Jean-Michel Ane´ et al. allowing karyotype analysis in Medicago truncatula lines Je- malong J5 and R-108-1,” Molecular Plant-Microbe Interac- tions, vol. 12, no. 11, pp. 947–950, 1999. [57] J. M. Ane´, J. Le´vy, P. Thoquet, et al., “Genetic and cytoge- netic mapping of DMI1, DMI2, and DMI3 genes of Medicago truncatula involved in Nod factor transduction, nodulation, and mycorrhization,” Molecular Plant-Microbe Interactions, vol. 15, no. 11, pp. 1108–1118, 2002. [58] O. Kulikova, G. Gualtieri, R. Geurts, et al., “Integration of the FISH pachytene and genetic maps of Medicago truncatula,” Plant Journal, vol. 27, no. 1, pp. 49–58, 2001. [59] O. Kulikova, R. Geurts, M. Lamine, et al., “Satellite repeats in the functional centromere and pericentromeric heterochro- matin of Medicago truncatula,” Chromosoma, vol. 113, no. 6, pp. 276–283, 2004. [60] E. Schnabel, O. Kulikova, R. V. Penmetsa, T. Bisseling, D. R. Cook, and J. Frugoli, “An integrated physical, genetic and cy- togenetic map around the sunn locus of Medicago truncat- ula,” Genome, vol. 46, no. 4, pp. 665–672, 2003. [61] F. W. Engler, J. Hatﬁeld, W. Nelson, and C. A. Soderlund, “Locating sequence on FPC maps and selecting a minimal tiling path,” Genome Research, vol. 13, no. 9, pp. 2152–2163, 2003. [62] N. D. Young, S. B. Cannon, S. Sato, et al., “Sequencing the genespaces of Medicago truncatula and Lotus japonicus,” Plant Physiology, vol. 137, no. 4, pp. 1174–1181, 2005. [63] C. D. Town, “Annotating the genome of Medicago truncat- ula,” Current Opinion in Plant Biology, vol. 9, no. 2, pp. 122– 127, 2006. [64] V. Stolc, M. P. Samanta, and W. Tongprasit, “Identiﬁcation of transcribed sequences in Arabidopsis thaliana by using high- resolution genone tiling arrays,” Proceedings of the National Academy of Sciences of the United States of America, vol. 102, no. 12, pp. 4453–4458, 2005. [65] J. M. Johnson, S. Edwards, D. Shoemaker, and E. E. Schadt, “Dark matter in the genome: evidence of widespread tran- scription detected by microarray tiling experiments,” Trends in Genetics, vol. 21, no. 2, pp. 93–102, 2005. [66] K. Yamada, J. Lim, J. H. Dale, et al., “Empirical analysis of transcriptional activity in the Arabidopsis Genome,” Science, vol. 302, no. 5646, pp. 842–846, 2003. [67] P. Bertone, M. Gerstein, and M. Snyder, “Applications of DNA tiling arrays to experimental genome annotation and regulatory pathway discovery,” Chromosome Research, vol. 13, no. 3, pp. 259–274, 2005. [68] P. A. Covitz, L. S. Smith, and S. R. Long, “Expressed sequence tags from a root-hair-enriched Medicago truncatula cDNA li- brary,” Plant Physiology, vol. 117, no. 4, pp. 1325–1332, 1998. [69] J. Gyo¨rgyey, D. Vaubert, J. I. Jime´nez-Zurdo, et al., “Analy- sis of Medicago truncatula nodule expressed sequence tags,” Molecular Plant-Microbe Interactions, vol. 13, no. 1, pp. 62– 71, 2000. [70] C. J. Bell, R. A. Dixon, A. D. Farmer, et al., “The Medicago genome initiative: a model legume database,” Nucleic Acids Research, vol. 29, no. 1, pp. 114–117, 2001. [71] E.-P. Journet, D. van Tuinen, J. Gouzy, et al., “Exploring root symbiotic programs in the model legume Medicago truncat- ula using EST analysis,” Nucleic Acids Research, vol. 30, no. 24, pp. 5579–5592, 2002. [72] A.-F. J. Lamblin, J. A. Crow, J. E. Johnson, et al., “MtDB: a database for personalized data mining of the model legume Medicago truncatula transcriptome,” Nucleic Acids Research, vol. 31, no. 1, pp. 196–201, 2003. 