Trichoderma: the genomics of opportunistic success, Nature Reviews Microbiology, vol.270, issue.10, pp.749-759, 2011. ,
DOI : 10.1038/nrmicro2637
PHYLIP (phylogeny inference package) version 3, 2005. ,
Cloning and expression analysis of a chitinase gene crchi1 from the mycoparasitic fungus Clonostachys rosea (syn. Gliocladium roseum), J Microbiol, vol.45, pp.422-430, 2007. ,
Food Security: The Challenge of Feeding 9 Billion People, Science, vol.327, issue.5967, pp.812-818, 2010. ,
DOI : 10.1126/science.1185383
Full-length transcriptome assembly from RNA-Seq data without a reference genome, Nature Biotechnology, vol.30, issue.7, pp.644-652, 2011. ,
DOI : 10.1101/GR.229202. ARTICLE PUBLISHED ONLINE BEFORE MARCH 2002
Estimating Gene Gain and Loss Rates in the Presence of Error in Genome Assembly and Annotation Using CAFE 3, Molecular Biology and Evolution, vol.30, issue.8, pp.1987-1997, 2013. ,
DOI : 10.1093/molbev/mst100
Fungi from the Lower Devonian Rhynie Chert: Mycoparasitism, American Journal of Botany, vol.81, issue.1, pp.29-37, 1994. ,
DOI : 10.2307/2445559
Plant-beneficial effects of Trichoderma and of its genes, Microbiology, vol.158, issue.1, pp.17-25, 2012. ,
DOI : 10.1099/mic.0.052274-0
MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects, BMC Bioinformatics, vol.12, issue.1, p.491, 2011. ,
DOI : 10.1101/gr.403602
Comparative molecular evolution of Trichoderma chitinases in response to mycoparasitic interactions, Evol Bioinform Online, vol.6, pp.1-26, 2010. ,
Reconstructing the early evolution of Fungi using a six-gene phylogeny, Nature, vol.18, issue.7113, pp.818-822, 2006. ,
DOI : 10.1038/nature05110
strain 'IK726', Australasian Plant Pathology, vol.107, issue.2, pp.95-101, 2007. ,
DOI : 10.1094/Phyto-84-398
The rapid generation of mutation data matrices from protein sequences, Bioinformatics, vol.8, issue.3, pp.275-282, 1992. ,
DOI : 10.1093/bioinformatics/8.3.275
6a-Hydroxyphaseollin: an Antifungal Chemical Induced in Soybean Hypocotyls by Phytophthora megasperma var. sojae, Phytopathology, vol.61, issue.9, pp.1084-1089, 1971. ,
DOI : 10.1094/Phyto-61-1084
Gene finding in novel genomes, BMC Bioinformatics, vol.5, issue.1, p.59, 2004. ,
DOI : 10.1186/1471-2105-5-59
Transcriptomic profiling to identify genes involved in Fusarium mycotoxin Deoxynivalenol and Zearalenone tolerance in the mycoparasitic fungus Clonostachys rosea, BMC Genomics, vol.15, issue.1, p.55, 2014. ,
DOI : 10.1093/molbev/msr121
Phylogenetic analysis of fungal ABC transporters, BMC Genomics, vol.11, issue.1, p.177, 2010. ,
DOI : 10.1186/1471-2164-11-177
Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma, Genome Biology, vol.12, issue.4, 2011. ,
DOI : 10.1093/bioinformatics/btm076
Revealed by Confocal Laser Scanning Microscopic Analysis Using the Green Fluorescent Protein as a Marker, Molecular Plant-Microbe Interactions, vol.15, issue.2, pp.172-179, 2002. ,
DOI : 10.1094/MPMI.2002.15.2.172
Clustal W and Clustal X version 2.0, Bioinformatics, vol.23, issue.21, pp.2947-2948, 2007. ,
DOI : 10.1093/bioinformatics/btm404
URL : https://hal.archives-ouvertes.fr/hal-00206210
Expansion of the enzymatic repertoire of the CAZy database to integrate auxiliary redox enzymes, Biotechnology for Biofuels, vol.6, issue.1, p.41, 2013. ,
DOI : 10.1186/1471-2148-12-186
URL : https://hal.archives-ouvertes.fr/hal-01268121
OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes, Genome Research, vol.13, issue.9, pp.2178-2189, 2003. ,
DOI : 10.1101/gr.1224503
The carbohydrate-active enzymes database (CAZy) in 2013, Nucleic Acids Research, vol.42, issue.D1, pp.490-495, 2014. ,
DOI : 10.1093/nar/gkt1178
