Sebacinales everywhere: previously overlooked ubiquitous fungal endophytes, PLoS One, vol.6, p.16793, 2011. ,
Disruption of signaling in a fungal-grass symbiosis leads to pathogenesis, Plant Physiol, vol.153, pp.1780-1794, 2010. ,
Fungal endophytes: diversity and functional roles, New Phytol, vol.182, pp.314-330, 2009. ,
Ectomycorrhizal fungi and the biotrophy-saprotrophy continuum, New Phytol, vol.178, pp.230-233, 2008. ,
The endophytic continuum, Mycol Res, vol.109, pp.661-686, 2005. ,
Contributions of rpb2 and tef1 to the phylogeny of mushrooms and allies (Basidiomycota, Fungi), Mol Phylogenet Evol, vol.43, pp.430-451, 2007. ,
Sebacinales: a hitherto overlooked cosm of heterobasidiomycetes with a broad mycorrhizal potential, Mycol Res, vol.108, pp.1003-1010, 2004. ,
Piriformospora indica, gen. et sp. nov., a new root-colonizing fungus, Mycologia, vol.90, pp.896-903, 1998. ,
Association of Piriformospora indica with Arabidopsis thaliana roots represents a novel system to study beneficial plant-microbe interactions and involves early plant protein modifications in the endoplasmic reticulum and at the plasma membrane, Physiologia Plantarum, vol.122, pp.465-477, 2004. ,
A cell wall extract from the endophytic fungus Piriformospora indica promotes growth of Arabidopsis seedlings and induces intracellular calcium elevation in roots, Plant J, vol.59, pp.193-206, 2009. ,
Salt tolerance of barley induced by the root endophyte Piriformospora indica is associated with a strong increase in antioxidants, New Phytol, vol.180, pp.501-510, 2008. ,
The root-colonizing endophyte Pirifomospora indica confers drought tolerance in Arabidopsis by stimulating the expression of drought stress-related genes in leaves, Mol Plant Microbe Interact, vol.21, pp.799-807, 2008. ,
The endophytic fungus Piriformospora indica reprograms barley to salt-stress tolerance, disease resistance, and higher yield, Proc Natl Acad Sci U S A, vol.102, pp.13386-13391, 2005. ,
Piriformospora indica promotes adventitious root formation in cuttings, Scientia Horticulturae, vol.112, pp.422-426, 2007. ,
A phosphate transporter from the root endophytic fungus Piriformospora indica plays a role in phosphate transport to the host plant, J Biol Chem, vol.285, pp.26532-26544, 2010. ,
The endophytic fungus Piriformospora indica stimulates the expression of nitrate reductase and the starch-degrading enzyme glucan-water dikinase in tobacco and Arabidopsis roots through a homeodomain transcription factor that binds to a conserved motif in their promoters, J Biol Chem, vol.280, pp.26241-26247, 2005. ,
The root endophytic fungus Piriformospora indica requires host cell death for proliferation during mutualistic symbiosis with barley, Proc Natl Acad Sci U S A, vol.103, pp.18450-18457, 2006. ,
, Mycorrhizal Symbiosis, 2008.
URL : https://hal.archives-ouvertes.fr/hal-01268065
Broad-spectrum suppression of innate immunity is required for colonization of Arabidopsis roots by the fungus Piriformospora indica, Plant Physiol, vol.156, pp.726-740, 2011. ,
Ethylene signalling and ethylene-targeted transcription factors are required to balance beneficial and nonbeneficial traits in the symbiosis between the endophytic fungus Piriformospora indica and Arabidopsis thaliana, New Phytol, vol.185, pp.1062-1073, 2010. ,
Calcium signaling in pathogenic and beneficial plant microbe interactions: what can we learn from the interaction between Piriformospora indica and Arabidopsis thaliana, Plant Signal Behav, vol.4, pp.1024-1027, 2009. ,
Manipulation of plant innate immunity and gibberellin as factor of compatibility in the mutualistic association of barley roots with Piriformospora indica, Plant J, vol.59, pp.461-474, 2009. ,
Systemic resistance in Arabidopsis conferred by the mycorrhizal fungus Piriformospora indica requires jasmonic acid signaling and the cytoplasmic function of NPR1, Plant Cell Physiol, vol.49, pp.1747-1751, 2008. ,
The role of auxins and cytokinins in the mutualistic interaction between Arabidopsis and Piriformospora indica, Mol Plant Microbe Interact, vol.21, pp.1371-1383, 2008. ,
