Legume Genomics Relevant to N2 Fixation

  • L. Schauser
  • M. Udvardi
  • S. Tabata
  • J. Stougaard
Part of the Nitrogen Fixation: Origins, Applications, and Research Progress book series (NITR, volume 7)


Nodule Development Symbiotic Nitrogen Fixation Lotus Japonicus Medicago Truncatula Model Legume 
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  1. Ané, J. M., Kiss, G. B., Riely, B. K., Penmetsa, R. V., Oldroyd, G. E. D., Ayax, C., et al.(2004). Medicago truncatula DMI1 required for bacterial and fungal symbioses in legumes. Science, 303, 1364-1367.PubMedCrossRefGoogle Scholar
  2. Arimura, G., Ozawa, R., Kugimiya, S., Takabayashi, J., and Bohlmann, J. (2004). Herbivore-induced defense response in a model legume. Two-spotted spider mites induce emission of (E)-β-ocimene and transcript accumulation of (E)-β -ocimene synthase in Lotus japonicus, Plant Physiol., 135,1976–1983.PubMedCrossRefGoogle Scholar
  3. Asamizu, E., Nakamura, Y., Sato, S., and Tabata, S. (2005). Comparison of the transcript profiles from the root and the nodulating root of the model legume Lotus japonicus by serial analysis of gene expression. Mol. Plant-Microbe Interact.,18, 487-498.PubMedCrossRefGoogle Scholar
  4. Barker, D. G., Bianchi, S., Blondon, F., Dattée, Y., Duc, G., Essad, S., et al.(1990). Medicago truncatula, a model plant for studying the molecular genetics of the rhizobium–legume symbiosis, Plant Mol. Biol. Rep.,8, 40–49.Google Scholar
  5. Barnett, M. J., Toman, C. J., Fisher, R. F., and Long, S. R. (2004). A dual-genome Symbiosis Chip for coordinate study of signal exchange and development in a prokaryote-host interaction. Proc. Natl. Acad. Sci. USA,101 ,16636-16641.PubMedCrossRefGoogle Scholar
  6. Bennett, M. D., and Leitch, I. J. (2004). Plant DNA C-values database (release 3.0, Dec. 2004) Scholar
  7. Blanc, G., and Wolfe, K. H. (2004). Widespread paleoploidity in model plant species inferred from age distributions of duplicate genes. Plant Cell 16,1667-1678.PubMedCrossRefGoogle Scholar
  8. Borisov, A. Y., Madsen, L. H., Tsyganov, V. E., Umehara, Y., Voroshilova, V. A., Batagov, A. O., et al. (2003). The sym35 gene required for root nodule development in pea is an ortholog of nin from Lotus japonicus. Plant Physiol., 131 , 009–1017.CrossRefGoogle Scholar
  9. Boutin, S. R., Young, N. D., Olson, T. C., Yu, Z. H., Shoemaker, R. C., and Vallejos, C. E. (1995). Genome conservation among three legume genera detected with DNA markers. Genome, 38, 928-937.PubMedGoogle Scholar
  10. Bowers, J. E., Chapman, B. A., Rong, J., and Paterson, A. H. (2003). Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature, 422, 433-438.PubMedCrossRefGoogle Scholar
  11. Buzas, D. M., Lohar, D., Sato, S., Nakamura, Y., Tabata, S., Vickers, C. E., et al. (2005). Promoter trapping in Lotus japonicus reveals novel root and nodule GUS expression domains. Plant Cell Physiol., 46, 202-1212.CrossRefGoogle Scholar
  12. Capoen, W., Goormachtig, S., De Rycke, R., Schroeyers, K., and Holsters, M. (2005). SrSymRK, a plant receptor essential for symbiosome formation. Proc. Natl. Acad. Sci. USA, 102, 10369-10374.PubMedCrossRefGoogle Scholar
  13. Catalano, C. M., Lane, W. S., and Sherrier, D. J. (2004). Biochemical characterization of symbiosome membrane proteins from Medicago truncatula root nodules. Electrophoresis, 25, 519-531.PubMedCrossRefGoogle Scholar
  14. Catoira, R., Galera, C ., de Billy, F., Penmetsa, R. V., Journet, E. P., Maillet, F., et al. (2000). Four genes of Medicago truncatula controlling components of a nod factor transduction pathway. Plant Cell, 12, 1647–1666.PubMedCrossRefGoogle Scholar
