10 [87] G. K. Agrawal, M. Yonekura, Y. Iwahashi, H. Iwahashi, and R. Rakwal, “System, trends and perspectives of proteomics in dicot plants—part III: unraveling the proteomes inﬂuenced by the environment, and at the levels of function and genetic relationships,” Journal of Chromatography B, vol. 815, no. 1-2, pp. 137–145, 2005. [88] G. K. Agrawal, M. Yonekura, Y. Iwahashi, H. Iwahashi, and R. Rakwal, “System, trends and perspectives of proteomics in di- cot plants—part II: proteomes of the complex developmen- tal stages,” Journal of Chromatography B, vol. 815, no. 1-2, pp. 125–136, 2005. [89] K. Zhang, C. McKinlay, C. H. Hocart, and M. A. Djordje- vic, “The Medicago truncatula small protein proteome and peptidome,” Journal of Proteome Research, vol. 5, no. 12, pp. 3355–3367, 2006. [90] F. Colditz, O. Nyamsuren, K. Niehaus, H. Eubel, H.-P. Braun, and F. Krajinski, “Proteomic approach: identiﬁcation of Med- icago truncatula proteins induced in roots after infection with the pathogenic oomycete Aphanomyces euteiches,” Plant Molecular Biology, vol. 55, no. 1, pp. 109–120, 2004. [91] C. M. Catalano, W. S. Lane, and D. J. Sherrier, “Biochemi- cal characterization of symbiosome membrane proteins from Medicago truncatula root nodules,” Electrophoresis, vol. 25, no. 3, pp. 519–531, 2004. [92] B. Valot, M. Dieu, G. Recorbet, M. Raes, S. Gianinazzi, and E. Dumas-Gaudot, “Identiﬁcation of membrane-associated proteins regulated by the arbuscular mycorrhizal symbiosis,” Plant Molecular Biology, vol. 59, no. 4, pp. 565–580, 2005. [93] B. Valot, S. Gianinazzi, and D.-G. Eliane, “Sub-cellular pro- teomic analysis of a Medicago truncatula root microsomal fraction,” Phytochemistry, vol. 65, no. 12, pp. 1721–1732, 2004. [94] U. Mathesius, G. Keijzers, S. H. A. Natera, J. J. Weinman, M. A. Djordjevic, and B. G. Rolfe, “Establishment of a root pro- teome reference map for the model legume Medicago trun- catula using the expressed sequence tag database for peptide mass ﬁngerprinting,” Proteomics, vol. 1, no. 11, pp. 1424– 1440, 2001. [95] B. S. Watson, V. S. Asirvatham, L. Wang, and L. W. Sumner, “Mapping the proteome of barrel medic (Medicago truncat- ula),” Plant Physiology, vol. 131, no. 3, pp. 1104–1123, 2003. [96] N. Imin, F. De Jong, U. Mathesius, et al., “Proteome reference maps of Medicago truncatula embryogenic cell cultures gen- erated from single protoplasts,” Proteomics, vol. 4, no. 7, pp. 1883–1896, 2004. [97] N. Imin, M. Nizamidin, D. Daniher, K. E. Nolan, R. J. Rose, and B. G. Rolfe, “Proteomic analysis of somatic embryoge- nesis in Medicago truncatula. Explant cultures grown under 6-benzylaminopurine and 1-naphthaleneacetic acid treat- ments,” Plant Physiology, vol. 137, no. 4, pp. 1250–1260, 2005. [98] Z. Lei, A. M. Elmer, B. S. Watson, R. A. Dixon, P. J. Mendes, and L. W. Sumner, “A two-dimensional electrophoresis pro- teomic reference map and systematic identiﬁcation of 1367 proteins from a cell suspension culture of the model legume Medicago truncatula,” Molecular and Cellular Proteomics, vol. 4, no. 11, pp. 1812–1825, 2005. [99] N. Amiour, G. Recorbet, F. Robert, S. Gianinazzi, and E. Dumas-Gaudot, “Mutations in DMI3 and SUNN modify the appressorium-responsive root proteome in arbuscular myc- orrhiza,” Molecular Plant-Microbe Interactions, vol. 19, no. 9, pp. 988–997, 2006. [100] J. Prayitno, B. G. Rolfe, and U. Mathesius, “The ethylene- insensitive sickle mutant of Medicago truncatula shows altered International Journal of Plant Genomics auxin transport regulation during nodulation,” Plant Physi- ology, vol. 142, no. 1, pp. 168–180, 2006. [101] M. K. Udvardi and W.