Posts Tagged ‘JGI’

Understanding the Polyporales Evolution

December 15th, 2013

The Saprotrophic Agaricomycetes Sequencing Consortium, lead by David Hibbett (Clark University) analyzed 10 currently available whole genomes of Polyporales, comparing them to known gene datasets. In a special issue of Mycologia, the consortium reported the phylogenomic and phylogenetic analyses of this ecologically-important group of wood-rotters. They also analyzed several single-copy genes to assess them for their potential as markers of relationships between members of this group.

This analysis yielded new details about the evolutionary relationships between species, which they detailed in several phylogenetic trees of several clades (residual polyporoid clade, plebioid clade, antrodia clade and core polyporoid clade).

An INRA-JGI Bastille Day tribute!

July 14th, 2013
In the spirit of Bastille Day, I enthuse (in French with English subtitles) about the Joint Genome Institute’s contributions to the field of fungal genomics:
I enjoyed shooting this video at the Fungal Genetics Conference in Asilomar in March 2013. Thanks to David Gilbert from the JGI, we had a lot of fun working with the video crew.

Photo: © france.fr

A Cornucopia of Mycorrhizal Genomes

February 23rd, 2013

Mycorrhizal symbioses are nearly universal in terrestrial plants. Based on host plant and characteristic symbiotic structures, several classes of mycorrhizal symbioses are currently recognised, with the two major types being the endocellular arbuscular mycorrhiza (AM) and the intercellular ectomycorrhiza (ECM). Mark Brundrett’s web site provides an excellent introduction to the different types of mycorrhizal symbioses. Briefly,

In AM association, the fungal hyphae penetrates host roots to form intracellular arbuscules and vesicles.

In ECM, colonizing hyphae remain in the intercellular, apoplastic space forming the Hartig net. They do not penetrate the root cells. ECM are mostly form by basidiomycetes (e.g., Amanita, Boletus, Sebacina), but some are formed with ascomycetes (e.g., Tuber, Terfezia).

Additionally, the ericoid mycorrhiza (ERM) has been regarded as the most specific of mycorrhizas because of its limitation to hosts belonging to a restricted number of families of the Ericales and the participation of a small group of ascomycetous fungi (e.g., Helotiales) as mycobionts in the association. Ericoid fungi form hyphal coils in outer cells of the narrow “hair roots” of plants in the family Ericaceae, such as Vaccinium and Calluna.

All orchids are myco-heterotrophic at some stage during their lifecycle and form orchid mycorrhizas with a range of basidiomycete fungi (e.g., Tulasnella). The mycobiont forms coils of hyphae within roots or stems of orchidaceous plants. This type of mycorrhiza is unique because the endophytic fungus supplies the plant with carbon during the heterotrophic seedling stage of orchidaceous plants. The mycorrhizal fungi are often Tulasnellales, a basidiomycetous order that contains plant parasites and saprobes capable of degrading complex carbohydrates, such as cellulose.

Whether these different types of mycorrhizal fungi forming strikingly different anatomical structures and with contrasted biology and ecology differ in their gene repertoires and symbiosis-related gene networks is currently unknown and tackling these major questions is the main impetus of the current Mycorrhizal Genomics Initiative lead by the JGI and INRA (see my previous posts ‘Mycorrhizal Genomics Initiative‘ and ‘Exploring the Mycorrhizal Genomes‘ )

The genome of 30 representatives of these various types of mycorrhizal symbioses are currently sequenced and these tremendous genomic resources are providing new highlights on the biology, genetic and ecology of these symbioses. The findings obtained previously on L. bicolor and T. melanosporum genomes suggested that the ECM condition represents a syndrome of variable traits and that mycorrhizal fungi share fewer functional similarities in their molecular ‘toolboxes’ than anticipated (Plett & Martin, 2011) and this hypothesis is confirmed by the newly available genomes. We see very different symbiosis-upregulated genes in the various mycorrhizal lineages suggesting that these are non-homologous ecologies and that there are many routes to the similar nutritional modes. Several talks and posters at the forthcoming 27th Fungal Genetics Conference in Asilomar will illustrate several breakthroughs obtained by the MGI consortium members.