Piriformospora indica affects plant growth by auxin production, Physiol Plant, vol.131, pp.581-589, 2007. ,
Pathogenomics of fungal plant parasites: what have we learnt about pathogenesis?, Curr Opin Plant Biol, vol.14, pp.392-399, 2011. ,
Signatures of adaptation to obligate biotrophy in the Hyaloperonospora arabidopsidis genome, Science, vol.330, pp.1549-1551, 2010. ,
Genome expansion and gene loss in powdery mildew fungi reveal tradeoffs in extreme parasitism, Science, vol.330, pp.1543-1546, 2010. ,
URL : https://hal.archives-ouvertes.fr/hal-02664949
Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium, Nature, vol.464, pp.367-373, 2010. ,
URL : https://hal.archives-ouvertes.fr/hal-00574227
The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis, Nature, vol.452, pp.88-92, 2008. ,
URL : https://hal.archives-ouvertes.fr/halsde-00261893
Tissueadapted invasion strategies of the rice blast fungus Magnaporthe oryzae, Plant Cell, vol.22, pp.3177-3187, 2010. ,
Reprogramming a maize plant: transcriptional and metabolic changes induced by the fungal biotroph Ustilago maydis, Plant J, vol.56, pp.181-195, 2008. ,
FM-dyes as experimental probes for dissecting vesicle trafficking in living plant cells, J Microsc, vol.214, pp.159-173, 2004. ,
URL : https://hal.archives-ouvertes.fr/hal-00122335
Assessing the gene space in draft genomes, Nucleic Acids Res, vol.37, pp.289-297, 2009. ,
Assessing the Performance of Single-Copy Genes for Recovering Robust Phylogenies, Syst Biol, vol.57, pp.613-627, 2008. ,
URL : https://hal.archives-ouvertes.fr/hal-02333207
Karyotype analysis, genome organization, and stable genetic transformation of the root colonizing fungus Piriformospora indica, Fungal Genet Biol, vol.46, pp.543-550, 2009. ,
The diploid genome sequence of Candida albicans, Proc Natl Acad Sci U S A, vol.101, pp.7329-7334, 2004. ,
The Pfam protein families database, Nucleic Acids Res, vol.38, pp.211-222, 2010. ,
URL : https://hal.archives-ouvertes.fr/hal-01294685
Genesis of a fungal non-self recognition repertoire, PLoS One, vol.2, p.283, 2007. ,
URL : https://hal.archives-ouvertes.fr/hal-00131937
Fungal incompatibility: evolutionary origin in pathogen defense, Bioessays, vol.31, pp.1201-1210, 2009. ,
An efficient algorithm for large-scale detection of protein families, Nucleic Acids Res, vol.30, pp.1575-1584, 2002. ,
CAFE: a computational tool for the study of gene family evolution, Bioinformatics, vol.22, pp.1269-1271, 2006. ,
LysM, a widely distributed protein motif for binding to (peptido)glycans, Mol Microbiol, vol.68, pp.838-847, 2008. ,
Conserved fungal LysM effector Ecp6 prevents chitin-triggered immunity in plants, Science, vol.329, pp.953-955, 2010. ,
A latrophilin/CL-1-like GPS domain in polycystin-1, Curr Biol, vol.9, pp.585-588, 1999. ,
Molecular characterization of a novel beta-1,3-exoglucanase related to mycoparasitism of Trichoderma harzianum, Gene, vol.226, pp.147-154, 1999. ,
A family of genes required for maintenance of cell wall integrity and for the stress response in Saccharomyces cerevisiae, Proc Natl Acad Sci U S A, vol.94, pp.13804-13809, 1997. ,
Carbohydrate-binding modules: fine-tuning polysaccharide recognition, Biochem J, vol.382, pp.769-781, 2004. ,
The CBEL glycoprotein of Phytophthora parasitica var-nicotianae is involved in cell wall deposition and adhesion to cellulosic substrates, J Cell Sci, vol.115, pp.4565-4575, 2002. ,
Cellulose binding domains of a Phytophthora cell wall protein are novel pathogen-associated molecular patterns, Plant Cell, vol.18, pp.1766-1777, 2006. ,
An expanded family of fungalysin extracellular metallopeptidases of Coprinopsis cinerea, Mycol Res, vol.112, pp.389-398, 2008. ,
The snf1 gene of Ustilago maydis acts as a dual regulator of cell wall degrading enzymes, Phytopathology, vol.100, pp.1364-1372, 2010. ,
The Cochliobolus carbonum SNF1 gene is required for cell wall-degrading enzyme expression and virulence on maize, Plant Cell, vol.12, pp.237-248, 2000. ,
Carbon repression in Aspergilli, FEMS Microbiol Lett, vol.151, pp.103-114, 1997. ,
