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Plant Molecular Biology

, Volume 54, Issue 3, pp 405–414 | Cite as

Characteristics of the Lotus Japonicus Gene Repertoire Deduced from Large-Scale Expressed Sequence Tag (EST) Analysis

  • Erika Asamizu
  • Yasukazu Nakamura
  • Shusei Sato
  • Satoshi Tabata
Article

Abstract

To perform a comprehensive analysis of genes expressed in a model legume, Lotus japonicus, a total of 74472 3′-end expressed sequence tags (EST) were generated from cDNA libraries produced from six different organs. Clustering of sequences was performed with an identity criterion of 95% for 50 bases, and a total of 20457 non-redundant sequences, 8503 contigs and 11954 singletons were generated. EST sequence coverage was analyzed by using the annotated L. japonicus genomic sequence and 1093 of the 1889 predicted protein-encoding genes (57.9%) were hit by the EST sequence(s). Gene content was compared to several plant species. Among the 8503 contigs, 471 were identified as sequences conserved only in leguminous species and these included several disease resistance-related genes. This suggested that in legumes, these genes may have evolved specifically to resist pathogen attack. The rate of gene sequence divergence was assessed by comparing similarity level and functional category based on the Gene Ontology (GO) annotation of Arabidopsis genes. This revealed that genes encoding ribosomal proteins, as well as those related to translation, photosynthesis, and cellular structure were more abundantly represented in the highly conserved class, and that genes encoding transcription factors and receptor protein kinases were abundantly represented in the less conserved class. To make the sequence information and the cDNA clones available to the research community, a Web database with useful services was created at http://www.kazusa.or.jp/en/plant/lotus/EST/.

