P. H. Graham and C. P. Vance, Update on Legume Utilization Legumes: Importance and Constraints to Greater Use, Plant Physiol, vol.131, pp.872-877, 2014.

G. E. Oldroyd, J. D. Murray, P. S. Poole, and J. A. Downie, The rules of engagement in the legume-rhizobial symbiosis, Annu. Rev. Genet, vol.45, pp.119-163, 2011.

H. Kouchi, How many peas in a pod? Legume genes responsible for mutualistic symbioses underground, Plant Cell Physiol, vol.51, pp.1381-97, 2010.

J. I. Sprent, Evolving ideas of legume evolution and diversity: a taxonomic perspective on the occurrence of nodulation, New Phytol, vol.174, pp.11-25, 2007.

E. Giraud, Legumes symbioses: absence of Nod genes in photosynthetic bradyrhizobia, Science, vol.316, pp.1307-1319, 2007.
URL : https://hal.archives-ouvertes.fr/halsde-00151340

K. Bonaldi, Nodulation of Aeschynomene afraspera and A. indica by photosynthetic Bradyrhizobium Sp. strain ORS285: the nod-dependent versus the nod-independent symbiotic interaction, Mol. Plant. Microbe. Interact, vol.24, pp.1359-71, 2011.

J. Arrighi, Aeschynomene evenia, a model plant for studying the molecular genetics of the nod-independent rhizobiumlegume symbiosis, Mol. Plant. Microbe. Interact, vol.25, pp.851-61, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00855572

R. M. Mitra, A Ca2+/calmodulin-dependent protein kinase required for symbiotic nodule development: Gene identification by transcript-based cloning, Proc. Natl. Acad. Sci. USA, vol.101, pp.4701-4706, 2004.

S. Stracke, A plant receptor-like kinase required for both bacterial and fungal symbiosis, Nature, vol.417, pp.959-62, 2002.

S. Gonzalez-rizzo, M. Crespi, and F. Frugier, The Medicago truncatula CRE1 cytokinin receptor regulates lateral root development and early symbiotic interaction with Sinorhizobium meliloti, Plant Cell, vol.18, pp.2680-93, 2006.
URL : https://hal.archives-ouvertes.fr/hal-00123705

S. Fabre, The Nod factor-independent nodulation in Aeschynomene evenia required the common plant-microbe symbiotic 'toolkit', Plant Physiol, vol.169, pp.2654-2664, 2015.

P. Czernic, Convergent Evolution of Endosymbiont Differentiation in Dalbergioid and Inverted Repeat-Lacking Clade Legumes Mediated by Nodule-Specific Cysteine-Rich Peptides, Plant Physiol, vol.169, pp.1254-1265, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01430710

X. Argout, Towards the understanding of the cocoa transcriptome: Production and analysis of an exhaustive dataset of ESTs of Theobroma cacao L. generated from various tissues and under various conditions, BMC Genomics, vol.9, p.512, 2008.

, SCIENTIFIC REPoRts |, vol.8, 2018.

M. C. Wildermuth, J. Dewdney, G. Wu, and F. M. Ausubel, Isochorismate synthesis is required to synthesize salicylic acid for plant defense, Nature, vol.414, pp.562-565, 2001.

T. Liu, Unconventionally secreted effectors of two filamentous pathogens target plant salicylate biosynthesis, Nat. Commun, vol.5, 2014.

D. P. Lohar, Transcript analysis of early nodulation events in Medicago truncatula, Plant Physiol, vol.140, pp.221-255, 2006.

T. Rey, NFP, a LysM protein controlling Nod factor perception, also intervenes in Medicago truncatula resistance to pathogens, New Phytol, vol.198, pp.875-886, 2013.

H. Kouchi and . Large-scale, Analysis of Gene Expression Profiles during Early Stages of Root Nodule Formation in a Model Legume, Lotus japonicus, DNA Res, vol.11, pp.263-274, 2004.

M. Libault, Complete Transcriptome of the Soybean Root Hair Cell, a Single-Cell Model, and Its Alteration in Response to Bradyrhizobium japonicum Infection, Plant Physiol, vol.152, pp.541-552, 2010.

C. Zipfel and G. E. Oldroyd, Plant signalling in symbiosis and immunity, Nature, vol.543, pp.328-336, 2017.

P. Gamas, M. Brault, M. F. Jardinaud, and F. Frugier, Cytokinins in Symbiotic Nodulation: When, Where, What For?, Trends Plant Sci, vol.22, pp.792-802, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01608674

S. Yan and X. Dong, Perception of the plant immune signal salicylic acid, Curr. Opin. Plant Biol, vol.20, pp.64-68, 2014.