As of writing, the mycorrhizal species sequenced, assembled and annotated span a wide section of the evolutionary tree of Ascomycota and Basidiomycota, and include ectomycorrhizal, ericoid and orchid symbionts as follows:

Ectomycorrhizal species:

  • Amanita muscaria,
  • Boletus edulis
  • Cenococcum geophilum,
  • Cortinarius glaucopus,
  • Hebeloma cylindrosporum h7  (v2.0),
  • Laccaria amethystina 08-1,
  • Laccaria bicolor (v2.0),
  • Paxillus involutus,
  • Paxillus rubicundulus,
  • Piloderma croceum F 1598,
  • Pisolithus microcarpus 441,
  • Pisolithus tinctorius 270,
  • Scleroderma citrinum FougA,
  • Suillus luteus UH-Slu-Lm8-n1,
  • Terfezia boudieri,
  • Tricholoma matsutake 945.

Orchid mycorrhizal species:

  • Tulasnella calospora AL13/4D
  • Sebacina vermifera MAFF 305830,

Ericoid mycorrhizal species

  • Oidiodendron maius Zn,
  • Meliniomyces bicolor,
  • Meliniomyces variabilis.

As of today, 20 mycorrhizal genomes have been released on the JGI MycoCosm web portal and 10 additional genomes will be publicly released by the end of 2013 (see also our MGI web portal).

In addition to these new genomes/transcriptomes, those of Rhizopogon vinicolor, Gyrodon lividus, Choiromyces venosus, Lactarius quietus, Leccinum scabrum, Thelephora terrestris, Tomentella sublilacina, Tuber aestivum, Tuber magnatum, Rhizoscyphus ericae are expected to be released in 2013.

The genomes of mycorrhizal species released over the last two years, combined with previous studies of the L. bicolor and T. melanosporum genomes, provides a rich foundation for future studies to elucidate the unique features of these ubiquitous plant symbionts. Let’s find the gems in these genetic blueprints!

Photo: Fruiting bodies of the ectomycorrhizal Fly Agaric (Amanita muscaria).

F1000 nominations

December 18th, 2012

Great news!!! A new nomination tool for the 1000 Fungal Genome Project has been released (http://genome.jgi-psf.org/pages/fungi-1000-projects.jsf) to entire research community.  Any JGI registered user can click on MycoCosm tree nodes at (jgi.doe.gov/fungi), choose ‘Nominate’ to suggest new fungal species for sequencing and provide DNA/RNA samples to fill the gaps in the Fungal Tree of Life.  The nominations can be made all year around; after review the approved candidates will be added to the list of JGI projects.

The guiding principle for sampling in F1000 is at the end of the project to have 2 representatives from all fungal families or family-level clades. This will require a lot of coordination across several JGI CSP projects, e.g. our Mycorrhizal Genome Initiative, the Forest Soil Metatranscriptome Project and the Saprotrophic Agaricomycotina project, and interactions with the community and systematics experts of given groups. The current nomination will help in selecting the most interesting suggestions from our community.

Photo: Mycena sp. belongs to a large genus of small saprotrophic mushrooms. Mycena galopus will be sequenced within the framework of the Forest Soil Metatranscriptome Project (CSP570) © F Martin

The Pizza Mushroom Genome

October 9th, 2012

The publication describing the genome from the Button Mushroom (Agaricus bisporus) was published online today  in the early Edition of the journal, the Proceedings of the National Academy of Sciences (PNAS). This paper represents a culmination of five years of work by many people from multiple institutions in France, U.S.A., U.K., The Netherlands, Finland and Germany. This was truly an amazing team effort between the JGI teams and the international consortium. Let’s see if the news coverage of this genome study is as good as the one received for the Black Truffle genome. After all, the Portobello mushroom is one of the most commonly and widely consumed mushrooms in the world.

Below is the abstract of our PNAS paper:

[Abstract. Agaricus bisporus is the model fungus for the adaptation,persistence, and growth in the humic-rich leaf-litter environment. Aside from its ecological role, A. bisporus has been an important component of the human diet for over 200 y and worldwide cultivation of the “button mushroom” forms a multibillion dollar industry. We present two A. bisporus genomes, their gene repertoires and transcript profiles on compost and during mushroom formation. The genomes encode a full repertoire of polysaccharide-degrading enzymes similar to that of wood-decayers. Comparative transcriptomics of mycelium grown on defined medium, casing-soil, and compost revealed genes encoding enzymes involved in xylan, cellulose, pectin, and protein degradation are more highly expressed in compost. The striking expansion of heme-thiolate peroxidases and β-etherases is distinctive from Agaricomycotina wood-decayers and suggests a broad attack on decaying lignin and related metabolites found in humic acid-rich environment. Similarly, up-regulation of these genes together with a lignolytic manganese peroxidase, multiple copper radical oxidases, and cytochrome P450s is consistent with challenges posed by complex humic-rich substrates. The gene repertoire and expression of hydrolytic enzymes in A. bisporus is substantially different from the taxonomically related ectomycorrhizal symbiont Laccaria bicolor. A common promoter motif was also identified in genes very highly expressed in humic-rich substrates. These observations reveal genetic and enzymatic mechanisms governing adaptation to the humic-rich ecological niche formed during plant degradation, further defining the critical role such fungi contribute to soil structure and carbon sequestration in terrestrial ecosystems. Genome sequence will expedite mushroom breeding for improved agronomic characteristics.]

