P. Graham and C. Vance, Legumes: Importance and Constraints to Greater Use, PLANT PHYSIOLOGY, vol.131, issue.3, pp.872-879, 2003.
DOI : 10.1104/pp.017004

R. Dixon and L. Sumner, Legume Natural Products: Understanding and Manipulating Complex Pathways for Human and Animal Health, PLANT PHYSIOLOGY, vol.131, issue.3, pp.878-85, 2003.
DOI : 10.1104/pp.102.017319

J. Duke, Handbook of legumes of economic importance, 1992.
DOI : 10.1007/978-1-4684-8151-8

I. Southon, F. Bisby, J. Buckingham, J. Harborne, and J. Zarucchi, International Legume Database and Information Service., Chapman & Hall Chemical Database, Phytochemical dictionary of the Leguminosae, 1994.

M. Gouy, S. Guindon, and O. Gascuel, SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building, Molecular Biology and Evolution, vol.27, issue.2, pp.221-225, 2010.
DOI : 10.1093/molbev/msp259

URL : https://hal.archives-ouvertes.fr/lirmm-00705187

M. Wink, Evolution of secondary metabolites from an ecological and molecular phylogenetic perspective, Phytochemistry, vol.64, issue.1, pp.3-19, 2003.
DOI : 10.1016/S0031-9422(03)00300-5

I. Rahioui, V. Eyraud, L. Karaki, F. Sasse, M. Carre-pierrat et al., Host range of the potential biopesticide Pea Albumin 1b (PA1b) is limited to insects, Toxicon, vol.89, pp.67-76, 2014.
DOI : 10.1016/j.toxicon.2014.07.004

URL : https://hal.archives-ouvertes.fr/hal-01449144

B. Delobel, A. Grenier, J. Gueguen, E. Ferrasson, and M. Mbaiguinam, Utilisation d'un polypeptide dérivé d'une albumine PA1b de légumineuse comme insecticide, pp.1-6500, 1998.

F. Gressent, D. Silva, P. Eyraud, V. Karaki, L. Royer et al., Pea Albumin 1 Subunit b (PA1b), a Promising Bioinsecticide of Plant Origin, Toxins, vol.3, issue.12, pp.1502-1519, 2011.
DOI : 10.3390/toxins3121502

URL : https://hal.archives-ouvertes.fr/hal-00666408

J. Gatehouse, J. Gilroy, M. Hoque, and R. Croy, ), Biochemical Journal, vol.225, issue.1, pp.239-286, 1985.
DOI : 10.1042/bj2250239

F. Gressent, G. Duport, I. Rahioui, Y. Pauchet, P. Bolland et al., Biological Activity and Binding Site Characteristics of the PA1b Entomotoxin on Insects from Different Orders, Journal of Insect Science, vol.7, issue.12, pp.1-10, 2007.
DOI : 10.1673/031.007.1201

URL : https://hal.archives-ouvertes.fr/hal-00391325

F. Gressent, I. Rahioui, and Y. Rahbe, Characterization of a high-affinity binding site for the pea albumin 1b entomotoxin in the weevil Sitophilus, European Journal of Biochemistry, vol.60, issue.11, pp.2429-2464, 2003.
DOI : 10.1016/S0041-0101(98)00149-4

URL : https://hal.archives-ouvertes.fr/hal-00402185

C. Chouabe, V. Eyraud, D. Silva, P. Rahioui, I. Royer et al., New Mode of Action for a Knottin Protein Bioinsecticide: PEA ALBUMIN 1 SUBUNIT b (PA1b) IS THE FIRST PEPTIDIC INHIBITOR OF V-ATPase, Journal of Biological Chemistry, vol.286, issue.42, pp.36291-36297, 2011.
DOI : 10.1074/jbc.M111.281055

J. Gelly, J. Gracy, Q. Kaas, D. Le-nguyen, A. Heitz et al., The KNOTTIN website and database: a new information system dedicated to the knottin scaffold, Nucleic Acids Research, vol.32, issue.90001, pp.156-165, 2004.
DOI : 10.1093/nar/gkh015

T. Higgins, P. Chandler, P. Randall, D. Spencer, L. Beach et al., Gene structure, protein structure, and regulation of the synthesis of a sulfurrich protein in pea seeds, J Biol Chem, vol.261, pp.11124-11154, 1986.