cDNA EST gene repertoire legume Lotus japonicus Web database 

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References

  1. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D.J. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl. Acids Res. 25: 3389–3402.CrossRefPubMedGoogle Scholar
  2. Arabidopsis Genome Initiative. 2000. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796–815.Google Scholar
  3. Asamizu, E., Kato, T., Sato, S., Nakamura, Y., Kaneko, T. and Tabata, S. 2003. Structural analysis of a Lotus japonicus genome. IV. Sequence features and mapping of 73 TAC clones which cover the 7.5 Mb regions of the genome. DNA Res. 10: 115–122.PubMedGoogle Scholar
  4. Asamizu, E., Nakamura, Y., Sato, S., Fukuzawa, H. and Tabata, S. 1999. A large scale structural analysis of cDNAs in a unicellular green alga, Chlamydomonas reinhardtii. I. Generation of 3433 non-redundant expressed sequence tags. DNA Res. 6: 369–373.PubMedGoogle Scholar
  5. Asamizu, E., Nakamura, Y., Sato, S. and Tabata, S. 2000a. Generation of 7137 non-redundant expressed sequence tags from a legume, Lotus japonicus. DNA Res. 7: 127–130.PubMedGoogle Scholar
  6. Asamizu, E., Nakamura, Y., Sato, S. and Tabata S. 2000b. A large scale analysis of cDNA in Arabidopsis thaliana: generation of 12,028 non-redundant expressed sequence tags from normalized and size-selected cDNA libraries. DNA Res. 7: 175–180.PubMedGoogle Scholar
  7. 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.PubMedGoogle Scholar
  8. Endo, M., Hakozaki, H., Kokubun, T., Masuko, H., Takahata, Y., Tsuchiya, T., Higashitani, A., Tabata, S. and Watanabe, M. 2002a. Generation of 919 expressed sequence tags from immature flower buds and gene expression analysis using expressed sequence tags in the model plant Lotus japonicus. Genes Genet. Syst. 77: 277–282.CrossRefPubMedGoogle Scholar
  9. Endo, M., Kokubun, T., Takahata, Y., Higashitani, A., Tabata, S. and Watanabe, M. 2000. Analysis of expressed sequence tags of flower buds in Lotus japonicus. DNA Res. 7: 213–216.PubMedGoogle Scholar
  10. Endo, M., Matsubara, H., Kokubun, T., Masuko, H., Takahata, Y., Tsuchiya, T., Fukuda, H., Demura, T. and Watanabe, M. 2002b. The advantages of cDNA microarray as an effective tool for identification of reproductive organ-specific genes in a model legume, Lotus japonicus. FEBS Lett. 514: 229–237.CrossRefPubMedGoogle Scholar
  11. Ewing, B. and Green, P. 1998. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8: 186–194.PubMedGoogle Scholar
  12. Ewing, B., Hillier, L., Wendl, M.C. and Green, P. 1998. Basecalling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8: 175–185.PubMedGoogle Scholar
  13. Gamas, P., de Billy, F. and Truchet, G. 1998. Symbiosis-specific expression of two Medicago truncatula nodulin genes, MtN1 and MtN13, encoding products homologous to plant defense proteins. Mol. Plant-Microbe Interact. 11: 393–403.PubMedGoogle Scholar
  14. Goff, S.A., Ricke, D., Lan, T.H., Presting, G., Wang, R., Dunn, M., Glazebrook, J., Sessions, A., Oeller, P., Varma, H., Hadley, D., Hutchison, D., Martin, C., Katagiri, F., Lange, B.M., Moughamer, T., Xia, Y., Budworth, P., Zhong, J., Miguel, T., Paszkowski, U., Zhang, S., Colbert, M., Sun, W.L., Chen, L., Cooper, B., Park, S., Wood, T.C., Mao, L., Quail, P., Wing, R., Dean, R., Yu, Y., Zharkikh, A., Shen, R., Sahasrabudhe, S., Thomas, A., Cannings, R., Gutin, A., Pruss, D., Reid, J., Tavtigian, S., Mitchell, J., Eldredge, G., Scholl, T., Miller, R.M., Bhatnagar, S., Adey, N., Rubano, T., Tusneem, N., Robinson, R., Feldhaus, J., Macalma, T., Oliphant, A. and Briggs, S. 2002. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296: 79–92.CrossRefPubMedGoogle Scholar
  15. Graham, M.A., Marek, L.F. and Shoemaker, R.C. 2002. Organization, expression and evolution of a disease resistance gene cluster in soybean. Genetics 162: 1961–1977.PubMedGoogle Scholar
  16. Handberg, K. and Stougaard, J. 1992. Lotus japonicus, an autogamous, diploid legume species for classical and molecular genetics. Plant J. 2: 487–496.Google Scholar
