Posts Tagged ‘ectomycorrhiza’

Alisha owenby lands an NSF DDIG

May 23rd, 2013

From Joey Spatafora Lab blog

[Alisha Owensby, PhD candidate in the lab, was recently awarded an NSF Doctoral Dissertation Improvement Grant (DDIG) for her proposal, “Evolutionary Genomics of Inter-Kingdom Host-Jumping in the Fungal Genus Elaphocordyceps“.  Way to go!  If you follow our blog, you know that Alisha is currently in Nancy, France working in the laboratory of Francis Martin at INRA.  She is working on the genome of Elaphomyces, one of the hosts of Elaphocordyceps.  This is a particularly challenging project as Elaphomyces does not culture and thus the genomic libraries are prepared from DNA and RNA extracted directly from sporocarps and are metagenomic in nature.  The photo is of Alisha working in Francis’ lab doing an RNA extraction.  Just a few more weeks and she’ll be back.  Bring wine and cheese!!]

Photo: Alisha and Nicolas extracting Elaphomyces RNA for RNA-Seq

A lovely fungus

October 12th, 2011

Annegret and Yohann took this photo of our favorite ectomycorrhizal fungus Laccaria bicolor (strain S238N) fruiting near its poplar host. Its whithish mycelium is seen growing on ectomycorrhizal roots.

Image: Fruiting body of Laccaria bicolor S238N (© INRA: A Kohler & Y Daguerre).

25 Mycorrhiza Genomes

May 13th, 2010

Exploring the Genome Diversity of Mycorrhizal Fungi to Unearth Symbiosis Evolution

TintinBy the end of May, we will submit a proposal to the JGI Community Sequencing Program 2011 for whole-genome shotgun sequencing and deep transcriptomics of 25 symbiotic mycorrhizal fungi aiming to develop a phylogeny-driven genomic encyclopedia of symbiotic fungi. This project will be developed under the umbrella of the JGI Fungal Genomics Program initiated in October 2009.

The analysis of the Laccaria bicolor and Tuber melanosporum genomes emphasized the importance of having sequence data for more than one representative of each phylum of ECM fungi. As today, only a few ECM species were targeted for genome sequencing because of an interest in a specific characteristic of the organism. The model species nominated by the ECM symbiosis community are Paxillus involutus (CSP 2008), Rhizopogon salebrosus (CSP 2009), and Pisolithus tinctorius and P. microcarpus (CSP 2010). They belong to the Boletales, a large phylum of symbiotic basidiomycetes. None of the sequence has been released yet.

In addition to the on-going sequencing of Pisolithus species, we now propose a two-year project to sequence the 23 following reference genomes for basidiomycetous and ascomycetous mycorrhizal fungi. These species have been selected based on their ecological and phylogenetic importance, ability to establish different types of mycorrhizal symbiosis, and the avalaibility of HMW DNA:

JGI Fungal Genome Programme (MycoCosm): The ascomycetous Cenococcum geophilum (Dothideomycetes) and basidiomycetous Hebeloma cylindrosporum (Agaricales, Cortinariaceae) ectomycorrhizal fungi have been selected within the JGI Fungal Genome Programme in October 2009. As of this writing, DNA has been extracted and shipped to JGI for sequencing.

Tier 1 [11 species]

Basidiomycotina: Amanita muscaria (Agaricales; Amanitaceae), Laccaria amethystina (Agaricales; Hydnangiaceae), Lactarius quietus (Russulales, oak-specific symbiont), Paxillus rubicundulus (Boletales, Paxilineae, alder-specific), Piloderma croceum (Atheliales), Suillus luteus (Boletales, Suillineae), Scleroderma citrinum (Boletales, Sclerodermataceae), Thelephora terrestris (Thelephorales), Sebacina vermifera (Sebacinales).

AscomycotinaMeliniomyces bicolor (Helotiales, forms both ericoid mycorrhizas and ectomycorrhizas), Rhizoscyphus ericeae (Helotiales, ericoid mycorrhizal fungus), Terfezia boudieri (Pezizales, Pezizaceae; forms both endo- and ectomycorrhizas).

