Archive for October, 2010

26th Fungal Genetics Conference 2011 at Asilomar

October 31st, 2010

26thFGCLogo640Time to register for the Fungal Genetics Conference 2011 at the Asilomar conference center. The registration site is now open and you have till December 14th, 2010 to register and submit your abstract. See you there.

What is the most abundant deposited fungal genus in GenBank?

October 30th, 2010

chanterelles

Jason Stajich wrote a few Perl and BioPerl scripts to analyze the distribution of fungal species with ribosomal DNA internal transcribed spacer ( ITS) sequences in NCBI GenBank. The whole spreadsheet of the data is public and available here and Jason’s comments are available on his blog post. According to this analysis, soil  Fusarium is the most abundant deposited genus. As stressed by Jason, the analyzed sequences are mainly from Sanger-based studies. The recent released of 454 seq’ing based fungal surveys will certainly change this current picture.

Sex Wars of the Truffle Grounds

October 28th, 2010

Tuber_melanosporumLa Truffe … encore et encore !!!

It’s been busy press days for our New Phytologist article on the distribution of mating-type (MAT) genes in a truffle ground! The news coverage  grows by the minute … just amazing how this ‘ultimate’ mushroom is causing a stir. It ‘s nice that this work is reaching a much broader audience (and for not much effort on our part!). Of course having the key words ‘truffle’ and ‘sex wars’ in the headline helped.

Here is the Press Release: “They are one of the most highly prized delicacies in the culinary world, but now scientists have discovered that black truffles are locked in a gender war for reproduction. The research, published in New Phytologist as the truffle season begins, represents a breakthrough in the understanding of truffle cultivation and distribution.

The teams, led by Dr Francesco Paolocci and Dr Andrea Rubini from the CNR Plant Genetics Institute in Perugia and by Dr Francis Martin from INRA in Nancy, carried out their research on the reproduction strategy of the highly prized black truffle, Tuber melanosporum, which is grown across southern Europe. During the truffle season, between late autumn and winter, fruiting truffles can grow up to 7cm in diameter, weighing up to 100g with a value often measured in hundreds of Euros.

‘Fruiting’ is the crucial part of the truffle life cycle, occurring when the fungi interacts with and colonises host plants, usually at the roots. However, the process which causes this transition from vegetative to reproductive state remains unknown.

“It is commonly believed that truffles, like other fungi, are homothallic, meaning that they reproduce themselves,” said Paolocci. “Because fungi that reproduce this way do not need a sexual partner it was believed that truffle cultivation relied only on the environment and nutrition, now we know that is wrong.”

Taking advantage of the information provided by the T. melanosporum genome sequencing project led by Martin and from molecular analyses carried out by the Italian team, research now proves that truffles do outcross, meaning they are a two gender species, with sexual reproduction occurring between strains of opposite mating types.

The team studied samples of wild black truffle strains on plants from a natural truffle ground near Spoleto in central Italy. The study revealed that black truffle strains of opposite gender were not evenly distributed beneath potentially productive soil patches.

The team then studied the dynamics of truffle strains on host plants, artificially inoculated with truffle spores and grown in a greenhouse, which showed that a competition occurs between strains to colonise the host plant roots even under controlled conditions.

The truffle fruiting season traditionally begins in late autumn but sexual reproduction is believed to occur in spring. The Italian team demonstrated that during the latter season strain of opposite gender are present in the soil samples next to colonised host plants and that the host plant colonising strain acts as maternal partner in the reproductive process.

These findings represent a breakthrough in the understanding of truffle reproduction tactics as well as the dynamics of black truffle strains in both open-field conditions and on host plants produced to boost truffle production.

“These results are of considerable practical use for optimising and increasing production in truffle fields,” concluded Paolocci. “It is of paramount interest to artificial truffle plantations to encourage a balance of strains of both mating types. Future investigations will allow us to determine whether the distribution of mating types is a factor that truly limits truffle fruiting body production.”

Andrea Rubini, Beatrice Belfiori, Claudia Riccioni, Sergio Arcioni, Francis Martin, Francesco Paolocci. Tuber melanosporum: mating type distribution in a natural plantation and dynamics of strains of different mating types on the roots of nursery-inoculated host plants. New Phytologist, 2010; DOI: 10.1111/j.1469-8137.2010.03493.x

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

Photo: The Black Truffle of Perigord (Tuber melanosporum) © C Murat -INRA.

Fall 2010 DOE JGI Newsletter

October 27th, 2010

primerThe Fall 2010 edition of the DOE Joint Genome Institute newsletter, The Primer, has arrived and can be downloaded here: http://go.usa.gov/aVu

Highlights include:

  • DOE JGI’s 2011 Community Sequencing Program Portfolio
  • Alga for Biodiesel Sequenced
  • Fungal Lessons on Breaking Biomass Better
  • Microbes That can Take the Heat
  • Fungus in the Forest
  • and more!

Aggregating, tagging and connecting biodiversity studies

October 10th, 2010

Beech

Recommended Reading: Aggregating, tagging and connecting biodiversity studies on the PLoS blog. This is a guest blog from David MindellBrian FisherPeter Roopnarine,Roderic Page and others who were closely involved in the development of the PLoS Hubs: Biodiversity launched on October 4th, 2010.

How to Crunch Plant Walls? … by Gene Transfer

October 2nd, 2010

11752Lateral gene transfer (LGT) between bacteria has largely been documented. The transmission of genes between fungi (e.g., Supernumerary chromosomes in a root-rot fungus, In Vino Veritas, Next-Generation Sequencing of Sordaria Genome), and between fungi and insects, such as aphids (see Tap the Vein that Bleeds), have also been reported. In contrast, data on LGT in animals is scarce. In the last issue of PNAS, Pierre Abad’s group from INRA is publishing their study of LGT in plant-parasitic nematodes. Their phylogenetic analysis of  genes coding for degrading enzymes acting on plant cell walls  (e.g., GH28 polygalacturonase, PL3 pectate lyase, GH43 arabinase, …)  from root-knot nematodes (such as Meloidogyne incognita and M. hapla) shows that these nematode enzymes were likely acquired from several independent bacterial sources. The authors hypothesized a series of acquisition through soil bacteria feeding or gene transfers from endosymbiotic bacteria. The  observed abundance of multigenic families (cellulases, pectate lyases, and expansins) in these plant-parasitic nematodes is likely due to a series of duplications that started after acquisition by LGT events. Selective advantage associated with transfer of these CAZyme genes probably has driven their duplications and facilitated fixation in the different populations and species of plant-parasitic nematodes.

In brief, when ‘worms gobble up genes from bugs’ (S. Kamoun) they were able to get access to the largest store of carbon in soil — is this fast-track evolution?

Danchin et al. (2010) Multiple lateral gene transfers and duplications have promoted plant parasitism ability in nematodes. Proc. Ntl. Acad. Sci., published online before print September 27, 2010, doi: 10.1073/pnas.1008486107.

Photo: Root-knot nematode © www.minlnv.nl