  15. Catoira, R., Timmers, A. C., Maillet, F., Galera, C., Penmetsa, R. V., Cook, D., et al. (2001). The HCL gene of Medicago truncatula controls Rhizobium-induced root hair curling. Development, 128, 1507–1518.PubMedGoogle Scholar
  16. Choi, H. K., Mun, J. H., Kim, D. J., Zhu, H., Baek, J. M., Mudge, J., et al. (2004). Estimating genome conservation between crop and model legume species. Proc. Natl. Acad. Sci. USA, 101, 15289–15294.CrossRefGoogle Scholar
  17. Colebatch, G., Kloska, S., Trevaskis, B., Freund, S., Altmann, T., and Udvardi, M. K. (2002). Novel aspects of symbiotic nitrogen fixation uncovered by transcript profiling with cDNA arrays. Mol. Plant-Microbe Interact., 15, 411–420.PubMedCrossRefGoogle Scholar
  18. Colebatch, G., Desbrosses, G., Ott, T., Krusell, L., Montanari, O., Kloska, S., et al. (2004). Global changes in transcription orchestrate metabolic differentiation during symbiotic nitrogen fixation in Lotus japonicus, Plant J., 39, 487–512.Google Scholar
  19. d’Erfurth, I., Cosson, V., Eschstruth, A., Lucas, H., Kondorosi, A., and Ratet, P. (2003). Efficient transposition of the Tnt1 tobacco retrotransposon in the model legume Medicago truncatula. Plant J., 34, 95-106.Google Scholar
  20. Desbrosses, G. G., Kopka, J., and Udvardi, M. K. (2005). Lotus japonicus metabolic profiling: Development of gas chromatography-mass spectrometry resources for the study of plant–microbe interactions. Plant Physiol., 137, 1302-1318.PubMedCrossRefGoogle Scholar
  21. Djordjevic, M. A. (2004). Sinorhizobium meliloti metabolism in the root nodule: A proteomic perspective. Proteomics, 4, 859-1872.CrossRefGoogle Scholar
  22. Dong, Q., Schlueter, S. D., and Brendel, V. (2004). PlantGDB, plant genome database and analysis tools. Nucleic Acids Res., 32, D354-D359.PubMedCrossRefGoogle Scholar
  23. Driscoll, B. T., and Finan, T. M. (1997). Properties of NAD(+)- and NADP(+)-dependent malic enzymes of Rhizobium (Sinorhizobium) meliloti and differential expression of their genes in nitrogen-fixing bacteroids. Microbiology, 143, 489-498.PubMedCrossRefGoogle Scholar
  24. El Yahyaoui, F., Küster, H., Ben Amor, B., Hohnjec, N., Pühler, A., Becker, A., et al. (2004). Expression profiling in Medicago truncatula identifies more than 750 genes differentially expressed during nodulation, including many potential regulators of the symbiotic program. Plant Physiol.,136, 3159-3176.PubMedCrossRefGoogle Scholar
  25. Endre, G., Kereszt, A., Kevei, Z., Mihacea, S., Kalo, P., and Kiss, G. B. (2002). A receptor kinase gene regulating symbiotic nodule development. Nature, 417, 962-966.PubMedCrossRefGoogle Scholar
  26. Fedorova, M., van de Mortel, J., Matsumoto, P. A., Cho, J., Town, C. D., VandenBosch, K. A., et al. (2002). Genome-wide identification of nodule-specific transcripts in the model legume Medicago truncatula. Plant Physiol.,130, 519-537.PubMedCrossRefGoogle Scholar
  27. Fiehn, O., Kopka, J., Dormann, P., Altmann, T., Trethewey, R. N., and Willmitzer, L. (2000). Metabolite profiling for plant functional genomics. Nature Biotechnol., 18, 1157–1161.CrossRefGoogle Scholar
  28. Flemetakis, E., Efrose, R. C., Desbrosses, G., Dimou, M., Delis, C., Aivalakis, G. et al., (2004). Induction and spatial organization of polyamine biosynthesis during nodule development in Lotus japonicus. Mol. Plant-Microbe Interact., 17, 1283–1293.PubMedCrossRefGoogle Scholar
  29. Forslund, K., Morant, M., Jørgensen, B., Olsen, C. E., Asamizu, E., Sato, S., et al. (2004). Biosynthesis of the nitrile glucosides rhodiocyanoside A and D and the cyanogenic glucosides lotaustralin and linamarin in Lotus japonicus. Plant Physiol., 135, 71–84.PubMedCrossRefGoogle Scholar
