The regulation of symbiotic N2 fixation: a conceptual model of N feedback from the ecosystem to the gene expression level, Lewis, Legumes of the World, pp.92-120, 1998. ,
DOI : 10.1078/1433-8319-00054
Legumes: Importance and Constraints to Greater Use Proteomics for exploiting diversity of lupin seed storage proteins and their use as nutraceuticals for health and welfare Calcium, kinases and nodulation signalling in legumes, Root Nodulation: A Paradigm for How Plant-Microbe Symbiosis Influences Host Developmental Pathways, pp.872-877, 2003. ,
Speak, friend, and enter: signalling systems that promote beneficial symbiotic associations in plants Long, Genes and signals in the Rhizobium-legume symbiosis, Nat. Rev. Microbiol. Plant Physiol, vol.11, issue.125, pp.252-263, 2001. ,
Sandal, others, Plant recognition of symbiotic bacteria requires two LysM receptor-like kinases, pp.425-585, 2003. ,
LysM domains mediate lipochitin???oligosaccharide recognition and Nfr genes extend the symbiotic host range, The EMBO Journal, vol.129, issue.17, pp.3923-3935, 2007. ,
DOI : 10.1038/sj.emboj.7601826
Depolarization of alfalfa root hair membrane potential by Rhizobium meliloti Nod factors, Science, vol.256, issue.5059, pp.998-1000, 1992. ,
DOI : 10.1126/science.10744524
From The Cover: A nucleoporin is required for induction of Ca2+ spiking in legume nodule development and essential for rhizobial and fungal symbiosis, Proceedings of the National Academy of Sciences, vol.328, issue.1, pp.359-364, 2006. ,
DOI : 10.1016/S0022-2836(03)00266-3
NUCLEOPORIN85 Is Required for Calcium Spiking, Fungal and Bacterial Symbioses, and Seed Production in Lotus japonicus, Plant Cell Online, vol.19, pp.610-624, 2007. ,
A Putative Ca2+ and Calmodulin-Dependent Protein Kinase Required for Bacterial and Fungal Symbioses, Science, vol.303, issue.5662, pp.303-1361, 2004. ,
DOI : 10.1126/science.1093038
Rhizobium???legume symbioses: the crucial role of plant immunity, Trends in Plant Science, vol.20, issue.3, 2015. ,
DOI : 10.1016/j.tplants.2014.11.008
Legume comparative genomics: progress in phylogenetics and phylogenomics, Current Opinion in Plant Biology, vol.9, issue.2, 2006. ,
DOI : 10.1016/j.pbi.2006.01.011
), an emerging health food: insights into plant-microbe interactions and legume evolution, Plant Biotechnology Journal, vol.9, issue.3, 2016. ,
DOI : 10.1371/journal.pone.0089030
URL : http://onlinelibrary.wiley.com/doi/10.1111/pbi.12615/pdf
An RNA-Seq Transcriptome Analysis of Orthophosphate-Deficient White Lupin Reveals Novel Insights into Phosphorus Acclimation in Plants, PLANT PHYSIOLOGY, vol.161, issue.2, pp.705-724, 2013. ,
DOI : 10.1104/pp.112.209254
Yellow lupin (Lupinus luteus L.) transcriptome sequencing: molecular marker development and comparative studies, BMC Genomics, vol.13, issue.1, p.425, 2012. ,
DOI : 10.1016/j.ympev.2008.03.009
An unusual infection mechanism and nodule morphogenesis in white lupin (Lupinus albus), New Phytologist, vol.203, issue.2, 2004. ,
DOI : 10.1016/S0092-8674(00)81284-2
Diversification of Lupine Bradyrhizobium Strains: Evidence from Nodulation Gene Trees, Applied and Environmental Microbiology, vol.73, issue.10, pp.3254-3264, 2007. ,
DOI : 10.1128/AEM.02125-06
Endosymbiotic bacteria nodulating a new endemic lupine Lupinus mariae-josephi from alkaline soils in Eastern Spain represent a new lineage within the Bradyrhizobium genus, Systematic and Applied Microbiology, vol.34, issue.3, pp.34-207, 2011. ,
DOI : 10.1016/j.syapm.2010.11.020
Symbiosis specificity in the legume - rhizobial mutualism, Cellular Microbiology, vol.21, issue.3, 2012. ,
DOI : 10.1094/MPMI-21-12-1600
Receptor-mediated exopolysaccharide perception controls bacterial infection, Nature, vol.523, pp.308-312, 2015. ,
Identification of a dominant gene in Medicago truncatula that restricts nodulation by Sinorhizobium meliloti strain Rm41, BMC Plant Biology, vol.14, issue.1, 2014. ,
DOI : 10.1099/00221287-84-1-188