9 [73] J. Liu, L. A. Blaylock, G. Endre, et al., “Transcript proﬁl- ing coupled with spatial expression analyses reveals genes in- volved in distinct developmental stages of an arbuscular my- corrhizal symbiosis,” Plant Cell, vol. 15, no. 9, pp. 2106–2123, 2003. [74] F. E. Yahyaoui, H. K u¨ster, B. B. Amor, et al., “Expression pro- ﬁling in Medicago truncatula identiﬁes more than 750 genes diﬀerentially expressed during nodulation, including many potential regulators of the symbiotic program,” Plant Physi- ology, vol. 136, no. 2, pp. 3159–3176, 2004. [75] K. Manthey, F. Krajinski, N. Hohnjec, et al., “Transcriptome proﬁling in root nodules and arbuscular mycorrhiza identi- ﬁes a collection of novel genes induced during Medicago trun- catula root endosymbioses,” Molecular Plant-Microbe Inter- actions, vol. 17, no. 10, pp. 1063–1077, 2004. [76] R. M. Mitra and S. R. Long, “Plant and bacterial symbi- otic mutants deﬁne three transcriptionally distinct stages in the development of the Medicago truncatula/Sinorhizobium meliloti Symbiosis,” Plant Physiology, vol. 134, no. 2, pp. 595– 604, 2004. [77] R. M. Mitra, S. L. Shaw, and S. R. Long, “Six nonnodulating plant mutants defective for Nod factor-induced transcrip- tional changes associated with the legume-rhizobia symbio- sis,” Proceedings of the National Academy of Sciences of the United States of America, vol. 101, no. 27, pp. 10217–10222, 2004. [78] D. P. Lohar, N. Sharopova, G. Endre, et al., “Transcript anal- ysis of early nodulation events in Medicago truncatula,” Plant Physiology, vol. 140, no. 1, pp. 221–234, 2006. [79] C. G. Starker, A. L. Parra-Colmenares, L. Smith, R. M. Mi- tra, and S. R. Long, “Nitrogen ﬁxation mutants of Medicago truncatula fail to support plant and bacterial symbiotic gene expression,” Plant Physiology, vol. 140, no. 2, pp. 671–680, 2006. [80] M. J. Barnett, C. J. Toman, R. F. Fisher, and S. R. Long, “A dual-genome Symbiosis Chip for coordinate study of signal exchange and development in a prokaryote-host interaction,” Proceedings of the National Academy of Sciences of the United States of America, vol. 101, no. 47, pp. 16636–16641, 2004. [81] N. Aziz, N. L. Paiva, G. D. May, and R. A. Dixon, “Transcrip- tome analysis of alfalfa glandular trichomes,” Planta, vol. 221, no. 1, pp. 28–38, 2005. [82] B. E. Deavours and R. A. Dixon, “Metabolic engineering of isoﬂavonoid biosynthesis in alfalfa,” Plant Physiology, vol. 138, no. 4, pp. 2245–2259, 2005. [83] L. Diatchenko, Y.-F. C. Lau, A. P. Campbell, et al., “Suppres- sion subtractive hybridization: a method for generating dif- ferentially regulated or tissue-speciﬁc cDNA probes and li- braries,” Proceedings of the National Academy of Sciences of the United States of America, vol. 93, no. 12, pp. 6025–6030, 1996. [84] A. Wulf, K. Manthey, J. Doll, et al., “Transcriptional changes in response to arbuscular mycorrhiza development in the model plant Medicago truncatula,” Molecular Plant-Microbe Interactions, vol. 16, no. 4, pp. 306–314, 2003. [85] L. Godiard, A. Niebel, F. Micheli, J. Gouzy, T. Ott, and P. Gamas, “Identiﬁcation of new potential regulators of the Medicago truncatula-Sinorhizobium meliloti symbiosis us- ing a large-scale suppression subtractive hybridization ap- proach,” Molecular Plant-Microbe Interactions, vol. 20, no. 3, pp. 321–332, 2007. [86] V. E. Velculescu, L. Zhang, B. Vogelstein, and K. W. Kin- zler, “Serial analysis of gene expression,” Science, vol. 270, no. 5235, pp. 484–487, 1995.