S. Louis, B. Delobel, F. Gressent, I. Rahioui, L. Quillien et al., Molecular and biological screening for insect-toxic seed albumins from four legume species, Plant Science, vol.167, issue.4, pp.705-719, 2004.
DOI : 10.1016/j.plantsci.2004.04.018

S. Louis, B. Delobel, F. Gressent, G. Duport, O. Diol et al., Broad screening of the legume family for variability in seed insecticidal activities and for the occurrence of the A1b-like knottin peptide entomotoxins, Phytochemistry, vol.68, issue.4, pp.521-556, 2007.
DOI : 10.1016/j.phytochem.2006.11.032

URL : https://hal.archives-ouvertes.fr/hal-00373359

K. Silverstein, W. Jr, H. Wu, B. Underwood, M. Graham et al., Small cysteine-rich peptides resembling antimicrobial peptides have been under-predicted in plants, The Plant Journal, vol.62, issue.2, pp.262-80, 2007.
DOI : 10.1111/j.1365-313X.2007.03136.x

Y. Zhang, M. Fernandez-aparicio, E. Wafula, M. Das, Y. Jiao et al., Evolution of a horizontally acquired legume gene, albumin 1, in the parasitic plant Phelipanche aegyptiaca and related species, BMC Evolutionary Biology, vol.13, issue.1, p.48, 2013.
DOI : 10.1093/bioinformatics/btq033

N. Young, F. Debelle, G. Oldroyd, R. Geurts, S. Cannon et al., The Medicago genome provides insight into the evolution of rhizobial symbioses, Nature, vol.151, pp.520-524, 2011.
DOI : 10.1038/nature10625

J. Schmutz, S. Cannon, J. Schlueter, J. Ma, T. Mitros et al., Genome sequence of the palaeopolyploid soybean, Nature, vol.22, issue.7278, pp.178-83, 2010.
DOI : 10.1038/nature08670

F. Ronquist, M. Teslenko, P. Van-der-mark, D. Ayres, A. Darling et al., MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space, Systematic Biology, vol.61, issue.3, pp.539-581, 2012.
DOI : 10.1093/sysbio/sys029

R. Varshney, C. W. Li, Y. Bharti, A. Saxena, R. Schlueter et al., Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers, Nature Biotechnology, vol.106, issue.1, pp.83-92, 2011.
DOI : 10.1093/nar/30.7.1575

R. Varshney, C. Song, R. Saxena, S. Azam, S. Yu et al., Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement, Nature Biotechnology, vol.30, issue.3, pp.240-246, 2013.
DOI : 10.1126/science.1176620

J. Schmutz, P. Mcclean, S. Mamidi, G. Wu, S. Cannon et al., A reference genome for common bean and genome-wide analysis of dual domestications, Nature Genetics, vol.132, issue.7, pp.707-720, 2014.
DOI : 10.1093/bioinformatics/bts444

J. Istvanek, M. Jaros, A. Krenek, and J. Repkova, Genome assembly and annotation for red clover (Trifolium pratense; Fabaceae), American Journal of Botany, vol.101, issue.2, pp.327-364, 2014.
DOI : 10.3732/ajb.1300340

N. Young, J. Mudge, and T. Ellis, Legume genomes: more than peas in a pod, Current Opinion in Plant Biology, vol.6, issue.2, pp.199-204, 2003.
DOI : 10.1016/S1369-5266(03)00006-2

J. Gracy, D. Le-nguyen, J. Gelly, Q. Kaas, A. Heitz et al., KNOTTIN: the knottin or inhibitor cystine knot scaffold in 2007, Nucleic Acids Research, vol.36, issue.Database, pp.314-323, 2007.
DOI : 10.1093/nar/gkm939

Q. Cronk, I. Ojeda, and R. Pennington, Legume comparative genomics: progress in phylogenetics and phylogenomics, Current Opinion in Plant Biology, vol.9, issue.2, pp.99-103, 2006.
DOI : 10.1016/j.pbi.2006.01.011