Read: Morin et al. (2012) Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche. Proceedings of the National Academy of Sciences, Early Edition.

Press releases:

JGI: Adaptable Button Mushroom Serves Up Biomass-Degrading Genes Critical to Managing the Planet’s Carbon Stores

INRA: Le génome du champignon de Paris décrypté

JGI Summer 2012 Primer

August 2nd, 2012

The summer edition of the U.S Department of Energy (DOE) Joint Genome Institute (JGI) newsletter The Primer is now available for download: http://bit.ly/JGI-Summer-Primer-2012

…featuring articles and images:

Features include:

  • A summary of the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting
  • Comparative Genomics of White Rot Fungi Providing Insight into Selective Ligninolysis
  • The Omics Response to the Deepwater Oil Spill
  • Assembling the Switchgrass Genome
  • Single-cell Genomics @ the DOE JGI
  • Save the Date for the 8th Annual Genomics of Energy & Environment Meeting MARCH 25-29, 2013 in WALNUT CREEK, CA
  • Other Publication Highlights

 

 

8th JGI Users Meeting

August 2nd, 2012


JGI Spring 2012 Primer

May 29th, 2012

The Spring 2012 edition of the DOE Joint Genome Institute (DOE JGI) newsletter The Primer is now available for download:
http://1.usa.gov/JGI-Primer-Spring-2012
and features highlights from the DOE JGI Genomics of Energy & Environment Meeting #7.

Videos of the talks from Meeting #7 are posted here:
http://bit.ly/JGI_Mtg7Videos


Be sure to Save the Date for meeting #8 the week of March 25-29, 2013.

JGI Fungal Jamboree

March 19th, 2012

The annual JGI Fungal Jamboree will start on Monday 19th at the Marriott Hotel in Walnut Creek. During the workshop, attendees will:

  • provide an update on their JGI program’s development during the last year and future plans,
  • discuss several important questions, including: (1) How to address current bottlenecks for future scale-up (target selection, DNA samples, analysis, publications)? (2) How to reach new groups of users and coordinate with other large genomics initiatives (e.g., 1K Chinese Fungal Genomes)? (3) What products in addition to sequencing JGI should be working on for mycologists? (4) What informatics/analytical needs should be addressed?
  • discuss strategic partnerships.

I will report on our two fungal programs, i.e. the Mycorrhizal Genomics Initiative and the Metatranscriptomics of Forest Soils.

    JGI Fungal Jamboree 2012

    February 15th, 2012

    Mycorrhizal Genomics Initiative: an Update

    January 18th, 2012

    I am writing to touch base about our JGI Mycorrhizal Genomics Initiative. As of today, the genome annotations publicly released are those of:

    The genome of Piloderma croceum and Tulasnella calospora are in the JGI annotation pipeline and should (hopefully) be available in the coming weeks. Those of Cenococcum geophilum, Sebacina vermifera, and Pisolithus tinctorius are in the final phase of sequencing, but Cenococcum and Pisolithus are difficult (large and polymorphic) genomes and JGI cannot give an estimated date of release.

    The transcriptome of free-living mycelium of C. geophilum, H. cylindrosporum, O. maius, P. involutus, P. croceum, P. microcarpus, P. tinctorius, Scleroderma citrinum, Sebacina vermifera and T. calospora are sequenced (RNA-Seq) and a series of dedicated databases are under construction.

    Finally, Igor Grigoriev, Joey Spatafora and I would like to invite you to Walnut Creek in mid-March 2012 to participate in several important JGI meetings:

    • Fungal Jamboree (March 19, 2011 8am-8pm) to discuss progress and coordination of large scale initiatives in fungal genomics: (1) Genomic Encyclopedia of Fungi, (2) 1000 fungal genomes, and (3) Fungal model systems and metagenomes (including our Mycorrhizal Genome Initiative).
    • JGI User Meeting (March 20-22, 2012: http://www.jgi.doe.gov/meetings/usermeeting/) and workshops including MycoCosm Tutorial (March 20, afternoon)

    You could access our recently opened MycorWeb portal dedicated to this project, Mycorrhizal Genomics Initiative, for links and updates.