Tier 2 [10 species]

Basidiomycotina: Boletus edulis (Boletales, Boletineae), Cantharellus cibarius (Cantharellales), Corticia cinnamomea (Hymenochaetales), Cortinarius glaucopus (Agaricales; Cortinariaceae), Gymnomyces xanthosporus (Russulales), Ramaria formosa (Gomphales), Tomentella sublilacina (Thelephorales), Tricholoma matsutake (Agaricales; Tricholomataceae), Tulasnella calospora (Cantharellales; Tulasnellaceae).

AscomycotinaMeliniomyces variabilis (Helotiales, root endophyte)

The Tier 1 taxa are proposed for sequencing in 2010. If sequencing capacity exists, Tier 2 taxa could be sequenced in 2011.

The proposed taxa include representatives of the major clades (orders or subclasses) of culturable Mycotina that contain mycorrhizal taxa. This phylogenetically based sample of the genomes that we propose would propel the field forward and allow us to answer fundamental questions about the evolution of this mutualism and the variation in function and interaction across the phylogenetic depth occupied by these organisms. The fact that mycorrhizal fungi appear to be independently derived from multiple saprobic lineages means that genomic data will provide independent assessments of what is required to become ectomycorrhizal. This initiative would be complementary to the project aiming to sequence the genome of the lignocellulose-degrading basidiomycetes submitted by Hibbett, Cullen, Eastwood and Martin to CSP2011.

Community Interest

The proposed genome sequences will be of great interest to diverse scientists with interests in 1) development and evolution of the mycorrhizal symbiosis; 2) carbon cycling and carbon sequestration in terrestrial ecosystems; 3) diverse aspects of fungal molecular biology; 4) molecular ecology of communities of mycorrhizal fungi; 5) plant health and domesticated bioenergy trees; 6) fungal phylogenetics; and 7) evolution of terrestrial ecosystems.

If you are interested by joining this exciting project and/or willing to provide a letter of support for this proposal, contact me.

Pisolithus genome sequencing on the road

August 10th, 2009

Piso_eucalyptOur proposal ‘Sequencing of the pan-global basidiomycetes Pisolithus tinctorius and Pisolithus microcarpus for increased knowledge of the ectomycorrhizal symbiosis’ to JGI’s Community Sequencing Program 2010 has been approved for WGS sequencing in this cycle. Pisolithus are puffball belonging to the Gasteroid group (Basidiomycota, Agaricomycotina; Agaricomycetes; Agaricomycetidae; Boletales; Sclerodermatineae; Pisolithaceae).

The Eucalyptus genome is near completion at the JGI. As part of the development of a broader community-based Eucalyptus genomics resource, and as a means of conducting informative comparative genomics among fungi, we have proposed the genome sequencing for Pisolithus microcarpus, a prominent eucalypt-specific ectomycorrhizal symbiont worldwide. We have also propose the sequencing of its close relative P. tinctorius forming symbiosis with pine species only and commercially used in U.S.A. for large scale mycorrhizal inoculation of pine plantations.

The objectives of this collaborative project between JGI and INRA is to: 1) build an assembled genome sequence (8X) database, 2) develop 200,000 ESTs and carry out protein shotgun sequencing for supporting the annotation of the two genomes, 3) annotate the P. microcarpus and P. tinctorius genomes, 4) investigate alteration in transcriptome upon ectomycorrhiza formation using custom NimbleGen exon arrays, 5) investigate the genomic polymorphism between eucalypt- and pine-associated Pisolithus using CGH arrays and/or Illumina sequencing, and 5) complete an initial comparative analysis between these Pisolithus and other sequenced fungi, such as Paxillus involutus, Serpula lacrymans and Rhizopogon salebrosus.

The availability of genome sequence from two related fungi that play such a critical role in tree growth and health will increase our understanding of the symbiosis host specificity.  This work will greatly complement efforts to understand and exploit eucalypt trees and will give researchers an unprecedented resource to aid in our understanding of the relationship between this tree and its favorite fungus.

Up to 240,000 ‘454’ ESTs of P. microcarpus (strain 441) has recently been sequenced by the Genoscope and assembled by our team. This resource will soon be available online at the INRA genome portal.