D. Silva, P. Rahioui, I. Laugier, C. Jouvensal, L. Meudal et al., Molecular Requirements for the Insecticidal Activity of the Plant Peptide Pea Albumin 1 Subunit b (PA1b), Journal of Biological Chemistry, vol.285, issue.43, pp.32689-94, 2010.
DOI : 10.1074/jbc.M110.147199

URL : https://hal.archives-ouvertes.fr/hal-00591660

I. Rahioui, C. Laugier, S. Balmand, D. Silva, P. Rahbé et al., Toxicity, binding and internalization of the pea-A1b entomotoxin in Sf9 cells, Biochimie, vol.89, issue.12, pp.1539-1582, 2007.
DOI : 10.1016/j.biochi.2007.07.021

URL : https://hal.archives-ouvertes.fr/hal-00391507

E. Yahyaoui, F. Kuster, H. , B. Amor, B. Hohnjec et al., Expression Profiling in Medicago truncatula Identifies More Than 750 Genes Differentially Expressed during Nodulation, Including Many Potential Regulators of the Symbiotic Program, PLANT PHYSIOLOGY, vol.136, issue.2, pp.3159-76, 2004.
DOI : 10.1104/pp.104.043612

P. Gamas, F. Niebel, N. Lescure, and J. Cullimore, Genes Induced During Root Nodule Development, Molecular Plant-Microbe Interactions, vol.9, issue.4, pp.233-275, 1996.
DOI : 10.1094/MPMI-9-0233

L. Hu and S. Liu, Genome-wide identification and phylogenetic analysis of the ERF gene family in cucumbers, Genetics and Molecular Biology, vol.34, issue.4, pp.624-657, 2011.
DOI : 10.1590/S1415-47572011005000054

F. Boutrot, N. Chantret, and M. Gautier, Genome-wide analysis of the rice and arabidopsis non-specific lipid transfer protein (nsLtp) gene families and identification of wheat nsLtp genes by EST data mining, BMC Genomics, vol.9, issue.1, p.86, 2008.
DOI : 10.1186/1471-2164-9-86

K. Olsen and J. Wendel, A Bountiful Harvest: Genomic Insights into Crop Domestication Phenotypes, Annual Review of Plant Biology, vol.64, issue.1, pp.47-70, 2013.
DOI : 10.1146/annurev-arplant-050312-120048

K. Hanada, Y. Nishiuchi, and H. Hirano, Amino acid residues on the surface of soybean 4-kDa peptide involved in the interaction with its binding protein, European Journal of Biochemistry, vol.264, issue.12
DOI : 10.1021/bi00247a019

T. Yamazaki, M. Takaoka, E. Katoh, K. Hanada, M. Sakita et al., A possible physiological function and the tertiary structure of a 4-kDa peptide in legumes, European Journal of Biochemistry, vol.253, issue.6, pp.1269-76, 2003.
DOI : 10.1126/science.283.5409.1911

Y. Watanabe, S. Barbashov, S. Komatsu, A. Hemmings, M. Miyagi et al., A Peptide that Stimulates Phosphorylation of the Plant Insulin-Binding Protein. Isolation, Primary Structure and cDNA Cloning, European Journal of Biochemistry, vol.167, issue.27, pp.167-72, 1994.
DOI : 10.1016/0005-2744(81)90106-6

X. Dun, J. Wang, L. Chen, J. Lu, F. Li et al., Activity of the plant peptide aglycin in mammalian systems, FEBS Journal, vol.12, issue.Suppl., pp.751-760, 2007.
DOI : 10.1111/j.1742-4658.2006.05619.x

A. Poth, M. Colgrave, R. Lyons, N. Daly, and D. Craik, Discovery of an unusual biosynthetic origin for circular proteins in legumes, Proceedings of the National Academy of Sciences, vol.108, issue.25, pp.10127-10159, 2011.
DOI : 10.1073/pnas.1103660108

G. Nguyen, S. Zhang, N. Nguyen, P. Nguyen, M. Chiu et al., Discovery and Characterization of Novel Cyclotides Originated from Chimeric Precursors Consisting of Albumin-1 Chain a and Cyclotide Domains in the Fabaceae Family, Journal of Biological Chemistry, vol.286, issue.27, pp.24275-87, 2011.
DOI : 10.1074/jbc.M111.229922

