesis are more complex in soybean.

As emphasized by the authors: “Soybean, one of the most important global sources of protein and oil, is now the first legume species with a complete genome sequence. It is, therefore, a key reference for the more than 20,000 legume species, and for the remarkable evolutionary innovation of nitrogen-fixing symbiosis”. The genome sequence has provided access to the first resistance gene for the devastating disease Asian Soybean Rust.

Schmutz et al. (2010) Genome sequence of the palaeopolyploid soybean. Nature 463, 178-183.

Photo from

A Time to Mourn

February 14th, 2010

It is with great sorrow that I write this post in memory to my friend Gopi Podila. The news of the shooting at University of Alabama has hit our headlines here in France early yesterday morning. When I’ve seen the mention of Alabama-Huntsville University, I read this headline and I find it hard to believe that Gopi was amongst the victims of this senseless, desperate act. No doubt Gopi was a very close and dear friend of me since his visit to Nancy in 98. Two years ago we enjoyed a diner at home and he told me how he was worrying to raise his daughters in a country were violence was so present. It is just terrible.

During the last decade, Gopi and I collaborated on several projects aiming to decipher the complex developmental mechanisms leading to the mycorrhiza symbiosis. Gopi’s effort was instrumental to the success of the Laccaria genome project. A few days ago, we were coordinating our deep sequencing activities aiming to improve the annotation 2.0 of this genome. He was a dedicated scientist that made significant scientific advances in the genetics of the mycorrhizal symbiosis.

Gopi was a gentle man who had a great smile and infectious laughter. My thoughts go out to Gopi’s wife and daughters.

Allow yourself to mourn, to be angry and sad about what we have lost.