: From 'Omics to the Field, Annual Review of Phytopathology, vol.48, issue.1, pp.395-417, 2010. ,
DOI : 10.1146/annurev-phyto-073009-114314
GUS and GFP transformation of the biocontrol strain Clonostachys rosea IK726 and the use of these marker genes in ecological studies, Mycological Research, vol.106, issue.7, pp.815-826, 2002. ,
DOI : 10.1017/S095375620200607X
Fungi evolved right on track, Mycologia, vol.101, issue.6, pp.810-822, 2009. ,
DOI : 10.3852/09-016
Three endochitinase-encoding genes identified in the biocontrol fungus Clonostachys rosea are differentially expressed, Current Genetics, vol.39, issue.2, pp.57-70, 2008. ,
DOI : 10.1007/s00294-008-0199-5
Structure and evolution of the Fusarium mating type locus: New insights from the Gibberella fujikuroi complex, Fungal Genetics and Biology, vol.48, issue.7, pp.731-740, 2011. ,
DOI : 10.1016/j.fgb.2011.03.005
Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina), Nature Biotechnology, vol.307, issue.5, pp.553-560, 2008. ,
DOI : 10.1038/nbt1403
Expression of Biomass-Degrading Enzymes Is a Major Event during Conidium Development in Trichoderma reesei, Eukaryotic Cell, vol.10, issue.11, pp.1527-1535, 2011. ,
DOI : 10.1128/EC.05014-11
Research in the Genome Era, Annual Review of Phytopathology, vol.51, issue.1, pp.105-129, 2013. ,
DOI : 10.1146/annurev-phyto-082712-102353
Secondary metabolism in Trichoderma - a genomic perspective, Microbiology, vol.158, issue.1, pp.35-45, 2012. ,
DOI : 10.1099/mic.0.053629-0
Mode of action of a non-pathogenic Fusarium oxysporum strain against Verticillium dahliae using Real Time QPCR analysis and biomarker transformation, Biological Control, vol.50, issue.1, pp.30-36, 2009. ,
DOI : 10.1016/j.biocontrol.2009.01.010
Clonostachys rosea BAFC3874 as a Sclerotinia sclerotiorum antagonist: mechanisms involved and potential as a biocontrol agent, Journal of Applied Microbiology, vol.34, issue.5, pp.1177-1186, 2011. ,
DOI : 10.1111/j.1365-2672.2011.04970.x
The pleiotropic drug ABC transporters from Saccharomyces cerevisiae, J Mol Microbiol Biotechnol, vol.3, pp.207-214, 2001. ,
Genera in <I>Bionectriaceae</I>, <I>Hypocreaceae</I>, and <I>Nectriaceae</I> (<I>Hypocreales</I>) proposed for acceptance or rejection, IMA Fungus, vol.4, issue.1, pp.41-51, 2013. ,
DOI : 10.5598/imafungus.2013.04.01.05
: The Role of an ABC Transporter Membrane Pump in the Interaction with Different Plant-Pathogenic Fungi, Molecular Plant-Microbe Interactions, vol.22, issue.3, pp.291-301, 2009. ,
DOI : 10.1094/MPMI-22-3-0291
Molecular cloning: a laboratory manual, 2001. ,
Classification of the Mycoparasite Gliocladium roseum in Clonostachys as C. rosea, Its Relationship to Bionectria ochroleuca, and Notes on Other Gliocladium-like Fungi, Mycologia, vol.91, issue.2, pp.365-385, 1999. ,
DOI : 10.2307/3761383
Chitinases of filamentous fungi: a large group of diverse proteins with multiple physiological functions, Fungal Biology Reviews, vol.22, issue.1, pp.36-42, 2008. ,
DOI : 10.1016/j.fbr.2008.03.002
A complete survey of Trichoderma chitinases reveals three distinct subgroups of family 18 chitinases, FEBS Journal, vol.162, issue.22, pp.5923-5939, 2005. ,
DOI : 10.1111/j.1742-4658.2005.04994.x
Molecular Evolution of Trichoderma Chitinases, Biotechnology and biology of Trichoderma, pp.67-78, 2014. ,
DOI : 10.1016/B978-0-444-59576-8.00005-9
Bacteria Gnotobiotic System for Studying Rhizosphere, Molecular Plant-Microbe Interactions, vol.9, issue.7, pp.600-607, 1996. ,
DOI : 10.1094/MPMI-9-0600
ABySS: A parallel assembler for short read sequence data, Genome Research, vol.19, issue.6, pp.1117-1123, 2009. ,
DOI : 10.1101/gr.089532.108
