Sliced black truffle. With egg. (e_calamar/flickr)

What information about those delicate fungal flavors and aromas will now yield itself to the prying machines of molecular biologists? French and Italian researchers announced in the journal Nature, that the genome of the Perigord black truffle (Tuber melanosporum) has been sequenced. Of course if you followed fungal news on twitter, you’d already know this, but better late than never!

Truffle Genome Reveals Genes for Sex

Read all about it in the New York Times article Unearthing the Secret Sex Lives of Truffles (while you still can, before they switch to a rumored pay-for-content model, perhaps soon after the iPad is released):

It turns out the truffles, too, have sex lives, said Dr. Francis Martin, a plant biologist at the University of Nancy in France and leader of the research team. The precious fungi had long been thought to lead an asexual existence, but Dr. Martin and his colleagues have found that they have two sexes, or mating types.

The information is of great significance to truffle growers, whom Dr. Martin now advises to inject roots with both sexes of truffle spore. The truffle then benefits from the purpose of sex, which is of course to generate new combinations of genes and fresh diversity.

The discovery of two mating types is a pretty strong bit of evidence that the organism undergoes sexual reproduction. This is a pretty big deal, considering most people thought the fungus reproduced asexually.

The original publication appeared online at the Nature website and lo and behold the full text of the Letter Périgord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis (by many many authors) is available online. See also Scientists scent a breakthrough in truffle trafficking.

Based on some snooping around the internet, I gather that the researchers on the truffle genome project have been working on it for at least two years.

“Mountain pine beetles (Dendroctonus ponderosae) have eaten their way through vast swathes of western North American pine forests, including around 15 million hectares in British Columbia alone. As the burrowing beetles tunnel under the bark to feed and lay eggs, they release spores of the blue-stain fungus (Grosmannia clavigera), which stops the production of a protective toxic resin released by the tree and allows the beetles to continue to infest.”

The research is important for several reasons. For one, it shows that data collected using different sequencing technologies can be combined to produce a whole-genome sequence. And, genetic data on several different organisms (the beetle, the fungus, and the host trees) is being looked at in a synergistic way to get more meaningful insights into the biological relationships between the organisms and how the disease progresses and spreads.

The original research paper, De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data, appears in the open access journal Genome Biology.

More:

Blue Stain Fungus (improve it!)

Blue Stain Fungi Thrive in Jack Pine

Blue Stain Fungi — An Important Part of the Mountain Pine Beetle Epidemic

Mountain Pine Beetle

“We want to understand the path that we’ve taken to high enzyme production because it isn’t exactly known what was done to these strains,” said Scott Baker, a DOE JGI scientist at Pacific Northwest National Laboratory who, along with Christian Kubicek of TU Vienna and Antoine Margeot of IFP, is a senior author of the paper published in the journal Proceedings of the National Academy of Sciences. “There were three mutations characterized previously that gave us some clues, but that just touched the tip of the iceberg. There’s over 200 mutations we found in the T. reesei genome across 60 genes. We now have a blueprint on which we can do future studies to see which genes are related to the enzymes. If you can produce more enzyme more efficiently, that makes your process — in this case the production of biofuel — more economical.”

I decided to see what else was going on with respect to fungi at PNNL, so I contacted the lab to ask about it. Researcher Scott Baker had this to say about fungal research at PNNL:

“Fungal biotechnology work at PNNL is aimed accelerating the development of fungal strains that have utility in the future renewable fuels and chemicals area. Fungi are very productive producers of enzymes and small molecules (i.e. organic acids and other chemical compounds). We want to understand the biological processes that underlie the high productivity of fungi.

“The T. reesei work that was recently published in PNAS is a great example of how the Joint Genome Institute (JGI) accelerates downstream biological research that our group and others will do. The work in our group is focused around fungal bioprocess development and optimization and fungal genome analysis, proteomics and molecular genetics (i.e. gene deletions, etc).

The lab has a fact sheet about the JGI Fungal Genome Program (PDF) (kindly sent by David Gilbert).

That’s a lot of “what ifs.” It works pretty well for animals, less so for plants. It will probably work for everything in the end. A key to success will be the availability of PCR primers to use in amplifying the chosen sequences from any fungus.

According to the CBS Fungal Diversity Center, “The term DNA barcoding was coined by Paul Hebert in 2003. The general idea was to create, and create fast, a simple, unified species identification system based on DNA sequence data. An international consortium (CBoL, Consortium for the Barcode of Life) was formed to come up with binding suggestions as what markers and protocols would be accepted for DNA barcoding and to act as mediator between the DNA barcoding community and other parties, i.e. GenBank, potential users, or technology developers. A coordinated approach in the DNA barcoding of fungi (or any other group of organisms) requires the careful selection and agreement upon a suitable marker region. ITS region of the ribosomal DNA has been widely used as a marker in fungal studies, but additional marker regions are needed for many groups of fungi, as the ITS region does not provide sufficient resolution at the species level.”

If interested in the topic, you might want to keep an eye on All Fungi Barcoding.

For a readable general introduction see DNA Barcode Initiative.

Some technical publications and initiatives:

Progress toward DNA barcoding the vast diversity of fungi

Towards barcode markers in Fungi: an intron map of Ascomycota mitochondria

Canadian Centre for DNA Barcoding: Fungi

Assessing the effect of varying sequence length on DNA barcoding of fungi

Prospects for fungus identification using CO1 DNA barcodes, with Penicillium as a test case

Aspergillus DNA barcoding-Progress so far

Can we barcode the fungi?

Although it's a good idea, this is not the kind of barcode we are talking about

According to the company website: “OpenHelix provides convenient and effective online tutorial suites on the most powerful and popular web-based free bioinformatics and genomics resources. The online narrated tutorial, which runs in just about any browser connected to the web, can be viewed from beginning to end or navigated using chapters and forward and backward sliders.”

I viewed the first two parts of the SGD webinar and was impressed. I plan to finish them out and then give SGD a spin to see how effective the training is. I’ll let you know how it works out.