Archive for March, 2010

Truffle Genome Unearthed

March 31st, 2010

Perigord_TruffleToday is a great day for me and the folks of the Tuber Genome Consortium. Well, it has finally happened, we have come to the point where the Black Truffle Genome manuscript is now online at Nature. (Martin et al. Perigord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis. Nature, advance online publication 28 March 2010 | doi:10.1038/nature08867). This paper represents a culmination of five years of work by many people from multiple institutions in France, Italy and Germany. This was truly an amazing team effort, with all sorts of people from the Genoscope in particular, going above and beyond the call of duty to make sure it happened and worked well despite the complexity of this genome packed with transposable elements. Annotation jamborees in such exquisite places as Parma, Torino and Alba will remain in my mind forever for the quality of the science discussed at these gatherings, but also for the great wines and food we enjoyed.

A Nature News article accompanies this, and you can have a look at that here:  Truffle’s savoury secret revealed. Our paper also made the New York Times–and not every genome does…. This one they managed to sex-up a bit: Unearthing the Sex Secrets of the Périgord Black Truffle.

I’m watching the news coverage of our genome grow by the minute … just amazing how this ‘ultimate’ mushroom is causing a stir. I have given dozen of interviews over the last two days. Actually most of my comments to the journalists were in the context of the science but they left them out and they were more interested in the ‘folksy’ stuff.

In this Nature letter, we report the sequence of the haploid genome of a T. melanosporum strain harvested in Provence. The sequence provides important insights into fungal sex and fruiting, and the evolution of symbiotic relationships between fungi and plant roots. At ~125 megabases, it is the largest and most complex fungal genome sequenced so far. This expansion results from a proliferation of transposable elements accounting for ~58% of the genome. In contrast, this genome only contains ~7,500 protein-coding genes with very rare multigene families. It lacks large sets of carbohydrate cleaving enzymes, but a few of them involved in degradation of plant cell walls are induced in symbiotic tissues. The latter feature and the upregulation of genes encoding for lipases and multicopper oxidases suggest that T. melanosporum degrades its host cell walls during colonization. One observation that we made concerned the presence of a secreted invertase. This might provide the fungus with much greater capability (than would be the case in the ECM basidiomycete Laccaria bicolor which is lacking this enzyme) to obtain direct access to host carbon via sucrose catabolism. It would explain the ability to yield such massive fruit bodies, the production of which must be a large drain on the resources of the host.

We spent a good deal of time then analyzing the data asking a pretty simple question – are there any differences in genomic features between the two sequenced ectomycorrhizal fungi, the basidiomycete Laccaria bicolor and the ascomycete T. melanosporum. Symbiosis development induces an increased expression of carbohydrate and amino acid transporters in both symbionts, but the comparison of genomic traits in the two ectomycorrhizal fungi showed that genetic predispositions for symbiosis—‘the symbiosis toolbox’—evolved along different ways in ascomycetes and basidiomycetes.

Worldwide demand for the black truffle has fuelled intense efforts at cultivation. So, I hope that analysing the genetic traits related to fruiting and symbiosis should ultimately help boost crop production.

Martin et al. (2010) Perigord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis. Nature 464, 1033-1038.

Photo: Perigord Black Truffle fruiting body. © C Murat – INRA.

Heading to Walnut Creek

March 20th, 2010

Fomitopsis pinicolaNext week a collection of international ‘afficionados’ exploring fungal genomes will be meeting in Walnut Creek (in the Bay  Area) at the JGI Basidiomycetes Jamboree.  I am hopeful we’ll come up with some strategies and principles that can guide how the increasing number of fungal genomes (e.g. Agaricus, Pleurotus, Serpula, Pisolithus, Paxillus)  can be more effectively mined and the resulting comparative analyses provided to mycologists and scientists interested by the eukaryote evolution (see also Jason’s blog post: ‘Preparing for meeting on Fungal Genome databases‘) . I expect that we will also be discussing how genome databases can be interconnected to facilitate comparative analyses between groups. The JGI Fungal Genome Initiative and the Genoscope DIKARYOME projects will likely generate >100 genomes of yeast and filamentous fungal genomes in the next two years. Added to the 200 currently available genomes, these novel genome sequences will undoubtly facilitate our understanding of  the  life history of Mycota and help us to explain their tremendous ability to colonize most ecosystems on Earth. I will keep you in the loop.

Photo:  Red-belted Polypore (Fomitopsis pinicola) © FM

v2 of Mucor circinelloides genome

March 7th, 2010

Mucor.mucedo.-.lindseyJGI has released v2 of the Mucor circinelloides genome. M. circinelloides is a dimorphic fungus belonging to the Zygomycota phylum. This mold has been studied mainly because of its dimorphism, light responses, high capacity for accumulating lipids, anaerobic and aerobic production of ethanol and gene silencing mechanisms (RNAi).

Assembly v2 is an improved assembly produced by the JGI Finishing Pipeline containing 26 scaffolds and 36.6 Mbp. After filtering for homology and expression support, a total of 11719 genes were structurally and functionally annotated.

See also The Mucor Genome Project.

Photo: © Wikipedia.

Watson meets Moore

March 7th, 2010

logo The US company Ion Torrent Systems announced on February 24th that it will award two Ion Personal Genome Machine sequencers in April 2010 through a grant program designed to help make DNA sequencing accessible to all scientists. Well, if you want your own portable, affordable electronic DNA sequencer it is the right time to apply ;-).

Ion Torrent sequencing technology is based on large arrays of chemical-sensitive field-effect transistors (FETs) to monitor changes in chemical processes relating to DNA synthesis. This third-generation sequencing platform requires no proprietary chemistries or optics because it’s based on a simple chemical reaction. When a nucleotide is incorporated into a strand of DNA by a polymerase, a hydrogen ion is released as a byproduct. That hydrogen ion carries a charge which is detected by proprietary ion sensor. If a nucleotide, A, T, G or C, is incorporated to a DNA template by the polymerase enzyme then the chemical signal (H+) is detected. Ion Torrent uses a high-density array of micro-machined wells to perform this simple chemical reaction in a massively parallel way. Each well holds a different DNA template. Beneath the wells is an ion-sensitive layer and beneath that a proprietary Ion sensor. The Ion Torrent sequencer is operating like a pH meter. Because this is direct detection, each nucleotide run happens in seconds and an entire run lasts about an hour. Ion Torrent chips are designed, manufactured and packaged like any other semiconductor chips.

The electronic sequencer will cost less than $50,000 and Ion Torrent claims that it will generate hundreds of millions of bases and millions of highly accurate reads per run, each several hundred bases in length … “c’est trop beau pour être vrai”.

Kevin Davies (Bio-IT World) provides technical details on the new instrument in his post “Electronic DNA Sensing and Ion Torrent Systems“.