  30. Geurts, R., Heidstra, R., Hadri, A. E., Downie, J. A., Franssen, H., Van Kammen, A., et al. (1997). Sym2 of pea is involved in a nodulation factor-perception mechanism that controls the infection process in the epidermis. Plant Physiol., 115, 351–359.PubMedGoogle Scholar
  31. Goff, S. A., Ricke, D., Lan, T. H., Presting, G., Wang, R., Dunn, M., et al. (2002). A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science, 296, 92-100.CrossRefGoogle Scholar
  32. Gonzales, M. D., Archuleta, E., Farmer, A., Gajendran, K., Grant, D., Shoemaker, R., et al. (2005). The Legume Information Service (LIS): An integrated information resource for comparative legume biology. Nucleic Acids Res., 33, D660-D665.PubMedCrossRefGoogle Scholar
  33. Gordon, A. J., Minchin, F. R., James, C. L., and Komina, O. (1999). Sucrose synthase in legume nodules is essential for nitrogen fixation. Plant Physiol., 120, 867-878.PubMedCrossRefGoogle Scholar
  34. Graham, M. A., Silverstein, K. A. T., Cannon, S. B., and VandenBosch, K. A. (2004). Computational identification and characterization of novel genes from legumes. Plant Physiol., 135, 1179-1197.PubMedCrossRefGoogle Scholar
  35. Green, L. S., and Emerich, D. W. (1997). The formation of nitrogen-fixing bacteroids is delayed but not abolished in soybean infected by an [alpha]-ketoglutarate dehydrogenase-deficient mutant of Bradyrhizobium japonicum. Plant Physiol., 114, 1359-1368.PubMedGoogle Scholar
  36. Handberg, K., and Stougaard, J. (1992). Lotus japonicus, an autogamous, diploid legume species for classical and molecular-genetics. Plant J., 2, 487–496.CrossRefGoogle Scholar
  37. Hayashi, M., Miyahara, A., Sato, S., Kato, T., Yoshikawa, M., Taketa, M., et al. (2001). Construction of a genetic linkage map of the model legume Lotus japonicus using an intraspecific F2 population, DNA Res., 8, 301–310.Google Scholar
  38. Imaizumi-Anraku. H., Takeda, N., Charpentier, M., Perry, J., Miwa, H., Umehara, Y.,et al. (2005). Plastid proteins crucial for symbiotic fungal and bacterial entry into plant roots. Nature, 433, 527-531.PubMedCrossRefGoogle Scholar
  39. Journet, E. P., van Tuinen, D., Gouzy, J., Crespeau, H., Carreau, V., Farmer, M. J., et al. (2002). Exploring root symbiotic programs in the model legume Medicago truncatula using EST analysis. Nucleic Acids Res.,30, 5579-5592.PubMedCrossRefGoogle Scholar
  40. Kalò, P., Seres, A., Taylor, S. A., Jakab, J., Kevei, Z., Kereszt, A., et al. (2004). Comparative mapping between Medicago sativa and Pisum sativum. Mol. Genet. Genomics,272, 235-246.PubMedCrossRefGoogle Scholar
  41. Kanamori, N., Madsen, L. H., Radutoiu, S., Frantescu, M., Quistgaard, E. M. H., Miwa, H., et al. (2006). A nucleoporin is required for induction of Ca2 + spiking in legume nodule development and essential for rhizobial and fungal symbiosis. Proc. Natl. Acad. Sci. USA, 103, 359-364.PubMedCrossRefGoogle Scholar
  42. Kato, T., Kaneko, T., Sato, S., Nakamura, Y., and Tabata, S. (2000). Complete structure of the chloroplast genome of a legume, Lotus japonicus. DNA Res.,7, 323-330.Google Scholar
  43. Kawaguchi, M., Imaizumi-Anraku, H., Koiwa, H., Niwa, S., Ikuta, A., Syono, K., and Akao, S. (2002). Root, root hair, and symbiotic mutants of the model legume Lotus japonicus. Mol. Plant-Microbe Interact.,15, 17-26.PubMedCrossRefGoogle Scholar
  44. Kawaguchi, K., Pedrosa-Harand, A., Yano, K., Hayashi, M., Murooka, Y., Saito, K., et al. (2005). Lotus burttii takes a position of the third corner in the Lotus molecular genetics triangle. DNA Res., 12, 69–77.PubMedCrossRefGoogle Scholar
  45. Kevei, Z., Seres, A., Kereszt, A., Kalo, P., Kiss, P., Toth, G., et al. (2005). Significant microsynteny with new evolutionary highlights is detected between Arabidopsis and legume model plants despite the lack of macrosynteny. Mol. Genet. Genomics,274, 644 – 657.PubMedCrossRefGoogle Scholar