    JGI Winter 2012 Primer

    January 11th, 2012

    The Winter 2012 edition of the DOE Joint Genome Institute newsletter, The Primer, is out and downloadable here: http://1.usa.gov/d0VkZt

    Highlights include:

    • DOE JGI Data Analysis Assets Featured in the Special Database Issue of Nucleic Acids Research, including: The Genome portal, IMGIMG/MPhytozome and GOLD.
    • 2012 Community Sequencing Program (CSP) Portfolio Announcement
    • Microbial Activity in Arctic Permafrost
    • DOE JGI Presentation Schedule at the Upcoming Plant & Animal Genome (PAG) Meeting: http://www.intlpag.org/web/

     

    JGI Fungal Genome Program update

    November 12th, 2011

    Some news from the JGI Fungal Genome Program By Igor Grigoriev:

    CSP2012 results were recently announced and eight new fungal projects were selected for the next year in tight competition with others. The winners included large scale genome sequencing projects (1000+ Fungal Genomes, thermophiles, Colletotrichum), functional genomics of model fungal organisms (Schizophyllum commune, Coprinopsis cinerea) and exploration of fungal systems (lichens, cow rumen guts, forest soils), all in good alignment with our strategic goals. We published a summary of CSP11 portfolio and Genomic Encyclopedia of Fungi in New Phytologist and Mycology journals.

    In order to discuss ongoing projects and better coordinate in future we would like to organize a fungal jamboree (tentatively on Mar 19, 2012) just before the JGI User meeting in Walnut Creek (Mar 20-22, 2012). The meeting will focus on bringing larger research community into discussions of the Genomic Encyclopedia of Fungi, 1000 fungal genomes, and fungal systems/metagenomics.

    The latest version of MycoCosm now offers 100+ fungal genomes to public. Since this is a relatively new system, we would like to get feedback from you and your colleagues using a 5 minutes online survey. This will help us to better assess your experience and needs and share this feedback with DOE, which will reveiw JGI programs next month. Please share this survey with your colleagues and ask them to complete it by the next week.

    Photo: The polypore Fomitopsis pinicola (© F Martin).

    1000 Fungal Genomes Project

    November 11th, 2011

     

    Our proposal to sequence 1000+ fungal genomes has been funded by the Joint Genome Institute (JGI) of the Department of Energy. Our consortium in collaboration with JGI has embarked on a five-year project to sequence 1000 fungal genomes from across the Fungal Tree of Life. The guiding principle for sampling in F1000 is at the end of the project to have 2 representatives from all fungal families or family-level clades. This will require a lot of coordination across several JGI CSP projects, e.g. our Mycorrhizal Genome Initiative, the Forest Soil Metatranscriptome Project and the Saprotrophic Agaricomycotina project, and interactions with the community and systematics experts of given groups.

    The team comprises Joseph Spatafora (Oregon State University), Jason Stajich (University of California at Riverside), Kevin McCluskey (Fungal Genetics Stock Center), Pedro Crous (Centraal Bureau voor Schimmelcultures, Netherlands), Gillian Turgeon (Cornell University), Daniel Lindner (USDA Forest Service), Kerry O’Donnell and Todd Ward (USDA ARS), Antonis Rokas (Vanderbilt University), Louise Glass (University of California at Berkeley), Betsy Arnold (University of Arizona), Igor Grigoriev (JGI DOE) and myself.

    The ‘1000 Fungal Genomes‘ site, set up by Jason Stajich’s group, represents a gathering of the information about the project and will link to additional resources tracking the progress of the project.

    DOE JGI 2012 Community Sequencing Program Portfolio

    November 4th, 2011

    Trillions Served: Massive, Complex Projects Dominate DOE JGI 2012 Community Sequencing Program Portfolio.