Transcriptional adaptation of Mycosphaerella graminicola to programmed cell death (PCD) of its susceptible wheat host, Mol Plant Microbe Interact, vol.20, pp.178-193, 2007. ,
The acetate regulatory gene facB of Aspergillus nidulans encodes a Zn(II)2Cys6 transcriptional activator, Mol Gen Genet, vol.254, pp.495-504, 1997. ,
Bioinformatic and expression analysis of the putative gliotoxin biosynthetic gene cluster of Aspergillus fumigatus, FEMS Microbiol Lett, vol.248, pp.241-248, 2005. ,
Fungal effector proteins, Annu Rev Phytopathol, vol.47, pp.233-263, 2009. ,
Effectors of biotrophic fungi and oomycetes: pathogenicity factors and triggers of host resistance, New Phytol, vol.183, pp.993-1000, 2009. ,
Emerging concepts in effector biology of plant-associated organisms, Mol Plant Microbe Interact, vol.22, pp.115-122, 2009. ,
A Secreted Effector Protein of Laccaria bicolor Is Required for Symbiosis Development, Curr Biol, vol.21, pp.1197-1203, 2011. ,
URL : https://hal.archives-ouvertes.fr/hal-02651071
A Secreted Fungal Effector of Glomus intraradices Promotes Symbiotic Biotrophy, Curr Biol, vol.21, pp.1204-1209, 2011. ,
Cooperative domains define a unique host cell-targeting signal in Plasmodium falciparuminfected erythrocytes, Proc Natl Acad Sci U S A, vol.100, pp.12402-12407, 2003. ,
Mechanism of malarial haem detoxification inhibition by chloroquine, Biochem J, vol.355, pp.333-338, 2001. ,
Plasmodium falciparum histidine-rich protein II binds to actin, phosphatidylinositol 4,5-bisphosphate and erythrocyte ghosts in a pH-dependent manner and undergoes coil-to-helix transitions in anionic micelles, Mol Biochem Parasitol, vol.128, pp.157-166, 2003. ,
Inhibition of antithrombin by Plasmodium falciparum histidine-rich protein II, Blood, vol.117, pp.6347-6354, 2011. ,
Analyses of genome architecture and gene expression reveal novel candidate virulence factors in the secretome of Phytophthora infestans, BMC Genomics, vol.11, p.637, 2010. ,
URL : https://hal.archives-ouvertes.fr/hal-01606572
Ancient class of translocated oomycete effectors targets the host nucleus, Proc Natl Acad Sci U S A, vol.107, pp.17421-17426, 2010. ,
Coevolution between a Family of Parasite Virulence Effectors and a Class of LINE-1 Retrotransposons, PLoS One, vol.4, p.7463, 2009. ,
Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus), Proc Natl Acad Sci U S A, vol.107, pp.11889-11894, 2010. ,
Simple cDNA normalization using kamchatka crab duplex-specific nuclease, Nucleic Acids Res, vol.32, p.37, 2004. ,
A rapid DNA isolation procedure for small quantities of fresh leaf tissue, Phytochemical bulletin, vol.19, pp.11-15, 1987. ,
A whole-genome assembly of Drosophila, Science, vol.287, pp.2196-2204, 2000. ,
Aggressive assembly of pyrosequencing reads with mates, Bioinformatics, vol.24, pp.2818-2824, 2008. ,
Base-calling of automated sequencer traces using phred. II. Error probabilities, Genome Res, vol.8, pp.186-194, 1998. ,
Quality scores and SNP detection in sequencing-by-synthesis systems, Genome Res, vol.18, pp.763-770, 2008. ,
EagleView: a genome assembly viewer for nextgeneration sequencing technologies, Genome Res, vol.18, pp.1538-1543, 2008. ,
De novo identification of repeat families in large genomes, Bioinformatics, vol.21, issue.1, pp.351-358, 2005. ,
The Universal Protein Resource (UniProt) in 2010, Nucleic Acids Res, vol.38, pp.142-148, 2010. ,
Basic local alignment search tool, J Mol Biol, vol.215, pp.403-410, 1990. ,
LTR_STRUC: a novel search and identification program for LTR retrotransposons, Bioinformatics, vol.19, pp.362-367, 2003. ,
Using RepeatMasker to identify repetitive elements in genomic sequences, Curr Protoc Bioinformatics Chapter, vol.4, p.10, 2009. ,
tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence, Nucleic Acids Res, vol.25, pp.955-964, 1997. ,
WebLogo: a sequence logo generator, Genome Res, vol.14, pp.1188-1190, 2004. ,
Ab initio gene finding in Drosophila genomic DNA, Genome Res, vol.10, pp.516-522, 2000. ,
Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training, Genome Res, vol.18, pp.1979-1990, 2008. ,
AUGUSTUS: ab initio prediction of alternative transcripts, Nucleic Acids Res, vol.34, pp.435-439, 2006. ,