  46. Kistner, C., Winzer, T., Pitzschke, A., Mulder, L., Sato, S., Kaneko, T., et al. (2005). Seven Lotus japonicus genes required for transcriptional reprogramming of the root during fungal and bacterial symbiosis. Plant Cell, 17, 2217-2229.PubMedCrossRefGoogle Scholar
  47. Kouchi, H., Shimomura, K., Hata, S., Hirota, A., Wu, G. J., Kumagai, H., et al., (2004). Large-scale analysis of gene expression profiles during early stages of root nodule formation in a model legume, Lotus japonicus. DNA Res., 11, 263–274.PubMedCrossRefGoogle Scholar
  48. Krusell, L., Madsen, L. H., Sato, S., Aubert, G., Genua, A., Szczyglowski, K., et al. (2002). Shoot control of root development and nodulation is mediated by a receptor-like kinase, Nature, 420, 422–426.Google Scholar
  49. Krusell, L., Krause, K., Ott, T., Desbrosses, G., Krämer, U., Sato, S., et al. (2005). The sulfate transporter SST1 is crucial for symbiotic nitrogen fixation in Lotus japonicus root nodules. Plant Cell, 17, 1625-1636.PubMedCrossRefGoogle Scholar
  50. Kuster, H., Hohnjec, N., Krajinski, F., El Yahyaoui, F., Manthey, K., Gouzy, J., et al. (2004). Construction and validation of cDNA-based Mt6k-RIT macro- and microarrays to explore root endosymbioses in the model legume Medicago truncatula. J. Biotechnol., 108, 95-113.PubMedCrossRefGoogle Scholar
  51. Lee, J. M., Grant, D., Vallejos, C. E., and Shoemaker, R. C. (2001). Genome organization in dicots. II Arabidopsis as a ’bridging species’ to resolve genome evolution events among legumes. Theoret. Appl. Genet.,103, 765-773.CrossRefGoogle Scholar
  52. Lévy, J, Bres, C., Geurts, R., Chalhoub, B., Kulikova, O., Duc, G., et al. (2004). A putative Ca2 + and calmodulin-dependent protein kinase required for bacterial and fungal symbioses. Science, 303, 1361-1364.PubMedCrossRefGoogle Scholar
  53. Limpens, E., Franken, C., Smit, P., Willemse, J., Bisseling, T., and Geurts, R. (2003). LysM domain receptor kinases regulating rhizobial Nod factor-induced infection. Science, 302, 630–633.PubMedCrossRefGoogle Scholar
  54. Lodwig, E. M., Hosie, A. H. F., Bourdés, A., Findlay, K., Allaway, D., Karunakaran, R., et al. (2003). Amino-acid cycling drives nitrogen fixation in the legume-Rhizobium symbiosis. Nature, 422, 722-726.PubMedCrossRefGoogle Scholar
  55. Lohar, D. P., Sharopova, N., Endre, G., Peñuela, S., Samac, D., Town, C., et al. (2006). Transcript analysis of early nodulation events in Medicago truncatula. Plant Physiol.,140, 221-234.PubMedCrossRefGoogle Scholar
  56. Lowe, T. 2005). Scholar
  57. Lynch, M. (2002). Genomics. Gene duplication and evolution. Science, 297, 945-947.PubMedCrossRefGoogle Scholar
  58. Lyons, L. A., Laughlin, T. F., Copeland, N. G., Jenkins, N. A., Womack, J. E., and O’Brien, S. J. (1997). Comparative anchor tagged sequences (CATS) for integrative mapping of mammalian genomes. Nature Genetics, 15, 47-56.PubMedCrossRefGoogle Scholar
  59. Madsen, E. B., Madsen, L. H., Radutoiu, S., Olbryt, M., Rakwalska, M., Szczyglowski, K., et al. (2003). A receptor kinase gene of the LysM type is involved in legume perception of rhizobial signals. Nature, 425, 637–640.PubMedCrossRefGoogle Scholar
  60. Madsen, L. H., Fukai, E., Radutoiu, S., Yost, C. K., Sandal, N., Schauser, L., et al. (2005). LORE1, an active low copy number TY3-gypsy retrotransposon family in the model legume Lotus japonicus. Plant J., 44, 372-381.PubMedCrossRefGoogle Scholar
  61. Manthey, K., Krajinski, F., Hohnjec, N., Firnhaber, C., Pühler, A., Perlick, A. M., et al. (2004). Transcriptome profiling in root nodules and arbuscular mycorrhiza identifies a collection of novel genes induced during Medicago truncatula root endosymbioses. Mol. Plant-Microbe Interact., 17, 1063-1077.PubMedCrossRefGoogle Scholar