The specificity-conferring code of adenylation domains in nonribosomal peptide synthetases, Chemistry & Biology, vol.6, issue.8, pp.493-505, 1999. ,
DOI : 10.1016/S1074-5521(99)80082-9
Gene prediction in eukaryotes with a generalized hidden markov model that uses hints from external sources, BMC Bioinformatics, vol.7, issue.1, p.62, 2006. ,
DOI : 10.1186/1471-2105-7-62
Investigating the beneficial traits of Trichoderma hamatum GD12 for sustainable agriculture???insights from genomics, Frontiers in Plant Science, vol.4, p.258, 2013. ,
DOI : 10.3389/fpls.2013.00258
A Multidrug Resistance Transporter in Magnaporthe Is Required for Host Penetration and for Survival during Oxidative Stress, THE PLANT CELL ONLINE, vol.18, issue.12, pp.3686-3705, 2006. ,
DOI : 10.1105/tpc.105.037861
Phylogenetic classification of Cordyceps and the clavicipitaceous fungi, Studies in Mycology, vol.57, pp.5-59, 2007. ,
DOI : 10.3114/sim.2007.57.01
MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods, Molecular Biology and Evolution, vol.28, issue.10, pp.2731-2739, 2011. ,
DOI : 10.1093/molbev/msr121
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3203626
MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0, Molecular Biology and Evolution, vol.30, issue.12, pp.2725-2729, 2013. ,
DOI : 10.1093/molbev/mst197
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3840312
Perithecial ascomycetes from the 400 million year old Rhynie chert: an example of ancestral polymorphism, Mycologia, vol.96, issue.97, pp.269-285, 2004. ,
Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training, Genome Research, vol.18, issue.12, pp.1979-1990, 2008. ,
DOI : 10.1101/gr.081612.108
Glisoprenins C, D and E, New Inhibitors of Appressorium Formation in Magnaporthe grisea, from Cultures of Gliocladium roseum. 1. Production and Biological Activities., The Journal of Antibiotics, vol.51, issue.2, pp.117-122, 1998. ,
DOI : 10.7164/antibiotics.51.117
Functional analysis of glycoside hydrolase family 18 and 20 genes in Neurospora crassa, Fungal Genetics and Biology, vol.49, issue.9, pp.717-730, 2012. ,
DOI : 10.1016/j.fgb.2012.06.013
Gliocladins A - C and Glioperazine ; Cytotoxic Dioxo- or Trioxopiperazine Metabolites from a Gliocladium Sp. Separated from a Sea Hare, HETEROCYCLES, vol.63, issue.5, pp.1123-1129, 2004. ,
DOI : 10.3987/COM-04-10037
Isolates from Strawberry, Plant Disease, vol.95, issue.10, pp.1302-1307, 2011. ,
DOI : 10.1094/PDIS-04-11-0317
A convenient growth medium for Neurospora (medium N) Microbial Genet Bull, pp.42-43, 1956. ,
A survey of nonribosomal peptide synthetase (NRPS) genes in Aspergillus nidulans, Fungal Genetics and Biology, vol.46, issue.1, pp.45-52, 2009. ,
DOI : 10.1016/j.fgb.2008.08.008
Comparative Genomics Provide Insights into Evolution of Trichoderma Nutrition Style, Genome Biology and Evolution, vol.6, issue.2, pp.379-390, 2014. ,
DOI : 10.1093/gbe/evu018
CVTree update: a newly designed phylogenetic study platform using composition vectors and whole genomes, Nucleic Acids Research, vol.37, issue.Web Server, pp.174-178, 2009. ,
DOI : 10.1093/nar/gkp278
PAML: a program package for phylogenetic analysis by maximum likelihood, Bioinformatics, vol.13, issue.5, pp.555-556, 1997. ,
DOI : 10.1093/bioinformatics/13.5.555
PAML 4: Phylogenetic Analysis by Maximum Likelihood, Molecular Biology and Evolution, vol.24, issue.8, pp.1586-1591, 2007. ,
DOI : 10.1093/molbev/msm088
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.322.1650
Jackknife and Bootstrap Tests of the Composition Vector Trees, Genomics, Proteomics & Bioinformatics, vol.8, issue.4, pp.262-267, 2010. ,
DOI : 10.1016/S1672-0229(10)60028-9