  17. Hayashi, M., Miyahara, A., Sato, S., Kato, T., Yoshikawa, M., Taketa, M., Hayashi, M., Pedrosa, A., Onda, R., Imaizumi-Anraku, H., Bachmair, A., Sandal, N., Stougaard, J., Murooka, Y., Tabata, S., Kawasaki, S., Kawaguchi, M. and Harada, K. 2001. Construction of a genetic linkage map of the model legume Lotus japonicus using an intraspecific F2 population. DNA Res. 8: 301–310.PubMedGoogle Scholar
  18. Imaizumi-Anraku, H., Kawaguchi, M., Koiwa, H., Akao, S. and Syono, K. 1997. Two ineffective-nodulating mutants of Lotus japonicus: different phenotypes caused by the blockage of endocytotic bacterial release and nodule mutation. Plant Cell Physiol. 38: 871–881.Google Scholar
  19. Ito, M., Miyamoto, J., Mori, Y., Fujimoto, S., Uchiumi, T., Abe, M., Suzuki, A., Tabata, S. and Fukui, K. 2000. Genome and chromosome dimensions of Lotus japonicus. J. Plant Res. 113: 435–442.Google Scholar
  20. Iusem, N.D., Bartholomew, D.M., Hitz, W.D. and Scolnik, P.A. 1993. Tomato (Lycopersicon esculentum) transcript induced by water deficit and ripening. Plant Physiol. 102: 1353–1354.CrossRefPubMedGoogle Scholar
  21. Kaneko, T., Asamizu, E., Kato, T., Sato, S., Nakamura, Y. and Tabata, S. 2003. Structural analysis of a Lotus japonicus genome. III. Sequence features and mapping of sixty-two TAC clones which cover the 6.7 Mb regions of the genome. DNA Res. 10: 27–33.PubMedGoogle Scholar
  22. 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.PubMedGoogle Scholar
  23. Kato, T., Sato, S., Nakamura, Y., Kaneko, T., Asamizu, E. and Tabata, S. 2003. Structural Analysis of a Lotus japonicus genome. V. Sequence features and mapping of sixty-four TAC clones which cover the 6.4 Mb regions of the genome. DNA Res. 10: 277–285.PubMedGoogle Scholar
  24. Kawaguchi, M. 2000. Lotus japonicus 'Miyakojima' MG-20: an early flowering accession suitable for indoor handling. J. Plant Res. 113: 507–509.Google Scholar
  25. Kouchi, H. and Hata, S. 1993. Isolation and characterization of novel nodulin cDNAs representing genes expressed at early stages of soybean nodule development. Mol. Gen. Genet. 238: 106–119.PubMedGoogle Scholar
  26. Krusell, L., Madsen, L.H., Sato, S., Aubert, G., Genua, A., Szczyglowski, K., Duc, G., Kaneko, T., Tabata, S., de Bruijn, F., Pajuelo, E., Sandal, N. and Stougaard, J. 2002. Shoot control of root development and nodulation is mediated by a receptor-like kinase. Nature 420: 422–426.CrossRefPubMedGoogle Scholar
  27. Lagercrantz, U. and Axelsson, T. 2000. Rapid evolution of the family of CONSTANS LIKE genes in plants. Mol. Biol. Evol. 17: 1499–1507.PubMedGoogle Scholar
  28. Martirani, L., Stiller, J., Mirabella, R., Alfano, F., Lamberti, A., Radutoiu, S.E., Iaccarino, M., Gresshoff, P.M. and Chiurazzi, M. 1999. T-DNA tagging of nodulation-and rootrelated genes in Lotus japonicus: expression patterns and potential for promoter trapping and insertional mutagenesis. Mol. Plant-Microbe Interact. 12: 275–284.Google Scholar
  29. Nakamura, Y., Kaneko, T., Asamizu, E., Kato, T., Sato, S. and Tabata, S. 2002. Structural analysis of a Lotus japonicus genome. II. Sequence features and mapping of sixty-five TAC clones which cover the 6.5 Mb regions of the genome. DNA Res. 9: 63–70.PubMedGoogle Scholar
  30. Nishimura, R., Hayashi, M., Wu, G.J., Kouchi, H., Imaizumi-Anraku, H., Murakami, Y., Kawasaki, S., Akao, S., Ohmori, M., Nagasawa, M., Harada, K. and Kawaguchi, M. 2002. HAR1 mediates systemic regulation of symbiotic organ development. Nature 420: 426–429.CrossRefPubMedGoogle Scholar
  31. Poulsen, C. and Podenphant, L. 2002. Expressed sequence tags from roots and nodule primordia of Lotus japonicus infected with Mesorhizobium loti. Mol. Plant-Microbe Interact. 15: 376–379.PubMedGoogle Scholar
  32. Sandal, N., Krusell, L., Radutoiu, S., Olbryt, M., Pedrosa, A., Stracke, S., Sato, S., Kato, T., Tabata, S., Parniske, M., Bachmair, A., Ketelsen, T. and Stougaard, J. 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