  62. Márquez, A. J., Betty, M., Garciá,-Calderòn, M., Pal’ove-Balang, P., Dìaz, P., and Monza, J. (2005). Nitrate assimilation in Lotus japonicus. J. Exp. Bot.,56, 1741-1749.PubMedCrossRefGoogle Scholar
  63. McDermott, T. R., Griffith, S. M., Vance, C. P., and Graham, P. H. (1989). Carbon metabolism in Bradyrhizobium japonicum bacteroids. FEMS Microbiol. Rev., 63, 327-340. Medicago truncatula sequencing resources (2005) Scholar
  64. Menancio-Hautea, D., Fatokun, C. A., Kumar, L., Danesh, D., and Young, N. D. (1993). Comparative genome analysis of mungbean (Vigna radiata L. Wilczek) and cowpea (Vigna unguiculata L. Walpers) using RFLP mapping data. Theoret. Appl. Genet., 86, 797-810.CrossRefGoogle Scholar
  65. Mitra, R. M., Gleason, C. A., Edwards, A., Hadfield, J., Downie, J. A., Oldroyd, G. E., et al. (2004a). A Ca2 +/calmodulin-dependent protein kinase required for symbiotic nodule development: Gene identification by transcript-based cloning. Proc. Natl. Acad. Sci. USA,101, 4701-4705.CrossRefGoogle Scholar
  66. Mitra, R. M., Shaw, S. L., and Long, S. R. (2004b). Six nonnodulating plant mutants defective for Nod factor-induced transcriptional changes associated with the legume-rhizobia symbiosis. Proc. Natl. Acad. Sci. USA,101, 10217-10222.CrossRefGoogle Scholar
  67. Morris, A. C., and Djordjevic, M. A. (2001). Proteome analysis of cultivar-specific interactions between Rhizobium leguminosarum biovar trifolii and subterranean clover cultivar Woogenellup. Electrophoresis,22, 586-598.PubMedCrossRefGoogle Scholar
  68. Morzhina, E. V., Tsyganov, V. E., Borisov, A. Y., Lebsky, V. K., and Tikhonovich, I. A. (2000). Four developmental stages identified by genetic dissection of pea (Pisum sativum L.) root nodule morphogenesis. Plant Sci., 155, 75-83.PubMedCrossRefGoogle Scholar
  69. Mudge, J, Cannon, S. B., Kalo, P., Oldroyd, G. E. D., Roe, B. A., Town, C. D., and Young, N. D. (2005). Highly syntenic regions in the genomes of soybean, Medicago truncatula, and Arabidopsis thaliana. BMC Plant Biol., 5, 15.PubMedCrossRefGoogle Scholar
  70. Murakami, Y., Miwa, H., Imaizumi-Anraku, H., Kouchi, H., Downie, A. J., Kawaguchi, M., et al. (2006). TINod (transcription initiator for nodulation) induces nodulation via an SH2-like domain in a manner analogous to STAT proteins of animals. NCBI Nucleotide Entrez (accession AB241457).Google Scholar
  71. Nishimura, R., Ohmori, M., Fujita, H., and Kawaguchi, M. (2002a). A Lotus basic leucine zipper protein with a RING-finger motif negatively regulates the developmental program of nodulation. Proc. Natl. Acad. Sci. USA, 99, 15206-15210.CrossRefGoogle Scholar
  72. Nishimura, R., Hayashi M., Wu, G. J., Kouchi, H., Imaizumi-Anraku, H., Murakami, Y., et al. (2002b). HAR1 mediates systemic regulation of symbiotic organ development. Nature, 420 , 426–429.CrossRefGoogle Scholar
  73. Noiraud, N., Maurousset, L., and Lemoine, R. (2001). Identification of a mannitol transporter, AgMaT1, in celery phloem. Plant Cell, 13, 695-705.PubMedCrossRefGoogle Scholar
  74. Nuccio, M. L., and Thomas, T. L. (1999). ATS1 and ATS3: Two novel embryo-specific genes in Arabidopsis thaliana. Plant Mol. Biol., 39, 1153-1163.PubMedCrossRefGoogle Scholar
  75. Oka-Kira, E., Tateno, K., Miura, K., Haga, T., Hayashi, M., Harada, K., et al. (2005). klavier (klv), a novel hypernodulation mutant of Lotus japonicus affected in vascular tissue organization and floral induction. Plant J., 44, 505-515.PubMedCrossRefGoogle Scholar
  76. Oldroyd, G. E. D., and Long, S. R. (2003). Identification and characterization of nodulation-signaling pathway 2, a gene of Medicago truncatula involved in Nod factor signaling. Plant Physiol., 131, 1027–1032.PubMedCrossRefGoogle Scholar