D. M. Goodstein, Phytozome: a comparative platform for green plant genomics, Nucleic Acids Res, vol.40, pp.1178-1186, 2012.

E. A. Howe, R. Sinha, D. Schlauch, and J. Quackenbush, RNA-Seq analysis in MeV, Bioinformatics, vol.27, pp.3209-3210, 2011.

C. Chaintreuil, A gene-based map of the Nod factor-independent Aeschynomene evenia sheds new light on the evolution of nodulation and legume genomes, DNA Res, vol.23, pp.365-76, 2016.
URL : https://hal.archives-ouvertes.fr/hal-02410329

B. Lefebvre, A remorin protein interacts with symbiotic receptors and regulates bacterial infection, Proc. Natl. Acad. Sci. USA, vol.107, pp.2343-2351, 2010.

L. Schauser, A. Roussis, J. Stiller, and J. Stougaard, A plant regulator controlling development of symbiotic root nodules, Nature, vol.402, pp.191-196, 1999.

M. Mbengue, The Medicago truncatula E3 Ubiquitin Ligase PUB1 Interacts with the LYK3 Symbiotic Receptor and Negatively Regulates Infection and Nodulation, Plant Cell, vol.22, pp.3474-3488, 2010.

J. D. Murray, 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, Plant J, vol.65, pp.244-52, 2011.

M. Groth, NENA, a Lotus japonicus homolog of Sec. 13, is required for rhizodermal infection by arbuscular mycorrhiza fungi and rhizobia but dispensable for cortical endosymbiotic development, Plant Cell, vol.22, pp.2509-2535, 2010.

H. Zhu, A novel ARID DNA-binding protein interacts with SymRK and is expressed during early nodule development in Lotus japonicus, Plant Physiol, vol.148, pp.337-384, 2008.

A. B. Heckmann, Lotus japonicus nodulation requires two GRAS domain regulators, one of which is functionally conserved in a non-legume, Plant Physiol, vol.142, pp.1739-50, 2006.

P. Smit, NSP1 of the GRAS protein family is essential for rhizobial Nod factor-induced transcription, Science, vol.308, pp.1789-91, 2005.

P. Kaló, Nodulation signaling in legumes requires NSP2, a member of the GRAS family of transcriptional regulators, Science, vol.308, pp.1786-1795, 2005.

E. Asamizu, Y. Shimoda, H. Kouchi, S. Tabata, and S. Sato, A positive regulatory role for LjERF1 in the nodulation process is revealed by systematic analysis of nodule-associated transcription factors of Lotus japonicus, Plant Physiol, vol.147, pp.2030-2040, 2008.

J. Couzigou, NODULE ROOT and COCHLEATA maintain nodule development and are legume orthologs of Arabidopsis BLADE-ON-PETIOLE genes, Plant Cell, vol.24, pp.4498-510, 2012.

E. Kiss, LIN, a novel type of U-box/WD40 protein, controls early infection by rhizobia in legumes, Plant Physiol, vol.151, pp.1239-1288, 2009.

K. Yano, CERBERUS, a novel U-box protein containing WD-40 repeats, is required for formation of the infection thread and nodule development in the legume-Rhizobium symbiosis, Plant J, vol.60, pp.168-80, 2009.

K. Shimomura, M. Nomura, S. Tajima, H. Kouchi, and . Ljnsring, a Novel RING Finger Protein, is Required for Symbiotic Interactions Between Mesorhizobium loti and Lotus japonicus, vol.47, pp.1572-1581, 2006.

D. Wang, A nodule-specific protein secretory pathway required for nitrogen-fixing symbiosis, Science, vol.327, pp.1126-1135, 2010.

E. Limpens, LysM domain receptor kinases regulating rhizobial Nod factor-induced infection, Science, vol.302, pp.630-633, 2003.

S. Radutoiu, Plant recognition of symbiotic bacteria requires two LysM receptor-like kinases, Nature, vol.425, pp.585-92, 2003.

G. V. Lohmann, Evolution and Regulation of the Lotus japonicus LysM Receptor Gene Family, Mol. Plant-Microbe Interact, vol.23, pp.510-521, 2010.

J. Arrighi, The Medicago truncatula lysine motif-receptor-like kinase gene family includes NFP and new nodule-expressed genes, Plant Physiol, vol.142, pp.265-79, 2006.