R gene-controlled host specificity in the legumerhizobia symbiosis, Proc. Natl. Acad. Sci, pp.18735-18740, 2010. ,
Strains, Molecular Plant-Microbe Interactions, vol.30, issue.5, pp.399-409, 2017. ,
DOI : 10.1094/MPMI-01-17-0009-R
URL : https://hal.archives-ouvertes.fr/hal-01608196
Strain-Ecotype Specificity in Sinorhizobium meliloti-Medicago truncatula Symbiosis Is Correlated to Succinoglycan Oligosaccharide Structure, Journal of Bacteriology, vol.189, issue.21, pp.7733-7740, 2007. ,
DOI : 10.1128/JB.00739-07
Handbook for Rhizobia: Methods in Legume-Rhizobium technology, p.9781461383772, 1994. ,
DOI : 10.1007/978-1-4613-8375-8
A quality control tool for high throughput sequence data, 2010. ,
De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis, Nature Protocols, vol.500, issue.8, pp.1494-1512, 2013. ,
DOI : 10.1038/ng.2295
Fast gapped-read alignment with Bowtie 2, Nature Methods, vol.9, issue.4, 1923. ,
DOI : 10.1093/bioinformatics/btp352
Corset: enabling differential gene expression analysis for de novo assembled transcriptomes, Genome Biol, vol.15, p.410, 2014. ,
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs, Bioinformatics, vol.31, issue.19, pp.31-3210, 2015. ,
DOI : 10.1093/nar/gks1116
Pfam: the protein families database, Pfam: the protein families database, pp.222-230, 2014. ,
DOI : 10.1093/nar/gks1200
URL : https://hal.archives-ouvertes.fr/hal-01294685
BLAST+: architecture and applications, BLAST+: architecture and applications, pp.421-431, 2009. ,
DOI : 10.1186/1471-2105-10-421
URL : https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-10-421?site=bmcbioinformatics.biomedcentral.com
HMMER web server: interactive sequence similarity searching, Nucleic Acids Research, vol.38, issue.suppl_2, pp.29-37, 2011. ,
DOI : 10.1093/nar/gkq394
URL : https://academic.oup.com/nar/article-pdf/39/suppl_2/W29/7628106/gkr367.pdf
SignalP 4.0: discriminating signal peptides from transmembrane regions, Nature Methods, vol.6, issue.10, pp.785-786, 2011. ,
DOI : 10.1016/0005-2795(75)90109-9
Predicting transmembrane protein topology with a hidden markov model: application to complete genomes11Edited by F. Cohen, Journal of Molecular Biology, vol.305, issue.3, pp.567-580, 2001. ,
DOI : 10.1006/jmbi.2000.4315
An improved genome release (version Mt4.0) for the model legume Medicago truncatula, BMC Genomics, vol.15, issue.1, p.312, 2014. ,
DOI : 10.1038/nprot.2012.068
URL : https://bmcgenomics.biomedcentral.com/track/pdf/10.1186/1471-2164-15-312?site=bmcgenomics.biomedcentral.com
Genome sequence of the palaeopolyploid soybean, Nature, vol.22, issue.7278, pp.463-178, 2010. ,
DOI : 10.1093/molbev/msl159
GC-Content Normalization for RNA-Seq Data, BMC Bioinformatics, vol.12, issue.1, p.480, 2011. ,
DOI : 10.1093/nar/30.4.e15
URL : https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-12-480?site=bmcbioinformatics.biomedcentral.com
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, Genome Biol, vol.15, 2014. ,
Primer3???new capabilities and interfaces, Primer3-- new capabilities and interfaces, pp.115-115, 2012. ,
DOI : 10.6026/97320630003282
URL : https://academic.oup.com/nar/article-pdf/40/15/e115/16967451/gks596.pdf
Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2???????CT Method, Methods, vol.25, issue.4, pp.402-408, 2001. ,
DOI : 10.1006/meth.2001.1262
Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes, Genome Biol, vol.3, pp.34-35, 2002. ,
mapman: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes, The Plant Journal, vol.132, issue.7, pp.914-939, 2004. ,
DOI : 10.1111/j.1365-313X.2004.02016.x
PageMan: an interactive ontology tool to generate, display, and annotate overview graphs for profiling experiments, BMC Bioinformatics, vol.7, issue.535, 2006. ,
The ade4 package: implementing the duality diagram for ecologists, J. Stat. Softw, vol.22, pp.1-20, 2007. ,
URL : https://hal.archives-ouvertes.fr/hal-00434575
