Skip to main content
SpringerLink
Log in

The transfer RNA genes in Oryza sativa L. ssp. indica

  • Published:
Science in China Series C: Life Sciences Aims and scope Submit manuscript

Abstract

The availability of the draft genome sequence of Oryza sativa L. ssp. indica has made it possible to study the rice tRNA genes. A total of 596 tRNA genes, including 3 selenocysteine tRNA genes and one suppressor tRNA gene are identified in 127551 rice contigs. There are 45 species of tRNA genes and the revised wobble hypothesis proposed by Guthrie and Abelson is perfectly obeyed. The relationship between codon usage and the number of corresponding tRNA genes is discussed. Redundancy may exist in the present list of tRNA genes and novel ones may be found in the future. A set of 33 tRNA genes is discovered in the complete chloroplast genome of Oryza sativa L. ssp. indica. These tRNA genes are identical to those in ssp. japonica identified by us independently from the origional annotation.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  1. Zhang, J. H., Wang, X. K., Kong, Z. C., Rice cultivation of Jiahu Remains in Henan Province, Science J. (in Chinese), 2002, 54(3): 3.

    Google Scholar 

  2. Yu, J., Hu, S. N., Wang, J. et al., A draft sequence of the rice (Oryza sativa L. ssp. indica) genome, Chinese Science Bulletin, 2001, 46(23): 1937–1941.

    Article  CAS  Google Scholar 

  3. Yu, J., Hu, S. N., Wang, J. et al., A draft sequence of the rice genome (Oryza sativa L. ssp. indica), Science, 2002, 296: 79.

    Article  PubMed  CAS  Google Scholar 

  4. Goff, S. A., Ricke, D., Lan, T. H. et al., A draft sequence of the rice genome (Oryza sativa L. ssp. japonica), Science, 2002, 296: 92.

    Article  PubMed  CAS  Google Scholar 

  5. Crick, F., Codon-anticodon pairings: the wobble hypothesis, Journal of Molecular Biology, 1966, 19: 548.

    Article  PubMed  CAS  Google Scholar 

  6. Guthrie, C., Abelson, J., Organization and expression of tRNA genes in Saccharomyces cerevisiae, in The Molecular Biology of the Yeast Saccharomyces: Metabolism and Gene Expression (eds. Strathern, J., et al.), New York: Cold Spring Harbor Laboratory Press, 1982, 487.

    Google Scholar 

  7. International Human Genome Sequencing Consortium, Initial sequencing and analysis of the human genome, Nature, 2002, 409: 860.

    Google Scholar 

  8. http://rna.wust1.edu/GtRDB/

  9. Rice GD at Beijing Genomics Institute: http://btn.genomics.org.cn/rice

  10. Hiratsuka, J., Shimada, H., Whittier, R. et al., The complete sequence of the rice (Oryza sativa) chloroplast genome: intermolecular recombination between distinct tRNA genes accounts for a major plastid DNA inversion during the evolution of the cereals, Molecular General Genetics, 1989, 217 (2–3): 185.

    Article  PubMed  CAS  Google Scholar 

  11. http://www.ncbi.nlm.nih.gov/

  12. Eddy, S. R., Non-coding RNA genes and the modern RNA world, Nature Reviews Genetics, 2001, 2: 919.

    Article  PubMed  CAS  Google Scholar 

  13. Lowe, T. M., Eddy, S. R., tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence, Nucleic Acids Research, 1997, 25: 955.

    Article  PubMed  CAS  Google Scholar 

  14. Altschul, S. F., Madden, T. L., Shaffer, A. A. et al., Gapped BLAST and PSI-BLAST: A new generation of protein database search programs, Nucleic Acids Research, 1997, 25: 3389.

    Article  PubMed  CAS  Google Scholar 

  15. Center for Bioinformatics, Peking University: http://www.cbi.pku.edu.cn/

  16. Thompson, J. D. et al., CLUSTALW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice, Nucleic Acids Research, 1994, 22: 4673.

    Article  PubMed  CAS  Google Scholar 

  17. http://www.tigr.org/

  18. http://www.kazusa.or.jp/codon/

  19. Srinivasan, G., James, C. M., Krzycki, J. A. et al., Pyrrolysine encoded by UAG in archaea: Charging of a UAG-decoding specialized tRNA, Science, 2002, 296: 1459.

    Article  PubMed  CAS  Google Scholar 

  20. Hao, B., Gong, W. M., Ferguson, T. K. et al., A new UAG-encoded residue in the structure of a methanogen methyltransferase, Science, 2002, 296: 1462.

    Article  PubMed  CAS  Google Scholar 

  21. Adams, M. D., Celniker, S. E., Holt, R. A. et al., The genome sequence of Drosophila melanogaster, Science, 2000, 287: 2185.

    Article  PubMed  Google Scholar 

  22. Goffeau, A., Barrell, B. G., Bussey, H. et al., Life with 6000 genes, Science, 1996, 274: 546.

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. College of Life Science, Peking University, 100871, Beijing, China

    Xiyin Wang & Xiaoli Shi

  2. Beijing Genomics Institute/Center of Genomics and Bioinformatics, Chinese Academy of Sciences, 101300, Beijing, China

    Xiyin Wang, Xiaoli Shi & Bailin Hao

  3. Department of Mathematics and Physics, Hebei Institute of Science and Technology, 063009, Tangshan, China

    Xiyin Wang

  4. The T-life Research Center, Fudan University, 200433, Shanghai, China

    Bailin Hao

Authors
  1. Xiyin Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Xiaoli Shi
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Bailin Hao
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Bailin Hao.

Additional information

These authors contributed equally to this work.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Wang, X., Shi, X. & Hao, B. The transfer RNA genes in Oryza sativa L. ssp. indica . Sci. China Ser. C.-Life Sci. 45, 504–511 (2002). https://doi.org/10.1360/02yc9055

Download citation

  • Received:

  • Issue Date:

  • DOI: https://doi.org/10.1360/02yc9055

Keywords

Search

Navigation