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The CNRGH is the French national research center which enables a response to scientific questions necessitating high throughput sequencing and genotyping thanks to the development and deployment of innovative integrated technologies. The organization of the CNRGH enables optimization of genetic and genomic research on human diseases by creating indispensable links between cohort constitution (DNA samples), identification of the responsible genes, and study of the transcriptome and epigenome.
List of the main projects of the Institut de Génomique
The symbiotic fungus Tuber melanosporum Vittad. (Perigord Black truffle) belongs to the Ascomycota (Pezizomycota, Pezizomycetes, Pezizales, Tuberaceae).
This soil fungus is endemic to calcareous soils in southern Europe and induces a beneficial ectomycorrhizal symbiosis on haselnut tree and oaks. The fungus requires a host tree to complete its life cycle and produce hypogeous fruit bodies, so-called truffles. The Perigord Black truffle is a highly appreciated delicacy for its delicate organoleptic properties (i.e., taste and perfumes). This is a 'national, cult-food', one of the worldwide recognized icone of the European gastronomy and culture, for which genomic information could act as a knowledge platform to improve its production and environmental persistence.
The ectomycorrhizal symbiosis and the truffle life cycle
ectomycorrhizal symbiotic relationship, long, branching fungal filaments known
as hyphae ramify between cells of the host root’s outer layers, form a sheath
around the root, and radiate outwards into the surrounding soil and litter. In
late Summer, extramatrical hyphae aggregate to form fruit body initials. The
latter developed to the fruit body during Fall and early Winter. The spores released
from mature truffles germinate in the following
Spring, producing a vegetative mycelium, which results in colonisation of tree
root tips and further development of the symbiosis completing the truffle life
Understanding the evolution of symbiosis in fungi
Besides one of the two symbiotic fungi thus far addressed by a genomic project, T. melanosporum is the first sequenced member of the Pezizales, a very large and heterogenous group of ascomycetous fungi presently devoid of any genomic coverage. There is currently debate about whether most ectomycorrhizal fungi are derived from a few ectomycorrhizal ancestors, with multiple losses of that lifestyle in many currently saprobic lineages, or whether the pattern is based strictly on many convergent gains of the mycorrhizal habit with no reversions to saprotrophy. The genome architectures of symbiotic fungi may bear tell-tale signs of their adaptation to the symbiotic lifestyle. To assess whether independent symbiosis events result in similar genomic signatures, we have sequenced the genome of T. melanosporum and compared it to the genome of the symbiotic basidiomycete Laccaria bicolor.
The French-Italian Tuber Genome Consortium
Following an initiative of the "Tree-Microbe Interactions" Unit at the INRA Center in Nancy, the Scientific Council of Genoscope formally approved the genome sequencing of the T. melanosporum in 2005.
A consortium of 10 French and Italian laboratories, including the INRA-Nancy, the Università degli studi di Parma, Istituto per la Protezione delle Piante del CNR di Torino, Istituto di Genetica Vegetale di Perugia and the Università degli Studi di Urbino, was formed to annotate and analyze the genome.
whole-genome shotgun strategy (WGS) was adopted for sequencing and assembling
the T. melanosporum draft genome.
All genomic DNA was obtained from the
vegetative mycelium of the haploid strain Mel28. Template DNA was extracted
from mycelium using the Genomic Tip DNA extraction kit (Qiagen). This DNA was
randomly sheared and size-fractionated to create libraries with roughly 3 kb
and 10 kb inserts. From these two libraries, 1,284,900 reads were obtained.
After trimming, the removal of multiple read attempts, and the exclusion of
overly-short reads, the pool of data available for the assembly consisted of
1,281,391 reads (10X total sequence redundancy). The data was assembled using the ARACHNE assembler.
After excluding redundant and short scaffolds, there remained 125 Mbp of
scaffold sequence (398 supercontigs, N50= 637 kb).
Contact : Patrick Wincker : pwincker .. At .. Genoscope.cns.fr (Genoscope) - Francis Martin : fmartin.. At .. nancy.inra.fr (INRA)
Laboratories involved: Laboratory for the Genomic Analysis of Eukaryotes , Sequencing Laboratory
CEA is a French government-funded technological research organisation in four main areas: low-carbon energies, defense and security, information technologies and health technologies. A prominent player in the European Research Area, it is involved in setting up collaborative projects with many partners around the world.