D. Cardoso, L. De-queiroz, R. Pennington, H. De-lima, E. Fonty et al., Revisiting the phylogeny of papilionoid legumes: New insights from comprehensively sampled early-branching lineages, American Journal of Botany, vol.99, issue.12, pp.1991-2013, 2012.
DOI : 10.3732/ajb.1200380

S. Ilgoutz, N. Knittel, J. Lin, S. Sterle, and K. Gayler, Transcription of genes for conglutin gamma and a leginsulin-like protein in narrow-leafed lupin, Plant Molecular Biology, vol.34, issue.4, pp.613-640, 1997.
DOI : 10.1023/A:1005868105651

M. Lavin, P. Herendeen, and M. Wojciechowski, Evolutionary Rates Analysis of Leguminosae Implicates a Rapid Diversification of Lineages during the Tertiary, Systematic Biology, vol.54, issue.4, pp.575-94, 2005.
DOI : 10.1080/10635150590947131

F. Marsolais, A. Pajak, F. Yin, M. Taylor, M. Gabriel et al., Proteomic analysis of common bean seed with storage protein deficiency reveals up-regulation of sulfur-rich proteins and starch and raffinose metabolic enzymes, and down-regulation of the secretory pathway, Journal of Proteomics, vol.73, issue.8, pp.1587-600, 2010.
DOI : 10.1016/j.jprot.2010.03.013

F. Yin, A. Pajak, R. Chapman, A. Sharpe, S. Huang et al., Analysis of common bean expressed sequence tags identifies sulfur metabolic pathways active in seed and sulfur-rich proteins highly expressed in the absence of phaseolin and major lectins, BMC Genomics, vol.20, issue.1, p.268, 2011.
DOI : 10.1002/(SICI)1522-2683(19991201)20:18<3551::AID-ELPS3551>3.0.CO;2-2

R. Legocki and D. Verma, Identification of ???nodule-specific??? host proteins (nodulins) involved in the development of Rhizobium-Legume symbiosis, Cell, vol.20, issue.1, pp.153-63, 1980.
DOI : 10.1016/0092-8674(80)90243-3

V. Eyraud, L. Karaki, I. Rahioui, C. Sivignon, D. Silva et al., Expression and Biological Activity of the Cystine Knot Bioinsecticide PA1b (Pea Albumin 1 Subunit b), PLoS ONE, vol.7, issue.12, p.81619, 2013.
DOI : 10.1371/journal.pone.0081619.s001

URL : https://hal.archives-ouvertes.fr/hal-00921788

A. Heitz, L. Chiche, D. Le-nguyen, and B. Castro, Proton 2D NMR and distance geometry study of the folding of Ecballium elaterium trypsin inhibitor, a member of the squash inhibitors family, Biochemistry, vol.28, issue.6, pp.2392-2400, 1989.
DOI : 10.1021/bi00432a009

D. Craik and U. Malik, Cyclotide biosynthesis, Current Opinion in Chemical Biology, vol.17, issue.4, pp.546-54, 2013.
DOI : 10.1016/j.cbpa.2013.05.033

A. Mitchell, H. Chang, L. Daugherty, M. Fraser, S. Hunter et al., The InterPro protein families database: the classification resource after 15 years, Nucleic Acids Research, vol.43, issue.D1, pp.213-234, 2015.
DOI : 10.1093/nar/gku1243

URL : https://hal.archives-ouvertes.fr/hal-01222896

R. Finn, A. Bateman, J. Clements, P. Coggill, R. Eberhardt et al., Pfam: the protein families database, Nucleic Acids Research, vol.42, issue.D1, pp.222-252, 2014.
DOI : 10.1093/nar/gkt1223

URL : https://hal.archives-ouvertes.fr/hal-01294685

I. Guefrachi, M. Nagymihaly, C. Pislariu, W. Van-de-velde, P. Ratet et al., Extreme specificity of NCR gene expression in Medicago truncatula, BMC Genomics, vol.15, issue.1, p.712, 2014.
DOI : 10.1371/journal.pgen.1002230

