Archive for September, 2010

Horn of Plenty

September 26th, 2010

Trompette des morts (Cratarellus cornucopioides)Today was a great day for mushroom hunting. We harvested full bags of Horn of Plenty (Cratarellus cornucopioides). This ectomycorrhizal symbiont is exceptionally worthy of its gourmet status — This is a very choice, flavorful mushroom. Some of my favorite black trumpet spots are only one km from home in the Champenoux State Forest, where there are plenty of oak and beech, which are the usual mycorrhizal tree partners with this symbiotic mushroom. Its somber color, and small size allows it to blend remarkably well into its surroundings, easily concealed by a dark forest’s decaying leaves.

I have not yet plan the genome sequencing of this mycorrhizal species, but who knows.

Pushing to the Limit

September 26th, 2010

Encephalitozoon intestinalisThe microsporidia are spore-forming unicellular fungal parasites, causing chronic, debilitating diseases to their animal hosts (human, insects, crustaceans, fish). These highly adapted fungi are characterized by a severe reduction, or even absence, of cellular components typical of eukaryotes such as mitochondria, Golgi apparatus and flagella. Lacking mitochondria and peroxysomes, these unicellular eukaryotes were first considered a deeply branching protist lineage, but they are now affiliated to the Fungi. These features previously recognized as primitive are instead highly derived adaptations to their obligate parasitic lifestyle (Corradi et al., 2009).

In the first issue of Nature Communications, Keeling’s group reports the genomic sequence of the microsporidian Encephalitozoon intestinalis. Its genome is extremely compacted with 2.3 Mbp — a 20% reduction from the  already severely reduced 2.9 Mbp genome of E. cuniculi. DNA was isolated from 500 million purified spores and used for Illumina sequencing, from which the entire genome was assembled de novo, resulting in an assembly of 137 scaffolds with an average coverage of 40×. The two species share a conserved gene content (~1,800 versus 2,000 protein-coding genes), order and density over most of their sequences. The majority of the size difference is due to gene loss, the protein-coding capacity of the two genomes is however very similar because most of the genes that are absent in E. intestinalis are duplicates of genes that were retained, or unidentified ORFs. Genome compaction is also reflected by reduced intergenic spacers and by the shortness of most putative proteins relative to their eukaryote orthologues. The exceptions are the subtelomeric regions, where E. intestinalis chromosomes are missing large gene blocks of sequence found in E. cuniculi. In the remaining gene-dense chromosome ‘cores’, the diminutive intergenic sequences and introns are actually more highly conserved than the genes themselves, suggesting that they have reached the limits of reduction for a fully functional genome … ‘getting rid of everything that is not essential for gene function’

Corradi N. et al. The complete sequence of the smallest known nuclear genome from the microsporidian Encephalitozoon intestinalis. Nature Communications 1, 78, doi:10.1038/ncomms1079

Katinka, M. D. et al. Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi . Nature 414, 450453 (2001).

Photo: Encephalitozoon intestinalis, © www.microbiologybytes.com

Mycorrhiza 25 Genomes project approved

September 22nd, 2010

IMG_7095I am glad to report that our proposals ‘ Exploring the Genome Diversity of Mycorrhizal Fungi to Understand the Evolution and Functioning of Symbiosis in Woody Shrubs and Trees ‘ and ‘Community proposal to sequence a diverse assemblage of saprotrophic Basidiomycota (Agaricomycotina) ‘ to JGI’s Community Sequencing Program was approved for sequencing this cycle. This is extremely exciting, because it means that sometime between this Fall and next Summer we will have a large set of new mycorrhizal and  saprotrophic Agaricomycotina genomes, followed later in 2011-12 by another set of genomes. By the end of 2011, we should be able to mine and compare 50 novel symbiotic and saprotrophic  genomes.

As of this writing, JGI 454 and Illumina machines are busily churning out DNA from Hebeloma cylindrosporum, Piloderma croceum, Cenococcum geophilum, Pisolithus tinctorius and P. microcarpus.  Amanita muscaria, Boletus edulis, Laccaria amethystina, Lactarius quietus, Paxillus rubicundulus, Suillus luteus, and Sebacina vermifera will soon be queuing for sequencing.

Photo: The Fly Agaric, Amanita muscaria © F Martin

26th Fungal Genetics Conference

September 22nd, 2010

asilomar

The preliminary program for the  Twenty Sixth Fungal Genetics Conference (FGC) is now online. The conference will be held on March 15- 20, 2011, at the Asilomar Conference Center in Pacific Grove, California. It will include four plenary sessions, twenty-four concurrent sessions and extensive poster viewing time. I am glad to chair the ‘Symbiosis‘ plenary session.

Several jamborees and workshops dealing with the on-going fungal genome sequencing projects  will take place during the conference. Igor Grigoriev and I would like to organize a workshop aiming to bridge fungal genomics and soil metagenomics between the FGC and the 6th JGI Users meeting (March 22 – 24, 2011, at Walnut Creek, California). I would like to hear your ideas about the best way to run this workshop.

The FGC Website is here: http://www.fgsc.net/26thFGC/

When blogs make sense

September 12th, 2010

IMG_0415When blogs make sense Nature 466 , 8 (01 July 2010) doi:10.1038/466008a.

I liked this editorial and its associated comments:

“Biologists and astronomers approach data sharing differently, but both need better public outreach.”

“Blogging is a way to improve public outreach.”

“Institutions need to recognize and to encourage such outreach explicitly”

“In fact, given … the highly specialized language in primary literature, blogs and online magazines may be the ONLY way to reach the public”.

“The free speech is one of the pillars of science”.

Photo: Little girl listening (Siena, Toscana) © F Martin

Zoo Genomics

September 9th, 2010

turkeyMulti-Platform Next-Generation Sequencing of the Domestic Turkey (Meleagris gallopavo) by Dalloul et al. has been published in PLOS Biology. The consortium has used a combination of Roche 454 and Illumina GAII, and unique assembly tools to sequence the genome of the agriculturally important turkey, Meleagris gallopavo. Their draft assembly comprises approximately 1.1 gigabases of which 917 megabytes are assigned to specific chromosomes.

Thelephoroid Fungi

September 5th, 2010

Thelephora terrestrisWe have just received 500,000 454 TTN ESTs of a series of ectomycorrhizal thelephoroid fungi: Thelephora terrestris, Tomentellopsis submollis and Tomentella stuposa. from the Genoscope. T. terrestris (Earthfan) is a very common ‘contaminant’ of seedlings grown in greenhouses and forest nurseries. The Thelephoraceae are one of the most abundant ectomycorrhizal basidiomycete group in boreal and temperate forests, but they often form fruiting bodies on dead woods. It remains to be determined whether their genome and transcriptome reflect this dual lifestyle.

Photo: Earthfan fruiting bodies © F Martin