R: A Language and Environment for Statistical Computing, R Foundation for Statistical Computing ,
Full-length transcriptome assembly from RNA-Seq data without a reference genome, Nature Biotechnology, vol.30, issue.7, pp.29-644, 2011. ,
DOI : 10.1101/GR.229202. ARTICLE PUBLISHED ONLINE BEFORE MARCH 2002
New data and phylogenetic placement of the enigmatic Old World lupin: Lupinus mariae-josephi H. Pascual, Genetic Resources and Crop Evolution, vol.31, issue.1, pp.101-114, 2011. ,
DOI : 10.1016/0031-9422(95)91890-D
Sallet, others, A laser dissection-RNAseq analysis highlights the activation of cytokinin pathways by nod factors in the Medicago truncatula root epidermis, Plant Physiol, pp.171-2256, 2016. ,
RNA-Seq Analysis of Differential Gene Expression Responding to Different Rhizobium Strains in Soybean (Glycine max) Roots, Front, Plant Sci, vol.7, 2016. ,
GRAS Proteins Form a DNA Binding Complex to Induce Gene Expression during Nodulation Signaling in Medicago truncatula, THE PLANT CELL ONLINE, vol.21, issue.2, pp.545-557, 2009. ,
DOI : 10.1105/tpc.108.064501
E3 Ubiquitin Ligase PUB1 Interacts with the LYK3 Symbiotic Receptor and Negatively Regulates Infection and Nodulation, The Plant Cell, vol.22, issue.10, pp.3474-3488, 2010. ,
DOI : 10.1105/tpc.110.075861
Vapyrin, a gene essential for intracellular progression of arbuscular mycorrhizal symbiosis, is also essential for infection by rhizobia in the nodule symbiosis of Medicago truncatula, The Plant Journal, vol.60, issue.2, pp.244-252, 2011. ,
DOI : 10.1111/j.1365-313X.2009.03943.x
The C2H2 Transcription Factor REGULATOR OF SYMBIOSOME DIFFERENTIATION Represses Transcription of the Secretory Pathway Gene VAMP721a and Promotes Symbiosome Development in Medicago truncatula, The Plant Cell, vol.25, issue.9, pp.3584-3601, 2013. ,
DOI : 10.1105/tpc.113.114017
Sucrose Synthase in Legume Nodules Is Essential for Nitrogen Fixation, Plant Physiology, vol.120, issue.3, pp.867-878, 1999. ,
DOI : 10.1104/pp.120.3.867
Genomic organization and expression properties of the MtSucS1 gene, which encodes a nodule-enhanced sucrose synthase in the model legume Medicago truncatula, Molecular and General Genetics MGG, vol.261, issue.3, pp.261-514, 1999. ,
DOI : 10.1007/s004380050995
MTGD: The Medicago truncatula Genome Database, Plant and Cell Physiology, vol.8, issue.1, pp.1-1, 2015. ,
DOI : 10.1186/1471-2164-8-278
Soybean Metabolites Regulated in Root Hairs in Response to the Symbiotic Bacterium Bradyrhizobium japonicum, PLANT PHYSIOLOGY, vol.153, issue.4, pp.1808-1822, 2010. ,
DOI : 10.1104/pp.110.157800
The Class II Trehalose 6-phosphate Synthase Gene PvTPS9 Modulates Trehalose Metabolism in Phaseolus vulgaris Nodules, Frontiers in Plant Science, vol.62, 2016. ,
DOI : 10.1093/jxb/erq295
enhances nodule biomass and bacteroid number in the common bean, New Phytologist, vol.30, issue.1, pp.194-206, 2013. ,
DOI : 10.1071/FP03002
Glutamine Synthetase in Legumes: Recent Advances in Enzyme Structure and Functional Genomics, Glutamine Synthetase in Legumes: Recent Advances in Enzyme Structure and Functional Genomics, pp.7994-8024103390, 2012. ,
DOI : 10.1038/329219a0
Two Phloem Nitrate Transporters, NRT1.11 and NRT1 Are Important for Redistributing Xylem-Borne Nitrate to Enhance Plant Growth, PLANT Physiol, vol.12, issue.163, pp.844-856, 2013. ,
Natural Resistance-Associated Macrophage Protein1 Is Required for Iron Uptake by Rhizobia-Infected Nodule Cells, Plant Physiology, vol.168, issue.1, pp.258-272, 2015. ,
DOI : 10.1104/pp.114.254672
The role of iron in nodulation and nitrogen fixation in Lupinus angustifolius L, New Phytologist, vol.40, issue.2, 1990. ,
DOI : 10.1016/0038-0717(85)90093-8
The Rules of Engagement in the Legume-Rhizobial Symbiosis, Annual Review of Genetics, vol.45, issue.1, pp.119-144, 2011. ,
DOI : 10.1146/annurev-genet-110410-132549
