Research Article | Open Access
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
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.
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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- H. Ellegren, “Microsatellites: simple sequences with complex evolution,” Nature Reviews Genetics, vol. 5, no. 6, pp. 435–445, 2004.
- 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.
- 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.
- T. Domazet-Loso and D. Tautz, “An evolutionary analysis of orphan genes in Drosophila,” Genome Research, vol. 13, no. 10, pp. 2213–2219, 2003.
- 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.
- 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.
- 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.
- A. Bairoch, “PROSITE: a dictionary of sites and patterns in proteins,” Nucleic Acids Research, vol. 19, supplement, pp. 2241–2245, 1991.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- S. Cruveiller, K. Jabbari, O. Clay, and G. Bernardi, “Incorrectly predicted genes in rice?” Gene, vol. 333, pp. 187–188, 2004.
- 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.
- 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.
- A. B. Carvalho and A. G. Clark, “Genetic recombination: intron size and natural selection,” Nature, vol. 401, no. 6751, p. 344, 1999.
- 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.
- 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.
- F. Chamas and E. L. Sabban, “Role of the 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.
- N. Amrani, R. Ganesan, S. Kervestin, D. A. Mangus, S. Ghosh, and A. Jacobson, “A faux-UTR promotes aberrant termination and triggers nonsense-mediated mRNA decay,” Nature, vol. 432, no. 7013, pp. 112–118, 2004.
- C.-H. C. Cheng and L. Chen, “Evolution of an antifreeze glycoprotein,” Nature, vol. 401, no. 6752, pp. 443–444, 1999.
- 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.
- 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.
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.