  77. Osteras, M., O’Brien, S. A. P., and Finan, T. M. (1997). Genetic analysis of mutations affecting pckA regulation in Rhizobium (Sinorhizobium) meliloti. Genetics, 147, 1521-1531.PubMedGoogle Scholar
  78. Ott, T., van Dongen, J. T., Gunther, C., Krusell, L., Desbrosses, G., Vigeolas, H., et al. (2005). Symbiotic leghemoglobins are crucial for nitrogen fixation in legume root nodules but not for general plant growth and development. Curr. Biol., 15, 531-535.PubMedCrossRefGoogle Scholar
  79. Pan, X., Stein, L., and Brendel, V. (2005). SynBrowse: A synteny browser for comparative sequence analysis. Bioinformatics, 21, 3461-3468.PubMedCrossRefGoogle Scholar
  80. Panter, S., Thomson, R., de Bruxelles, G., Laver, D., Trevaskis, B., and Udvardi, M. (2000). Identification with proteomics of novel proteins associated with the peribacteroid membrane of soybean root nodules. Mol. Plant-Microbe Interact., 13, 325-333.PubMedCrossRefGoogle Scholar
  81. Parniske, M., and Downie, J. A. (2003). Plant biology: Locks, keys and symbioses. Nature, 425, 569-570.PubMedCrossRefGoogle Scholar
  82. Penmetsa, R. V., and Cook, D. R. (1997). A legume ethylene-insensitive mutant hyperinfected by its rhizobial symbiont. Science, 275, 527-530.PubMedCrossRefGoogle Scholar
  83. Perry, J. A., Wang, T. L., Welham, T. J., Gardner, S., Pike, J. M., Yoshida, S., et al. (2003). A TILLING reverse genetics tool and a web-accessible collection of mutants of the legume Lotus japonicus. Plant Physiol., 131, 866–871.PubMedCrossRefGoogle Scholar
  84. Pfeil, B. E., Schlueter, J. A., Shoemaker, R. C., and Doyle, J. J. (2005). Placing paleopolyploidy in relation to taxon divergence: A phylogenetic analysis in legumes using 39 gene families. Syst. Biol., 54, 441-454.PubMedCrossRefGoogle Scholar
  85. Pontius, J. U., Wagner, L., and Schuler, G. D. (2003). UniGene: A unified view of the transcriptome. In: The NCBI Handbook. Bethesda, MD: National Center for Biotechnology Information. pp. 21-1 - 21-12.Google Scholar
  86. Quackenbush, J., Cho, J., Lee, D., Liang, F., Holt, I., Karamycheva, S., et al. (2001). The TIGR Gene Indices: Analysis of gene transcript sequences in highly sampled eukaryotic species. Nucleic Acids Res., 29, 159-164.PubMedCrossRefGoogle Scholar
  87. Radutoiu, S., Madsen, L. H., Madsen, E. B., Felle, H. H., Umehara, Y., Grønlund, M., et al. (2003). Plant recognition of symbiotic bacteria requires two LysM receptor-like kinases. Nature, 425, 585–592.PubMedCrossRefGoogle Scholar
  88. Sagan, M., Morandi, D., Tarenghi, E., and Duc, G. (1995). Selection of nodulation and mycorrhizal mutants in the model plant Medicago truncatula (Gaertn) after γ -ray mutagenesis. Plant Sci., 111, 63–71CrossRefGoogle Scholar
  89. Sagan, M., de Larembergue, H., and Morandi, D. (1998). Genetic analysis of symbiosis mutants in Medicago truncatula. In C. Elmerich, A. Kondorosi, and W. E. Newton (Eds.), Biological nitrogen fixation for the 21 st century.(pp. 317–318). Dordrecht, The Netherlands: Kluwer Academic Publishers.Google Scholar
  90. Salse, J., Piégu, B., Cooke, R., and Delseny, M. (2002). Synteny between Arabidopsis thaliana and rice at the genome level: A tool to identify conservation in the ongoing rice genome sequencing project. Nucleic Acids Res., 30, 2316-2328.PubMedCrossRefGoogle Scholar
  91. Salse, J., Piégu, B., Cooke, R., and Delseny, M. (2004). New in silico insight into the synteny between rice (Oryza sativa L.) and maize (Zea mays L.) highlights reshuffling and identifies new duplications in the rice genome. Plant J., 38, 396-409.PubMedCrossRefGoogle Scholar