Root Transcriptome Reveals a Massive and Early Interaction between Nodulation Factor and Ethylene Signals, Deep Sequencing of the Medicago truncatula Root Transcriptome Reveals a Massive and Early Interaction between Nodulation Factor and Ethylene Signals, pp.233-265101500350, 1104. ,
DOI : 10.1104/pp.15.00350
An ERF Transcription Factor in Medicago truncatula That Is Essential for Nod Factor Signal Transduction, THE PLANT CELL ONLINE, vol.19, issue.4, pp.1221-1234, 2007. ,
DOI : 10.1105/tpc.106.048264
Manipulation of Auxin Transport in Plant Roots during Rhizobium Symbiosis and Nematode Parasitism, THE PLANT CELL ONLINE, vol.21, issue.9, pp.2553-2562, 2009. ,
DOI : 10.1105/tpc.109.069617
5-like class 2 KNOX transcription factors are involved in Medicago truncatula symbiotic nodule organ development, New Phytol, vol.213, issue.4, pp.822-837, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-01606064
Cytokinin action in plant development, Current Opinion in Plant Biology, vol.12, issue.5, pp.527-538, 2009. ,
DOI : 10.1016/j.pbi.2009.07.002
EFD Is an ERF Transcription Factor Involved in the Control of Nodule Number and Differentiation in Medicago truncatula, THE PLANT CELL ONLINE, vol.20, issue.10, pp.2696-2713, 2008. ,
DOI : 10.1105/tpc.108.059857
Abscisic Acid Coordinates Nod Factor and Cytokinin Signaling during the Regulation of Nodulation in Medicago truncatula, THE PLANT CELL ONLINE, vol.20, issue.10, pp.2681-2695, 2008. ,
DOI : 10.1105/tpc.108.061739
Abscisic acid sensor RCAR7/PYL13, specific regulator of protein phosphatase coreceptors, Proc. Natl. Acad. Sci, pp.5741-5746, 2014. ,
DOI : 10.1111/j.1365-313X.2007.03234.x
Arabidopsis Calcium-Dependent Protein Kinase AtCPK32 Interacts with ABF4, a Transcriptional Regulator of Abscisic Acid-Responsive Gene Expression, and Modulates Its Activity, PLANT PHYSIOLOGY, vol.139, issue.4, pp.1750-1761, 2005. ,
DOI : 10.1104/pp.105.069757
Relationship between gibberellin, ethylene and nodulation in Pisum sativum, New Phytologist, vol.125, issue.3, pp.829-842, 2011. ,
DOI : 10.1104/pp.125.2.627
Mechanistic action of gibberellins in legume nodulation, Journal of Integrative Plant Biology, vol.10, issue.10, pp.971-978, 2014. ,
DOI : 10.1146/annurev.arplant.59.032607.092804
Complete Transcriptome of the Soybean Root Hair Cell, a Single-Cell Model, and Its Alteration in Response to Bradyrhizobium japonicum Infection, PLANT PHYSIOLOGY, vol.152, issue.2, pp.541-552, 2010. ,
DOI : 10.1104/pp.109.148379
DELLA proteins are common components of symbiotic rhizobial and mycorrhizal signalling pathways, Nature Communications, vol.2 ,
DOI : 10.1038/nprot.2007.199
DELLA Proteins and Their Interacting RING Finger Proteins Repress Gibberellin Responses by Binding to the Promoters of a Subset of Gibberellin-Responsive Genes in Arabidopsis, The Plant Cell, vol.25, issue.3, pp.927-943, 2013. ,
DOI : 10.1105/tpc.112.108951
Flavonoids: biosynthesis, biological functions, and biotechnological applications, Frontiers in Plant Science, vol.3, 2012. ,
DOI : 10.3389/fpls.2012.00222
Silencing the Flavonoid Pathway in Medicago truncatula Inhibits Root Nodule Formation and Prevents Auxin Transport Regulation by Rhizobia, THE PLANT CELL ONLINE, vol.18, issue.7, 2006. ,
DOI : 10.1105/tpc.105.038232
Flavones and flavonols play distinct critical roles during nodulation of Medicago truncatula by Sinorhizobium meliloti, Plant J, vol.57, 2009. ,
Distinct, crucial roles of flavonoids during legume nodulation, Trends in Plant Science, vol.12, issue.7, pp.282-285, 2007. ,
DOI : 10.1016/j.tplants.2007.06.006
Phytochemical and Immunocytochemical Evidence for the Accumulation of 2???-Hydroxylupalbigenin in Lupin Nodules and Bacteroids, Molecular Plant-Microbe Interactions, vol.8, issue.1, pp.131-137, 1995. ,
DOI : 10.1094/MPMI-8-0131
symbiotic association, Journal of Experimental Botany, vol.46, issue.2, pp.231-237, 1995. ,
DOI : 10.1093/jxb/46.2.231
The role of the secondary cell wall in plant resistance to pathogens, Frontiers in Plant Science, vol.10, issue.46, 2014. ,
DOI : 10.1111/j.1364-3703.2009.00558.x