-R. Scheible, “GRAS genes and the symbiotic green revolution,” Science, vol. 308, no. 5729, pp. 1749–1750, 2005. [102] S. Laugesen, E. Messinese, S. Hem, et al., “Phosphoproteins analysis in plants: a proteomic approach,” Phytochemistry, vol. 67, no. 20, pp. 2208–2214, 2006. [103] R. N. Trethewey, A. J. Krotzky, and L. Willmitzer, “Metabolic proﬁling: a rosetta stone for genomics?” Current Opinion in Plant Biology, vol. 2, no. 2, pp. 83–85, 1999. [104] C. D. Broeckling, D. V. Huhman, M. A. Farag, et al., “Metabolic proﬁling of Medicago truncatula cell cultures re- veals the eﬀects of biotic and abiotic elicitors on metabolism,” Journal of Experimental Botany, vol. 56, no. 410, pp. 323–336, 2005. [105] H. Suzuki, M. S.S. Reddy, M. Naoumkina, et al., “Methyl jas- monate and yeast elicitor induce diﬀerential transcriptional and metabolic re-programming in cell suspension cultures of the model legume Medicago truncatula,” Planta, vol. 220, no. 5, pp. 696–707, 2005. [106] H. Jenkins, N. Hardy, M. Beckmann, et al., “A proposed framework for the description of plant metabolomics experi- ments and their results,” Nature Biotechnology, vol. 22, no. 12, pp. 1601–1606, 2004. [107] H. Jenkins, H. Johnson, B. Kular, T. Wang, and N. Hardy, “Toward supportive data collection tools for plant metabolomics,” Plant Physiology, vol. 138, no. 1, pp. 67–77, 2005. [108] J. Bowman, Arabidopsis: An Atlas of Morphology and Develop- ment, Springer, New York, NY, USA, 1994. [109] D. Moreau, C. Salon, and N. Munier-Jolain, “A framework for the analysis of genetic variability in Medicago truncatula,” in Proceedings of the 2nd International Conference on Legume Genomics and Genetics, p. 286, Dijon, France, June 2004. [110] M. D. Gonzales, E. Archuleta, A. Farmer, et al., “The legume information system (LIS): an integrated information re- source for comparative legume biology,” Nucleic Acids Re- search, vol. 33, pp. D660–D665, 2005. [111] M. Fedorova, J. van de Mortel, P. A. Matsumoto, et al., “Genome-wide identiﬁcation of nodule-speciﬁc transcripts in the model legume Medicago truncatula,” Plant Physiology, vol. 130, no. 2, pp. 519–537, 2002. [112] P. Mergaert, K. Nikovics, Z. Kelemen, 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, no. 1, pp. 161–173, 2003. [113] M. A. Graham, K. A.T. Silverstein, S. B. Cannon, and K. A. VandenBosch, “Computational identiﬁcation and char- acterization of novel genes from legumes,” Plant Physiology, vol. 135, no. 3, pp. 1179–1197, 2004. [114] H. K u¨ster, A. Becker, C. Firnhaber, et al., “Development of bioinformatic tools to support EST-sequencing, in sil- ico and microarray-based transcriptome proﬁling in mycor- rhizal symbioses,” Phytochemistry, vol. 68, no. 1, pp. 19–32, 2007. [115] S. B. Cannon, J. A. Crow, M. L. Heuer, et al., “Databases and information integration for the Medicago truncatula genome and transcriptome,” Plant Physiology, vol. 138, no. 1, pp. 38– 46, 2005. [116] E. Urbanczyk-Wochniak and L. W. Sumner, “MedicCyc: a biochemical pathway database for Medicago truncatula,” Bioinformatics, vol. 23, no. 11, pp. 1418–1423, 2007.