    ‘The 2012 Community Sequencing Program (CSP) call invited researchers to submit proposals for projects that advance capabilities in fields such as plant-microbe interactions, microbes involved in carbon capture and greenhouse gas emission, and metagenomics—the characterization of complex collections of microbes from particular environmental niches. The total allocation for the coming year’s CSP portfolio will exceed 30 trillion bases (terabases or Tb), a 100-fold increase compared with just two years ago, when just a third of a terabase was allocated to more than 70 projects. This amounts to the equivalent of at least 10,000 human genomes in data …’ Read more

     

    Photo:  The boreal forest, one of the ecosystem investigated by the CSP 2012 program. Denali Natl Park, Alaska  (© F Martin)

    7th Annual DOE JGI User Meeting

    October 24th, 2011

    The 7th Annual DOE JGI User Meeting ‘Genomics of Energy & Environment’ will be held at the Marriott Hotel in Walnut Creek, California on March 20 – 22, 2012.

    Scientists interested in how genomics applies to bioenergy and environmental issues are invited to attend the annual DOE Joint Genome Institute Genomics of Energy & Environment Meeting. This international gathering of researchers with an interest in sequence-based science offers three days of presentations, tours, workshops, and poster sessions.

    Topics: Synthetic biology & biodesign, Systems biology/transcriptional networks, Application of single cell genomics in microbial ecology and bioprospecting, Genomic analysis of biofuel traits in maize and switchgrass, Cloud computing as a platform for large scale sequence analysis, Ocean viruses: towards population genomics, understanding virus-host interactions, and accessing the uncultured, Omics in the Arctic: Genome-enabled contributions to carbon cycle and biogeochemical research in high-latitude ecosystems, and Ancient DNA

     

    JGI Fall 2011 Primer

    October 24th, 2011

    The Fall edition of the U.S Department of Energy (DOE) Joint Genome Institute (JGI) newsletter The Primer is now available for download:

    …featuring articles and images:

    • Tagging enzymes that can take the heat
    • Carbon fixation in the dark ocean
    • Linking fungi to boreal forests
    • Notable publications & more…

     

    1st Mycorrhizal Genomics Workshop

    August 21st, 2011

    We are organizing the 1st Mycorrhizal Genomics Workshop at the INRA center in Champenoux (France), on September 28-29, 2011. The aim of the workshop is (1) to establish the current status of the JGI CSP  ‘25 Mycorrhizal Genomes‘ project, (2) to train people to use the JGI annotation tools, and (3) to bring together future annotators for discussing the data sets which will be generated by machine annotations and manual curations. The format of the workshop will be roughly equally split between informal presentations (summarizing the current findings), what we hope will be spirited discussion and brainstorming about how to take advantage of the genome sequences to inform our understanding of symbiosis and fungal biology.

    A group of six mycorrhizal species have been selected for the first analyses. These include:

    • the unpublished Laccaria bicolor v2.0,
    • the annotated unpublished Paxillus involutus (Boletales) (thanks to Anders Tunlid),
    • Oidiodendron maius (Leotiomycetes): assembly and automated annotation done, RNA-Seq ESTs are available,
    • Hebeloma cylindrosporum (Agaricales, Cortinariaceae): assembly done, annotation on-going, RNA-Seq ESTs are available,
    • Pisolithus microcarpus (Boletales): assembly done, RNA-Seq ESTs are available,
    • Piloderma croceum (Atheliales): assembly on-going, RNA-Seq on-going.

    Thanks to David Hibbett, these genomes will be compared to the current set of yet unpublished genomes of >15 saprotrophic agaricomycotina.

    Seven additional mycorrhizal species are in the scope of work for 2011 from JGI: Cenococcum geophilum, Sebacina vermifera, Suillus luteus, Scleroderma citrinum, Terfezia boudieri, Tulasnella calospora, and Tricholoma matsutake. gDNA preps have either been shipped to JGI or are on-going in our lab.

    The rest of the Tier 1 and Tier 2 species are on hold until we are able to extract enough DNA of the requested quality (Amanita muscaria, Boletus edulis, Lactarius quietus, Meliniomyces spp., Paxillus rubicundulus, Rhizoscyphus ericeae, Tomentella sublilacina) or find the culture for growing the mycelium (Cantharellus cibarius, Coltricia cinnamomea, Gymnomyces xanthosporus, Ramaria formosa).

    Photo: The Aspen/Fly Agaric ectomycorrhizal symbiosis.  The fruiting body of the symbiotic Amanita muscaria is produced by the underground mycelium associated to its host-plant, a small aspen seedling. MSA Mushroom Forey, Large Animal Research Station, University of Fairbanks, AK (© F Martin).