  92. Sandal, N., Krusell, L., Radutoiu, S., Olbryt, M., Pedrosa, A., Stracke, S., et al. (2002). A genetic linkage map of the model legume Lotus japonicus and strategies for fast mapping of new loci. Genetics, 161, 1673–1683.PubMedGoogle Scholar
  93. Sandal, N., Petersen, T. R., Murray, J., Umehara, Y., Karas, B., Yano, K., et al. (2006). Genetics of symbiosis in Lotus japonicus: Recombinant inbred lines, comparative genetic maps, and map position of 35 symbiotic loci. Mol. Plant-Microbe Interact., 19, 80-91.PubMedCrossRefGoogle Scholar
  94. Saski, C., Lee, S. B., Daniell, H., Wood, T. C., Tomkins, J., Kim, H. G., et al. (2005). Complete chloroplast genome sequence of Glycine max and comparative analyses with other legume genomes. Plant Mol. Biol., 59, 309-322.PubMedCrossRefGoogle Scholar
  95. Schauser, L., Roussis, A., Stiller, J., and Stougaard, J. (1999). A plant regulator controlling development of symbiotic root nodules. Nature, 402, 191–195.PubMedCrossRefGoogle Scholar
  96. Schauser, L., Fredslund, J., Madsen, L. H., Sandal, N., and Stougaard, J. (2005). A computational pipeline towards the development of comparative anchor tagged sequence (CATS) markers. In M. O. Humphrey (Ed.), Molecular breeding for the improvement of forage crop and turf. (pp. 73-81). Wageningen, The Netherlands: Wageningen Academic Publishers.Google Scholar
  97. Schnabel, E., Journet, E. P., de Carvalho-Niebel, F, Duc, G., and Frugoli, J. (2005). The Medicago truncatula SUNN gene encodes a CLV1-like leucine-rich repeat receptor kinase that regulates nodule number and root length. Plant Mol. Biol., 58, 809–822.PubMedCrossRefGoogle Scholar
  98. Schlueter, J. A., Dixon, P., Granger, C., Grant, D., Clark, L., Doyle, J. J. and Shoemaker, R. C. (2004). Mining EST databases to resolve evolutionary events in major crop species. Genome, 47, 868-876.PubMedCrossRefGoogle Scholar
  99. Searle, I. R., Men, A. E., Laniya, T. S., Buzas, D. M., Iturbe-Ormaetxe, I., Carroll, B. J., et al. (2003). Long-distance signaling in nodulation directed by a CLAVATA1-like receptor kinase. Science, 299, 109–112.PubMedCrossRefGoogle Scholar
  100. Smit, P., Raedts, J., Portyanko, V., Debellé, F., Gough, C., Bisseling, T., et al. (2005). NSP1 of the GRAS protein family is essential for rhizobial Nod factor-induced transcription. Science, 308, 1789-1791.PubMedCrossRefGoogle Scholar
  101. Starker, C. G., Parra-Colmenares, A. L., Smith, L., Mitra, R. M., and Long, S. R. (2006). Nitrogen fixation mutants of Medicago truncatula fail to support plant and bacterial symbiotic gene expression. Plant Physiol., 141, 671-680.CrossRefGoogle Scholar
  102. Stein, L. D., Mungall, C., Shu, S., Caudy, M., Mangone, M., Day, A., et al., (2002). The generic genome browser: A building block for a model organism system database. Genome Res., 12, 1599-1610.PubMedCrossRefGoogle Scholar
  103. Stracke, S., Kistner, C., Yoshida, S., Mulder, L., Sato, S., Kaneko, T., et al. (2002). A plant receptor-like kinase required for both bacterial and fungal symbiosis, Nature, 417, 959–962.Google Scholar
  104. Suganuma, N., Yamamoto, A., Itou, A., Hakoyama, T., Banba, M., Hata, S., et al. (2004). cDNA macroarray analysis of gene expression in ineffective nodules induced on the Lotus japonicus sen1 mutant. Mol. Plant-Microbe Interact., 17, 1223-1233.PubMedCrossRefGoogle Scholar
  105. Szczyglowski, K., Shaw, R. S., Wopereis, J., Copeland, S., Hamburger, D., Kasiborski, B., et al. (1998). Nodule organogenesis and symbiotic mutants of the model legume Lotus japonicus. Mol. Plant-Microbe Interact., 11, 684-697.Google Scholar
  106. Thöny-Meyer, L., and Kunzler, P. (1996). TheBradyrhizobium japonicum aconitase gene (acnA) is important for free-living growth but not for an effective root nodule symbiosis. J. Bacteriol., 178, 6166-6172.PubMedGoogle Scholar
