International Journal of Genomics

International Journal of Genomics / 2007 / Article

Research Article | Open Access

Volume 2007 |Article ID 021676 | https://doi.org/10.1155/2007/21676

Wen-Jiu Guo, Ping Li, Jun Ling, Shao-Ping Ye, "Significant Comparative Characteristics between Orphan and Nonorphan Genes in the Rice (Oryza sativa L.) Genome", International Journal of Genomics, vol. 2007, Article ID 021676, 7 pages, 2007. https://doi.org/10.1155/2007/21676

Significant Comparative Characteristics between Orphan and Nonorphan Genes in the Rice (Oryza sativa L.) Genome

Academic Editor: Stephen Oliver
Received25 Sep 2006
Accepted16 Apr 2007
Published17 Sep 2007

Abstract

Microsatellites are short tandem repeats of one to six bases in genomic DNA. As microsatellites are highly polymorphic and play a vital role in gene function and recombination, they are an attractive subject for research in evolution and in the genetics and breeding of animals and plants. Orphan genes have no known homologs in existing databases. Using bioinformatic computation and statistical analysis, we identified 19,26 orphan genes in the rice (Oryza sativa ssp. Japanica cv. Nipponbare) proteome. We found that a larger proportion of orphan genes are expressed after sexual maturation and under environmental pressure than nonorphan genes. Orphan genes generally have shorter protein lengths and intron size, and are faster evolving. Additionally, orphan genes have fewer PROSITE patterns with larger pattern sizes than those in nonorphan genes. The average microsatellite content and the percentage of trinucleotide repeats in orphan genes are also significantly higher than in nonorphan genes. Microsatellites are found less often in PROSITE patterns in orphan genes. Taken together, these orphan gene characteristics suggest that microsatellites play an important role in orphan gene evolution and expression.

Supplementary Materials

The orphan and nonorphan genes are concluded using NCBI-BLAST program as described in the materials and methods section in the paper. The front part of table is the 1926 orphan genes and later is the 20439 nonorphan genes. The gene name column in the table is the TIGR's model name and the description column is TIGR annotation. The sequences of each gene can be used as base sequences to design microsatellite marker primers for genetic analysis and molecular marker assistant breeding. Markers deduced from orphan genes should be more efficient and that from nonorphan genes less efficient according to the inferences in the discussion and conclusion sections in the paper.

