July 31st, 2014 by Francis Martin
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In 2003, the Poplar Mesocosm Sequencing project was launched to sequence the genome of three Populus-associated fungi, the ectomycorrhizal (EM) basidiomycete Laccaria bicolor, the arbuscular mycorrhizal (AM) glomeromycete Rhizophagus irregularis (formerly Glomus intraradices), and the poplar leaf rust Melampsora larici-populina. The publication of the genome sequence of L. bicolor was a landmark event for the mycorrhizal community. It has been rapidly followed by the release of the genome of the iconic edible EM Tuber melanosporum, the Périgord black truffle and more recently, by the genome of Rhizophagus irregularis. These genomes have provided unprecedented knowledge about the structure and functioning of the mycorrhizal fungal species and their interactions with their host plants. Genome-wide transcript profilings have also led to the identification of master genes with crucial roles in symbiosis formation, such as those coding for Mycorrhiza-induced Small Secreted Proteins (MiSSPs) controling plant immunity and development.
An international effort, referred as to the Mycorrhiza 25 Genomes Project and then the Mycorrhizal Genomics Initiative (MGI), aiming to unearth the evolution and functioning of mycorrhizal symbioses through large-scale genome sequencing has been launched in 2011. As of writing, this initiative targets a set of 35 fungal species that are able to form various types of mycorrhizal symbioses, i.e., EM, arbuscular, ericoid and orchid mycorrhizae (see my previous posts ‘Mycorrhizal Genomics Initiative‘ and ‘Exploring the Mycorrhizal Genomes‘ ). Sequencing is carried out at JGI and Genoscope in the framework of the JGI Community Science Program, the 1000 Fungal Genomes Project and the TuberEvol project. Comparison of these genomes should facilitate the characterization of the genetic mechanisms that underpin the formation and evolution of ecologically-relevant mycorrhizal symbioses and characterization of genes selectively associated with particular symbiotic patterns.
The fungal species sequenced have been selected based on: (1) their phylogenetic position, (2) their ecological relevance, and (3) their ability to establish different types of mycorrhizal symbiosis. As of today, genomic sequences and gene repertoires are publicly available for 28 mycorrhizal fungi, including 24 ectomycorrhizal species, 3 ericoid species, 2 orchid mycorrhizal species and 1 arbuscular mycorrhizal species (see Table below & see the JGI MycoCosm Mycorrhizal Fungi portal.
Genomes of the sequenced mycorrhizal fungi range in size from about 36 Mb, as in the case of Rhizopogon vinicolor, to a 193 Mb, as in Tuber magnatum (Table). Repetitive DNA, mostly in the form of transposable elements (TE), is responsible for the bulk of the variation. A striking feature is the wide variation in repetitive DNA content (from 3.6 % for H. cylindrosporum to 58.3% for T. magnatum). Predicted gene contents range from about 7500 for T. melanosporum to ~28000 genes for Rhizophagus irregularis.
We are drafting a paper summarizing the main conclusions from the analysis of the first series of mycorrhizal genomes. Stay tune!
||Amanita muscaria Koide v1.01
||Boletus edulis v1.01
||Cenococcum geophilum 1.58 v2.01
||Choiromyces venosus 120613-1 v1.01
||Cortinarius glaucopus AT 2004 276 v2.01
||Gyrodon lividus BX v1.01
||Hebeloma cylindrosporum h7 v2.01
||Laccaria amethystina LaAM-08-1 v1.01
||Laccaria bicolor 81306 v1.01
||Laccaria bicolor D101 v1.01
||Laccaria bicolor S238N-H70 v1.01
||Laccaria bicolor S238N-H82 v1.01
||Laccaria bicolor S238N-H82xH70 v1.01
||Laccaria bicolor v2.01
||Meliniomyces bicolor E v2.03
||Meliniomyces variabilis F v1.03
||Morchella conica CCBAS932 v1.01
||Oidiodendron maius Zn v1.03
||Paxillus involutus ATCC 200175 v1.01
||Paxillus rubicundulus Ve08.2h10 v1.01
||Piloderma croceum F 1598 v1.01
||Pisolithus microcarpus 441 v1.01
||Pisolithus tinctorius Marx 270 v1.0
||Rhizophagus irregularis DAOM 181602 v1.02
||Rhizopogon vinicolor AM-OR11-026 v1.01
||Scleroderma citrinum Foug A v1.01
||Sebacina vermifera MAFF 305830 v1.04
||Suillus brevipes v1.01
||Suillus luteus UH-Slu-Lm8-n1 v1.01
||Terfezia boudieri S1 v1.01
||Tricholoma matsutake 945 v3.01
||Tuber magnatum v1.01
||Tuber melanosporum v1.01
||Tulasnella calospora AL13/4D v1.04
||Wilcoxina mikolae CBS 423.85 v1.01
February 19th, 2014 by Francis Martin
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The JGI User Meeting, Genomics of Energy and the Environment, will be held March 18-20 in Walnut Creek, CA.