P. Mergaert, K. Nikovics, Z. Kelemen, N. Maunoury, D. Vaubert et al., A Novel Family in Medicago truncatula Consisting of More Than 300 Nodule-Specific Genes Coding for Small, Secreted Polypeptides with Conserved Cysteine Motifs, PLANT PHYSIOLOGY, vol.132, issue.1, pp.161-73, 2003.
DOI : 10.1104/pp.102.018192

URL : https://hal.archives-ouvertes.fr/hal-00134878

S. Altschul, T. Madden, A. Schäffer, J. Zhang, Z. Zhang et al., Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Research, vol.25, issue.17, pp.3389-402, 1997.
DOI : 10.1093/nar/25.17.3389

C. Bru, E. Courcelle, S. Carrere, Y. Beausse, S. Dalmar et al., The ProDom database of protein domain families: more emphasis on 3D, Nucleic Acids Research, vol.33, issue.Database issue, pp.212-217, 2005.
DOI : 10.1093/nar/gki034

URL : https://hal.archives-ouvertes.fr/hal-01214150

S. Eddy, Accelerated Profile HMM Searches, PLoS Computational Biology, vol.21, issue.10, p.1002195, 2011.
DOI : 10.1371/journal.pcbi.1002195.g006

J. Bendtsen, H. Nielsen, G. Von-heijne, and S. Brunak, Improved Prediction of Signal Peptides: SignalP 3.0, Journal of Molecular Biology, vol.340, issue.4, pp.783-95, 2004.
DOI : 10.1016/j.jmb.2004.05.028

A. Bairoch, R. Apweiler, C. Wu, W. Barker, B. Boeckmann et al., The Universal Protein Resource (UniProt), Nucleic Acids Research, vol.33, issue.Database issue, pp.154-163, 2005.
DOI : 10.1093/nar/gki070

K. Katoh and D. Standley, MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability, Molecular Biology and Evolution, vol.30, issue.4, pp.772-80, 2013.
DOI : 10.1093/molbev/mst010

S. Guindon, J. Dufayard, V. Lefort, M. Anisimova, W. Hordijk et al., New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0, Systematic Biology, vol.59, issue.3, pp.307-328, 2010.
DOI : 10.1093/sysbio/syq010

URL : https://hal.archives-ouvertes.fr/lirmm-00511784

S. Le and O. Gascuel, Accounting for Solvent Accessibility and Secondary Structure in Protein Phylogenetics Is Clearly Beneficial, Systematic Biology, vol.59, issue.3, pp.277-87, 2010.
DOI : 10.1093/sysbio/syq002

URL : https://hal.archives-ouvertes.fr/lirmm-00511776

Z. Yang, PAML: a program package for phylogenetic analysis by maximum likelihood, Bioinformatics, vol.13, issue.5, pp.555-561, 1997.
DOI : 10.1093/bioinformatics/13.5.555

D. Mita, S. Siol, and M. , EggLib: processing, analysis and simulation tools for population genetics and genomics, BMC Genetics, vol.13, issue.1, p.27, 2012.
DOI : 10.1186/1471-2105-12-134

URL : https://hal.archives-ouvertes.fr/hal-01268349

J. Romiguier, E. Figuet, N. Galtier, E. Douzery, B. Boussau et al., Fast and Robust Characterization of Time-Heterogeneous Sequence Evolutionary Processes Using Substitution Mapping, PLoS ONE, vol.1, issue.3, p.33852, 2012.
DOI : 10.1371/journal.pone.0033852.s003

URL : https://hal.archives-ouvertes.fr/hal-00965722

F. Sievers, A. Wilm, D. Dineen, T. Gibson, K. Karplus et al., Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega, Molecular Systems Biology, vol.7, issue.1, p.539, 2011.
DOI : 10.1093/nar/gkn174

D. Silva, P. Strzepa, A. Jouvensal, L. Rahioui, I. Gressent et al., A folded and functional synthetic PA1b: An interlocked entomotoxic miniprotein, Biopolymers, vol.358, issue.5, pp.436-480, 2009.
DOI : 10.1002/bip.21217

URL : https://hal.archives-ouvertes.fr/hal-00391296