  107. Thoquet, P., Ghérardi, M., Journet, E. P., Kereszt, A., Ané, J. M., Prosperi, J. M., et al. (2002). The molecular genetic linkage map of the model legume Medicago truncatula: An essential tool for comparative legume genomics and the isolation of agronomically important genes. textitBMC Plant Biol., 2, 1.PubMedCrossRefGoogle Scholar
  108. Thykjaer, T., Stiller, J., Handberg, K., Jones, J., and Stougaard, J. (1995). The maize transposable element Ac is mobile in the legume Lotus japonicus. Plant Mol. Biol., 27, 981–993.PubMedCrossRefGoogle Scholar
  109. Uchiumi, T., Ohwada, T., Itakura, M., Mitsui, H., Nukui, N., Dawadi, P., et al. (2004). Expression islands clustered on the symbiosis island of the Mesorhizobium loti genome. J. Bacteriol., 186, 2439–2448.PubMedCrossRefGoogle Scholar
  110. Udvardi, M. K., and Day, D. A. (1997). Metabolite transport across symbiotic membranes of legume nodules. Annu. Rev. Plant Physiol. Plant Mol. Biol., 48, 493-523.PubMedCrossRefGoogle Scholar
  111. Vance, C. P. (2000). Amide biosynthesis in root nodules of temperate legumes. In E. Triplett (Ed.), Prokaryotic nitrogen fixation: A model system for the analysis of a biological process.(pp. 589-607). Wymondham, UK: Horizon Scientific Press.Google Scholar
  112. van Kammen, A. (1984). Suggested nomenclature for plant genes involved in nodulation and symbiosis. Plant Mol. Biol. Rep., 2, 43-45.Google Scholar
  113. Wagner, C., Sefkow, M., and Kopka, J. (2003). Construction and application of a mass spectral and retention time index database generated from plant GC/EI-TOF-MS metabolite profiles. Phytochemistry, 62, 887–900.PubMedCrossRefGoogle Scholar
  114. Wan, J., Torres, M., Ganapathy, A., Thelen, J., DaGue, B. B., Mooney, B., et al. (2005). Proteomic analysis of soybean root hairs after infection by Bradyrhizobium japonicum. Mol. Plant-Microbe Interact., 18, 458-467.PubMedCrossRefGoogle Scholar
  115. Webb, K. J., Robbins, M., Wang, T. L., Parniske, M., and Márquez, A. J. (2005). Mutagenesis. In A. J. Márquez (Ed.), Lotus japonicus handbook. (pp. 177-186). Dordrecht, The Netherlands: Springer.Google Scholar
  116. Webb, K. J., Skot, L., Nicholson, M. N., Jorgensen, B., and Mizen, S. (2000). Mesorhizobium loti increases root-specific expression of a calcium-binding protein homologue identified by promoter tagging in Lotus japonicus. Mol. Plant–Microbe Interact., 13, 606-616.PubMedCrossRefGoogle Scholar
  117. Wienkoop, S., and Saalbach, G. (2003). Proteome analysis. Novel proteins identified at the peribacteroid membrane from Lotus japonicus root nodules. Plant Physiol., 131, 1080-1090.PubMedCrossRefGoogle Scholar
  118. Yan, H. H., Mudge, J., Kim. D. J., Shoemaker, R. C., Cook, D. R., and Young, N. D. (2004). Comparative physical mapping reveals features of microsynteny between Glycine max, Medicago truncatula, and Arabidopsis thaliana. Genome, 47, 141-155.PubMedCrossRefGoogle Scholar
  119. Young, N. D., Cannon, S. B., Sato, S., Kim, D., Cook, D. R., Town, C. D., et al. (2005). Sequencing the genespaces of Medicago truncatula and Lotus japonicus. Plant Physiol., 137, 1174-1181.Google Scholar

Copyright information

© Springer Science+Business Media B.V. 2008

Authors and Affiliations

  • L. Schauser
    • 1
  • M. Udvardi
    • 2
  • S. Tabata
    • 3
  • J. Stougaard
    • 4
  1. 1.Bioinformatics Research CenterHøegh-Guldbergs Gade 10 Building 1090Denmark
  2. 2.Molecular Plant Nutrition GroupMax Planck Institute of Molecular Plant PhysiologyAm Mühlenberg 1Germany
  3. 3.Kazusa DNA Research Institute,1532-3 YanaKisarazuJapan
  4. 4.Department of Molecular BiologyUniversity of AarhusGustav Wieds Vej 10Denmark

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