  33. Sato, S., Kaneko, T., Nakamura, Y., Asamizu, E., Kato, T. and Tabata, S. 2001. Structural analysis of a Lotus japonicus genome. I. Sequence features and mapping of fifty-six TAC clones which cover the 5.4 Mb regions of the genome. DNA Res. 8: 311–318.PubMedGoogle Scholar
  34. Savenstrand, H., Brosche, M. and Strid, A. 2002. Regulation of gene expression by low levels of ultraviolet-B radiation in Pisum sativum: isolation of novel genes by suppression subtractive hybridisation. Plant Cell Physiol. 43: 402–410.CrossRefPubMedGoogle Scholar
  35. Schauser, L., Handberg, K., Sandal, N., Stiller, J., Thykjaer, T., Pajuelo, E., Nielsen, A. and Stougaard, J. 1998. Symbiotic mutants deficient in nodule establishment identified after T-DNA transformation of Lotus japonicus. Mol. Gen. Genet. 259: 414–423.CrossRefPubMedGoogle Scholar
  36. Schauser, L., Roussis, A., Stiller, J. and Stougaard, J. 1999. A plant regulator controlling development of symbiotic root nodules. Nature 402: 191–195.CrossRefPubMedGoogle Scholar
  37. Seki, M., Narusaka, M., Kamiya, A., Ishida, J., Satou, M., Sakurai, T., Nakajima, M., Enju, A., Akiyama, K., Oono, Y., Muramatsu, M., Hayashizaki, Y., Kawai, J., Carninci, P., Itoh, M., Ishii, Y., Arakawa, T., Shibata, K., Shinagawa, A. and Shinozaki, K. 2002. Functional annotation of a fulllength Arabidopsis cDNA collection. Science 296: 141–145.CrossRefPubMedGoogle Scholar
  38. Shimada, N., Akashi, T., Aoki, T. and Ayabe, S. 2000. Induction of isoflavonoid pathway in the model legume Lotus japonicus: molecular characterization of enzymes involved in phytoalexin biosynthesis. Plant Sci. 160: 37–47.CrossRefPubMedGoogle Scholar
  39. Szczyglowski, K., Hamburger, D., Kapranov, P. and de Bruijn, F.J. 1997. Construction of a Lotus japonicus late nodulin expressed sequence tag library and identification of novel nodule-specific genes. Plant Physiol. 114: 1335–1346.CrossRefPubMedGoogle Scholar
  40. Szczyglowski, K., Shaw, R.S., Wopereis, J., Copeland, S., Hamburger, D., Kasiborski, B., Dazzo, F.B. and de Bruijn, F.J. 1998. Nodule organogenesis and symbiotic mutants of the model legume Lotus japonicus. Mol. Plant-Microbe Interact. 11: 684–697.Google Scholar
  41. Vicient, C.M. and Delseny, M. 1999. Isolation of total RNA from Arabidopsis thaliana seeds. Anal. Biochem. 268: 412–413.CrossRefPubMedGoogle Scholar
  42. 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.PubMedGoogle Scholar
  43. Young, N.D. 2000. The genetic architecture of resistance. Curr. Opin. Plant Biol. 3: 285–290.CrossRefPubMedGoogle Scholar
  44. Young, N.D, Mudge, J. and Ellis, T.H. 2003. Legume genomes: more than peas in a pod. Curr. Opin. Plant Biol. 6: 199–204.CrossRefPubMedGoogle Scholar
  45. Yu, J., Hu, S., Wang, J., Wong, G.K., Li, S., Liu, B., Deng, Y., Dai, L., Zhou, Y., Zhang, X., Cao, M., Liu, J., Sun, J., Tang, J., Chen, Y., Huang, X., Lin, W., Ye, C., Tong, W., Cong, L., Geng, J., Han, Y., Li, L., Li, W., Hu, G., Huang, X., Li, W., Li, J., Liu, Z., Li, L., Liu, J., Qi, Q., Liu, J., Li, L., Li, T., Wang, X., Lu, H., Wu, T., Zhu, M., Ni, P., Han, H., Dong, W., Ren, X., Feng, X., Cui, P., Li, X., Wang, H., Xu, X., Zhai, W., Xu, Z., Zhang, J., He, S., Zhang, J., Xu, J., Zhang, K., Zheng, X., Dong, J., Zeng, W., Tao, L., Ye, J., Tan, J., Ren, X., Chen, X., He, J., Liu, D., Tian, W., Tian, C., Xia. H., Bao, Q., Li, G., Gao, H., Cao, T., Wang, J., Zhao, W., Li, P., Chen, W., Wang, X., Zhang, Y., Hu, J., Wang, J., Liu, S., Yang, J., Zhang, G., Xiong, Y., Li, Z., Mao, L., Zhou, C., Zhu, Z., Chen, R., Hao, B., Zheng, W., Chen, S., Guo, W., Li, G., Liu, S., Tao, M., Wang, J., Zhu, L., Yuan, L. and Yang, H. 2002. A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296: 79–92.CrossRefPubMedGoogle Scholar

Copyright information

© Kluwer Academic Publishers 2004

Authors and Affiliations

  • Erika Asamizu
    • 1
  • Yasukazu Nakamura
    • 1
  • Shusei Sato
    • 1
  • Satoshi Tabata
    • 1
  1. 1.Kazusa DNA Research InstituteChibaJapan

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