This year looks like a particularly exciting meeting, with great speakers and a diversity of interesting topics. The agenda and other details for this meeting can be found at http://www.jgi.doe.gov/meetings/usermeeting/
December 15th, 2013 by Francis Martin
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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).
October 16th, 2013 by Francis Martin
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The Annual Meeting 2013 of the Lab of Excellence ARBRE will be held at INRA-Nancy on Monday 21st October, 2013.
The primary objective of this meeting will be to present the projects awarded funding by the Labex call for proposals in 2012. It will aim to highlight and discuss the most noteworthy achievements during the first year of Labex ARBRE, specific to research units and those in each thematic area (Research, Valuation, Training-Dissemination). Projects selected for funding from the 2013 call for proposals will also be presented. The day will end with a strategy discussion moderated by project leaders from each thematic area who will focus on how to strengthen relationships between thematic actions and areas of research.
For the detailed meeting agenda please click here – Agenda
August 15th, 2013 by Francis Martin
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Wilson EO (2013) Letters to a Young Scientist.
New York: Liveright (W.W. Norton). 245 p. ISBN 978-0871403773 (hardcover). US$21.95.
Read the book review by: Simberloff D (2013) The Passion Principle. PLoS Biol 11(8): e1001629. doi:10.1371/journal.pbio.1001629
July 14th, 2013 by Francis Martin
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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.
June 26th, 2013 by Francis Martin
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Must read …
The Transition from a Phytopathogenic Smut Ancestor to an Anamorphic Biocontrol Agent Deciphered by Comparative Whole-Genome Analysis
[Abstract. Pseudozyma flocculosa is related to the model plant pathogen Ustilago maydis yet is not a phytopathogen but rather a biocontrol agent of powdery mildews; this relationship makes it unique for the study of the evolution of plant pathogenicity factors. The P. flocculosa genome of ~23 Mb includes 6877 predicted protein coding genes. Genome features, including hallmarks of pathogenicity, are very similar in P. flocculosa and U. maydis, Sporisorium reilianum, and Ustilago hordei. Furthermore, P. flocculosa, a strict anamorph, revealed conserved and seemingly intact mating-type and meiosis loci typical of Ustilaginales. By contrast, we observed the loss of a specific subset of candidate secreted effector proteins reported to influence virulence in U. maydis as the singular divergence that could explain its nonpathogenic nature. These results suggest that P. flocculosa could have once been a virulent smut fungus that lost the specific effectors necessary for host compatibility. Interestingly, the biocontrol agent appears to have acquired genes encoding secreted proteins not found in the compared Ustilaginales, including necrosis-inducing-Phytophthora-protein- and Lysin-motif- containing proteins believed to have direct relevance to its lifestyle. The genome sequence should contribute to new insights into the subtle genetic differences that can lead to drastic changes in fungal pathogen lifestyles.]
June 22nd, 2013 by Francis Martin
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We welcome Dr. Jessy Labbé, a former lab Ph.D. student, who joins us from the Biosciences Division at Oak Ridge National Laboratory (TE, USA). Within the framework of the DOE Plant-Microbe Interfaces project, Jessy is working with François Le Tacon and myself on the QTL for mycorrhiza formation in poplar. He is funded by the LabeX ARBRE.
May 23rd, 2013 by Francis Martin
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Collins C, Keane TM, Turner DJ, O’Keeffe G, Fitzpatrick DA, Doyle S (2013) Genomic and Proteomic Dissection of the Ubiquitous Plant Pathogen, Armillaria mellea: Towards a New Infection Model System. J Proteome Research, DOI: 10.1021/pr301131t
Armillaria mellea is a major plant pathogen. Yet, no large-scale ‘-omic’ data are available to enable new studies, and limited experimental models are available to investigate basidiomycete pathogenicity. Here we reveal that the A. mellea genome comprises 58.35 Mb, contains 14,473 gene models, of average length 1575 bp (4.72 introns/gene). Tandem mass spectrometry identified 921 mycelial (n = 629 unique) and secreted (n = 183 unique) proteins. Almost 100 mycelial proteins were either species-specific or previously unidentified at the protein level. A number of proteins (n = 111) were detected in both mycelia and culture supernatant extracts. Signal sequence occurrence was fourfold greater for secreted (50.2%) compared to mycelial (12%) proteins. Analyses revealed a rich reservoir of carbohydrate degrading enzymes, laccases and lignin peroxidases in the A. mellea proteome, reminiscent of both basidiomycete and ascomycete glycodegradative arsenals. We discovered that A. mellea exhibits a specific killing effect against Candida albicans, during co-culture. Proteomic investigation of this interaction revealed the unique expression of defensive and potentially offensive A. mellea proteins (n = 30). Overall, our data reveal new insights into the origin of basidiomycete virulence and we present a new model system for further studies aimed at deciphering fungal pathogenic mechanisms.]
Photo: Fruiting body of Armillaria mellea © F Martin