CYGD: the Comprehensive Yeast Genome Database, Nucleic Acids Res, vol.33, pp.364-368, 2005. ,
URL : https://hal.archives-ouvertes.fr/inria-00339841
Automated generation of heuristics for biological sequence comparison, BMC Bioinformatics, vol.6, p.31, 2005. ,
Using the Generic Genome Browser (GBrowse), Curr Protoc Bioinformatics Chapter, vol.9, p.9, 2007. ,
BLAT-the BLAST-like alignment tool, Genome Res, vol.12, pp.656-664, 2002. ,
FUNYBASE: a FUNgal phYlogenomic dataBASE, BMC Bioinformatics, vol.9, p.456, 2008. ,
PEDANT covers all complete RefSeq genomes, Nucleic Acids Res, vol.37, pp.408-411, 2009. ,
Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research, Bioinformatics, vol.21, pp.3674-3676, 2005. ,
WoLF PSORT: protein localization predictor, Nucleic Acids Res, vol.35, pp.585-587, 2007. ,
Predicting subcellular localization of proteins based on their N-terminal amino acid sequence, J Mol Biol, vol.300, pp.1005-1016, 2000. ,
Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites, Protein Eng, vol.10, pp.1-6, 1997. ,
A hidden Markov model for predicting transmembrane helices in protein sequences, Proc Int Conf Intell Syst Mol Biol, vol.6, pp.175-182, 1998. ,
RXLR effectors of plant pathogenic oomycetes, Curr Opin Microbiol, vol.10, pp.332-338, 2007. ,
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res, vol.25, pp.3389-3402, 1997. ,
SMART 6: recent updates and new developments, Nucleic Acids Res, vol.37, pp.229-232, 2009. ,
DOG 1.0: illustrator of protein domain structures, Cell Res, vol.19, pp.271-273, 2009. ,
The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools, Nucleic Acids Res, vol.25, pp.4876-4882, 1997. ,
Paup -a Computer-Program for Phylogenetic Inference Using Maximum Parsimony, J Gen Physiol, vol.102, pp.9-9, 1993. ,
, Contig assembly, vol.70, pp.75-89, 1997.
Isolation and characterisation of Pitef1 encoding the translation elongation factor EF-1 alpha of the root endophyte Piriformospora indica, Plant Biology, vol.2, pp.687-692, 2000. ,
Analysis of relative gene expression data using real-time quantitative PCR and the 2(T)(-Delta Delta C) method, Methods, vol.25, pp.402-408, 2001. ,
Electrophoretic karyotypes and genome sizing of the pathogenic fungus Paracoccidioides brasiliensis, J Clin Microbiol, vol.36, pp.742-747, 1998. ,
The Multivesicular Body-Localized GTPase ARFA1b/1c Is Important for Callose Deposition and ROR2 Syntaxin-Dependent Preinvasive Basal Defense in Barley, Plant Cell, vol.22, pp.3831-3844, 2010. ,
Thionin in cell walls and papillae of barley in compatible and incompatible interactions with Erysiphe graminis f. sp. hordei, Phys Mol Plant Pathol, vol.43, pp.343-352, 1993. ,
Bayesian inference of phylogeny and its impact on evolutionary biology, Science, vol.294, pp.2310-2314, 2001. ,
MUSCLE: a multiple sequence alignment method with reduced time and space complexity, BMC Bioinformatics, vol.5, p.113, 2004. ,
Protein structure prediction on the Web: a case study using the Phyre server, Nat Protoc, vol.4, pp.363-371, 2009. ,
DNA fragmentation in cereal roots indicative of programmed root cortical cell death, Physiol Plant, vol.111, pp.365-372, 2001. ,
Natural (Non-Pathogenic) Death of the Cortex of Wheat and Barley Seminal Roots, as Evidenced by Nuclear Staining with Acridine-Orange, Plant and Soil, vol.60, pp.255-274, 1981. ,
Visualizing profile-profile alignment: pairwise HMM logos, Bioinformatics, vol.21, pp.2912-2913, 2005. ,
Analysis of subgroup C of fungal chitinases containing chitinbinding and LysM modules in the mycoparasite Trichoderma atroviride, Glycobiology, vol.21, pp.122-133, 2011. ,
Analyzing real-time PCR data by the comparative C(T) method, Nat Protoc, vol.3, pp.1101-1108, 2008. ,
Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans, Nature, vol.461, pp.393-398, 2009. ,
URL : https://hal.archives-ouvertes.fr/hal-02668530
Circular genome visualization and exploration using CGView, Bioinformatics, vol.21, pp.537-539, 2005. ,
ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences, Nucleic Acids Res, vol.32, pp.11-16, 2004. ,