J. Arrighi, The RPG gene of Medicago truncatula controls Rhizobium-directed polar growth during infection, Proc. Natl. Acad. Sci. USA 105, pp.9817-9839, 2008.

C. H. Haney and S. Long, Plant flotillins are required for infection by nitrogen-fixing bacteria, Proc. Natl. Acad. Sci. USA, vol.107, pp.478-83, 2010.

J. Combier, The MtMMPL1 early nodulin is a novel member of the matrix metalloendoproteinase family with a role in Medicago truncatula infection by Sinorhizobium meliloti, Plant Physiol, vol.144, pp.703-719, 2007.

F. D. Niebel, N. Lescure, J. V. Cullimore, and P. Gamas, The Medicago truncatula MtAnn1 gene encoding an annexin is induced by Nod factors and during the symbiotic interaction with Rhizobium meliloti, Mol. Plant. Microbe. Interact, vol.11, pp.504-517, 1998.

H. J. Yoon, Lotus japonicus SUNERGOS1 encodes a predicted subunit A of a DNA topoisomerase VI that is required for nodule differentiation and accommodation of rhizobial infection, Plant J, vol.78, pp.811-832, 2014.

T. Suzaki, Endoreduplication-mediated initiation of symbiotic organ development in Lotus japonicus, Development, vol.141, pp.2441-2445, 2014.

M. Bourcy, Medicago truncatula DNF2 is a PI-PLC-XD-containing protein required for bacteroid persistence and prevention of nodule early senescence and defense-like reactions, New Phytol, vol.197, pp.1250-1261, 2013.
URL : https://hal.archives-ouvertes.fr/hal-02403239

F. Berrabah, A nonRD receptor-like kinase prevents nodule early senescence and defense-like reactions during symbiosis, New Phytol, vol.203, pp.1305-1314, 2014.
URL : https://hal.archives-ouvertes.fr/hal-02410361

F. Maillet, Fungal lipochitooligosaccharide symbiotic signals in arbuscular mycorrhiza, Nature, vol.469, pp.58-63, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00577122

K. Bonaldi, The Nod factor-independent symbiotic signaling pathway: development of Agrobacterium rhizogenes-mediated transformation for the legume Aeschynomene indica, Mol. Plant. Microbe. Interact, vol.23, pp.1537-1581, 2010.

J. F. Marsh, Medicago truncatula NIN is essential for rhizobial-independent nodule organogenesis induced by autoactive calcium/calmodulin-dependent protein kinase, Plant Physiol, vol.144, pp.324-359, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00159989

F. Clavijo, The Casuarina NIN gene is transcriptionally activated throughout Frankia root infection as well as in response to bacterial diffusible signals, New Phytol, vol.208, pp.887-903, 2015.

C. Ahn, U. Park, and P. Park, Increased salt and drought tolerance by D-ononitol production in transgenic Arabidopsis thaliana, Biochem. Biophys. Res. Commun, vol.415, pp.669-674, 2011.

N. Takeda, S. Sato, E. Asamizu, S. Tabata, and M. Parniske, Apoplastic plant subtilases support arbuscular mycorrhiza development in Lotus japonicus, Plant J, vol.58, pp.766-77, 2009.

, SCIENTIFIC REPoRts |, vol.8, 2018.

F. Molouba, Photosynthetic bradyrhizobia from Aeschynomene spp. are specific to stem-nodulated species and form a separate 16S ribosomal DNA restriction fragment length polymorphism group, Appl. Environ. Microbiol, vol.65, pp.3084-94, 1999.

D. Vallenet, MicroScope-an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data, Nucleic Acids Res, vol.41, pp.636-647, 2013.

Z. Ning, A. J. Cox, and J. C. Mullikin, SSAHA: a fast search method for large DNA databases, Genome Res, vol.11, pp.1725-1734, 2001.

H. Li, The Sequence Alignment/Map format and SAMtools, Bioinformatics, vol.25, pp.2078-2079, 2009.

A. R. Quinlan and I. M. Hall, BEDTools: a flexible suite of utilities for comparing genomic features, Bioinformatics, vol.26, pp.841-843, 2010.

S. Anders and W. Huber, Differential expression analysis for sequence count data, Genome Biol, vol.11, p.106, 2010.

M. W. Pfaffl, A new mathematical model for relative quantification in real-time RT-PCR, Nucleic Acids Res, vol.29, p.45, 2001.