  1. Supplemantary Table 1

References

  1. Y.-C. Li, A. B. Korol, T. Fahima, A. Beiles, and E. Nevo, “Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review,” Molecular Ecology, vol. 11, no. 12, pp. 2453–2465, 2002. View at: Publisher Site | Google Scholar
  2. V. V. Symonds and A. M. Lloyd, “An analysis of microsatellite loci in Arabidopsis thaliana: mutational dynamics and application,” Genetics, vol. 165, no. 3, pp. 1475–1488, 2003. View at: Google Scholar
  3. A. C. Frantz, L. C. Pope, P. J. Carpenter et al., “Reliable microsatellite genotyping of the Eurasian badger (Meles meles) using faecal DNA,” Molecular Ecology, vol. 12, no. 6, pp. 1649–1661, 2003. View at: Publisher Site | Google Scholar
  4. A. Selvi, N. V. Nair, N. Balasundaram, and T. Mohapatra, “Evaluation of maize microsatellite markers for genetic diversity analysis and fingerprinting in sugarcane,” Genome, vol. 46, no. 3, pp. 394–403, 2003. View at: Publisher Site | Google Scholar
  5. C. M. Ruitberg, D. J. Reeder, and J. M. Butler, “STRBase: a short tandem repeat DNA database for the human identity testing community,” Nucleic Acids Research, vol. 29, no. 1, pp. 320–322, 2001. View at: Publisher Site | Google Scholar
  6. D. Huang, Q. Yang, C. Yu, and R. Yang, “Development of the X-linked tetrameric microsatellite markers HumDXS6803 and HumDXS9895 for forensic purpose,” Forensic Science International, vol. 133, no. 3, pp. 246–249, 2003. View at: Publisher Site | Google Scholar
  7. A. Urquhart, C. P. Kimpton, T. J. Downes, and P. Gill, “Variation in short tandem repeat sequences—a survey of twelve microsatellite loci for use as forensic identification markers,” International Journal of Legal Medicine, vol. 107, no. 1, pp. 13–20, 1994. View at: Publisher Site | Google Scholar
  8. H. Ellegren, “Microsatellites: simple sequences with complex evolution,” Nature Reviews Genetics, vol. 5, no. 6, pp. 435–445, 2004. View at: Publisher Site | Google Scholar
  9. E. Nevo, “Evolution of genome-phenome diversity under environmental stress,” Proceedings of the National Academy of Sciences of the United States of America, vol. 98, no. 11, pp. 6233–6240, 2001. View at: Publisher Site | Google Scholar
  10. D. Field and C. Wills, “Abundant microsatellite polymorphism in Saccharomyces cerevisiae, and the different distributions of microsatellites in eight prokaryotes and S. cerevisiae, result from strong mutation pressures and a variety of selective forces,” Proceedings of the National Academy of Sciences of the United States of America, vol. 95, no. 4, pp. 1647–1652, 1998. View at: Publisher Site | Google Scholar
  11. T. Domazet-Loso and D. Tautz, “An evolutionary analysis of orphan genes in Drosophila,” Genome Research, vol. 13, no. 10, pp. 2213–2219, 2003. View at: Publisher Site | Google Scholar
  12. M. Long, E. Betrán, K. Thornton, and W. Wang, “The origin of new genes: glimpses from the young and old,” Nature Reviews Genetics, vol. 4, no. 11, pp. 865–875, 2003. View at: Publisher Site | Google Scholar
  13. Q. Yuan, S. Ouyang, J. Liu et al., “The TIGR rice genome annotation resource: annotating the rice genome and creating resources for plant biologists,” Nucleic Acids Research, vol. 31, no. 1, pp. 229–233, 2003. View at: Publisher Site | Google Scholar
  14. S. Kikuchi, K. Satoh, T. Nagata et al., “Collection, mapping, and annotation of over 28,000 cDNA clones from Japonica rice,” Science, vol. 301, no. 5631, pp. 376–379, 2003. View at: Publisher Site | Google Scholar
  15. A. Bairoch, “PROSITE: a dictionary of sites and patterns in proteins,” Nucleic Acids Research, vol. 19, supplement, pp. 2241–2245, 1991. View at: Google Scholar
  16. A. Gattiker, E. Gasteiger, and A. Bairoch, “ScanProsite: a reference implementation of a PROSITE scanning tool,” Applied Bioinformatics, vol. 1, no. 2, pp. 107–108, 2002. View at: Google Scholar
  17. S. Temnykh, G. DeClerck, A. Lukashova, L. Lipovich, S. Cartinhour, and S. McCouch, “Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential,” Genome Research, vol. 11, no. 8, pp. 1441–1452, 2001. View at: Publisher Site | Google Scholar