     

    JGI Summer 2011 Primer

    July 15th, 2011

    The summer edition of the U.S Department of Energy (DOE) Joint Genome Institute (JGI) newsletter The Primer is now available for download: http://1.usa.gov/orAs40

    …featuring articles and images:

    • Report from the 2011 Sequencing, Finishing and Analysis in the Future (SFAF) Meeting held in Santa Fe, NM, June 1–3, 2011
    • DOE Funds Restored Wetlands Study
    • Countering Rust Fungal Outbreaks
    • Detailing Lignin’s Development
    • Notable Publications & more…

     

    The Dry Rot Genome & Wood Decay Machinery in Forest Fungi

    July 14th, 2011

    The other good news of this Bastille Day: our paper on the Serpula lacrymans genome is reported online July 14 in Science Express.

    The Domestic Dry Rot (Serpula lacrymans, Basidiomycete, Coniophoraceae) comprises two subgroups, S. lacrymans var shastensis, found in montane conifer forests in the Himalayan foothills, and S. lacrymans var lacrymans, cause of building dry rot, which diverged in historic time [Kauserud et al. (2007) Mol. Ecol. 16: 3350-3360]. This brown rot fungus is the most damaging destroyer of wood construction materials in temperate regions. It has a powerful capacity for cellulolysis and mycelial colonization of coarse solid materials. It has been suggested that Northern Europe buildings offer a substitute environment for the forest floor in the Himalayan foothills where wild isolates of S. lacrymans have been spotted.

    As most brown rot fungi, S. lacrymans selectively depolymerises the lignin component of wood lignocellulose to assess and degrade cellulose. Brown rot wood decay involves an initial non-enzymic attack on the wood cell wall  generating hydroxyl radicals (∙OH) extracellularly via  the Fenton reaction. Residues from fungal brown rot of wood compose most of the carbon sequestered in boreal forest soil.

    Serpula’ capacity to break down the cellulose in wood led to its selection for sequencing by the U.S. Department of Energy (DOE) Joint Genome Institute (JGI) in the Community Sequencing Program 2007, with the goal of identifying the enzymes involved in the wood decay process and using the information to improve cellulosic biofuels production. Within the framework of the MycoCosm project, we have also compared the genome of S. lacrymans to the available genomes of white-rotters and the ectomycorrhizal symbiont Laccaria bicolor to study the evolution of ecological lifestyles in forest fungi and how the plant cell wall decomposing machinery of fungi underlies their functional diversity in forests. This study is published online July 14 in Science Express by Dan Eastwood and the Serpula Genome Consortium.

    The genome of S. lacrymans S7.9 was 42.8 Mbp, containing 12,917 gene predictions. Comparative and functional genomics of S. lacrymans showed that the evolution of both ectomycorrhizal biotrophy and brown rot saprotrophy were accompanied by reductions and losses in specific protein families, such as the enzymes degrading plant cell wall polysaccharides. Brown rot and ectomycorrhizal fungi have the fewest hydrolytic CAZy genes. Brown rot fungi have fewest oxidoreductases, due, not to gene losses, but to gene duplications in white rot species. This finding suggests that Serpula had cast off the energetically expensive apparatus of ligninolysis and acquired alternative mechanisms of initial attack of lignocellulose. It appears that S. lacrymans synthesized high level of variegatic acid, an iron-reducing phenolate, to enhance the Fenton’s reaction in contact with wood.

    We are also suggesting that the loss of aggressive ligninolysis might have permitted brown rot transitions to biotrophic ectomycorrhiza in Boletales. Analysis of the ‘soon-to-be released’ genomes from the ECM Boletales, Paxillus involutus and Pisolithus microcarpus, will facilitate the study of this lifestyle transition which tremendously impacted the fungi’s role in the global carbon cycle.

    The non-aggressive lineage, S. lacrymans var. shastensis, residing naturally in North America and Asia, has also been sequenced at JGI. This should help in understanding the evolution from  the non-aggressive to aggressive  Serpula strains.

    Eastwood et al. (2011) The Plant Cell Wall–Decomposing Machinery Underlies the Functional Diversity of Forest Fungi. Science DOI: 10.1126/science.1205411.

    Biofuels study gives clue to forest ecosystems. University of Oxford News & Stories.

    Understanding Dry Rot Fungus to Make Fuel. New Energy & Fuel.

    Breaking down cellulose without blasting lignin: “Dry rot” genome offers lessons for biofuel pretreatment. The JGI News.

     

    Photo: Serpula lacrymans resupinate fruiting body © G Elsner