  18. M. Morgante, M. Hanafey, and W. Powell, “Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes,” Nature Genetics, vol. 30, no. 2, pp. 194–200, 2002. View at: Publisher Site | Google Scholar
  19. G. Toth, Z. Gaspari, and J. Jurka, “Microsatellites in different eukaryotic genomes: surveys and analysis,” Genome Research, vol. 10, no. 7, pp. 967–981, 2000. View at: Publisher Site | Google Scholar
  20. J. E. Stajich, D. Block, K. Boulez et al., “The Bioperl toolkit: Perl modules for the life sciences,” Genome Research, vol. 12, no. 10, pp. 1611–1618, 2002. View at: Publisher Site | Google Scholar
  21. S. F. Altschul, T. L. Madden, A. A. Schäffer et al., “Gapped BLAST and PSI-BLAST: a new generation of protein database search programs,” Nucleic Acids Research, vol. 25, no. 17, pp. 3389–3402, 1997. View at: Publisher Site | Google Scholar
  22. S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, “Basic local alignment search tool,” Journal of Molecular Biology, vol. 215, no. 3, pp. 403–410, 1990. View at: Publisher Site | Google Scholar
  23. G. M. Rubin, M. D. Yandell, J. R. Wortman et al., “Comparative genomics of the eukaryotes,” Science, vol. 287, no. 5461, pp. 2204–2215, 2000. View at: Publisher Site | Google Scholar
  24. S. Cruveiller, K. Jabbari, O. Clay, and G. Bernardi, “Incorrectly predicted genes in rice?” Gene, vol. 333, pp. 187–188, 2004. View at: Publisher Site | Google Scholar
  25. K. Jabbari, S. Cruveiller, O. Clay, J. Le Saux, and G. Bernardi, “The new genes of rice: a closer look,” Trends in Plant Science, vol. 9, no. 6, pp. 281–285, 2004. View at: Publisher Site | Google Scholar
  26. L. S. Wyrwicz, M. von Grotthuss, J. Pas, L. Rychlewski, and S. Kikuchi, “How unique is the rice transcriptome?” Science, vol. 303, no. 5655, p. 168, 2004. View at: Publisher Site | Google Scholar
  27. A. B. Carvalho and A. G. Clark, “Genetic recombination: intron size and natural selection,” Nature, vol. 401, no. 6751, p. 344, 1999. View at: Publisher Site | Google Scholar
  28. M. Long, M. Deutsch, W. Wang, E. Betrán, F. G. Brunet, and J. Zhang, “Origin of new genes: evidence from experimental and computational analyses,” Genetica, vol. 118, no. 2-3, pp. 171–182, 2003. View at: Publisher Site | Google Scholar
  29. D. J. Lipman, A. Souvorov, E. V. Koonin, A. R. Panchenko, and T. A. Tatusova, “The relationship of protein conservation and sequence length,” BMC Evolutionary Biology, vol. 2, no. 1, p. 20, 2002. View at: Publisher Site | Google Scholar
  30. F. Chamas and E. L. Sabban, “Role of the 5 untranslated region (UTR) in the tissue-specific regulation of rat tryptophan hydroxylase gene expression by stress,” Journal of Neurochemistry, vol. 82, no. 3, pp. 645–654, 2002. View at: Publisher Site | Google Scholar
  31. N. Amrani, R. Ganesan, S. Kervestin, D. A. Mangus, S. Ghosh, and A. Jacobson, “A faux3-UTR promotes aberrant termination and triggers nonsense-mediated mRNA decay,” Nature, vol. 432, no. 7013, pp. 112–118, 2004. View at: Publisher Site | Google Scholar
  32. C.-H. C. Cheng and L. Chen, “Evolution of an antifreeze glycoprotein,” Nature, vol. 401, no. 6752, pp. 443–444, 1999. View at: Publisher Site | Google Scholar
  33. Y. Kashi, D. King, and M. Soller, “Simple sequence repeats as a source of quantitative genetic variation,” Trends in Genetics, vol. 13, no. 2, pp. 74–78, 1997. View at: Publisher Site | Google Scholar
  34. B. Charlesworth, J. A. Coyne, and N. H. Barton, “The relative rates of evolution of sex chromosomes and autosomes,” American Naturalist, vol. 130, no. 1, pp. 113–146, 1987. View at: Publisher Site | Google Scholar

Copyright © 2007 Wen-Jiu Guo et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


More related articles

 PDF Download Citation Citation
 Order printed copiesOrder
Views321
Downloads842
Citations

Related articles

Article of the Year Award: Outstanding research contributions of 2020, as selected by our Chief Editors. Read the winning articles.