Journal of Life Science (생명과학회지)

Korean Society of Life Science (한국생명과학회)
권호 표지
DOI QR코드

DOI QR Code

The Rates of Synonymous and Nonsynonymous Substitutions in Sorbus aucuparia Using Nuclear and Chloroplast Genes

핵 및 엽록체 유전자를 이용한 유럽마가목에서 동의 및 비동의치환율

  • Huh, Man-Kyu (Department of Molecular Biology, Dongeui University)
  • 허만규 (동의대학교 분자생물학과)
  • Received : 2010.01.12
  • Accepted : 2010.03.08
  • Published : 2010.04.30
Download PDF
⟨ Previous Next ⟩

Abstract

The rates of synonymous and nonsynonymous nucleotide substitutions were studied for sequences of nuclear and chloroplast genes in Sorbus aucuparia. Results suggested that DNA evolution in this species had taken place, on average, at a slower rate in the chloroplast genes than in the nuclear genes: a rate variation pattern similar to those observed in eudicot plants. Within the nucleus, the synonymous substitution rates (Ks) (2.45-2.60) were two-fold higher than nonsynonymous substitution rates (Ka) (1.15-1.30). More notably, the values of Ks (1.20-1.26) were about six-fold higher than those of Ka (0.26-0.42) within the chloroplast genome. Ka/Ks ratios for nuclear and chloroplast genes of S. aucuparia had mean values of 0.178 and 0.056, respectively. A Ka/Ks ratio < 1 indicated negative (purifying) selection. The chloroplast genes had a lower effective number of codons (ENC) values (22.4-32.2) than those of nuclear genes (35.8-38.7). The analysis of the G+C content indicated that the chloroplast genes in this investigation had a higher preference for synonymous codons ending with A and T (G+C content range, 28.4-29.1%) where there was a slight bias toward codons ending with G+C (63.2-64.2%) in the nuclear genome.

유럽마가목에서 핵 및 엽록체 유전자의 서열을 이용하여 동의 및 비동의치환율을 산출하였다. 유럽마가목 엽록체 유전자의 서열은 핵 유전자에 비해 평균적으로 움진화가 느리게 일어나고 있음을 나타내었으며 다른 쌍자엽식물과 유사하였다. 핵에서 동의치환율(Ks)은 2.45-2.60이었으며 비동의치환율(Ka=1.15-1.30)보다 약 2배 정도 높았다. 엽록체에서 Ks는 1.20-1.26이었으며 엽록체에서 Ka (0.26-0.42) 보다 약 6배 높았다. 유럽마가목에서 핵 및 엽록체 Ka/Ks은 각각 0.178과 0.056이었다. 이 Ka/Ks의 비율이 1보다 작다는 것은 음의 도태에 있다는 것을 나타낸다. 엽록체 유전자는 유효유전자코돈(ENC)이 22.4-32.2로 핵의 값(35.8-38.7)에 비해 낮았다. G+C 함량 분석에서 엽록체 유전자는 동의코돈 A와 T에 대해 높은 선호성(G+C 함량은 28.4-29.1%에 불과)을 나타낸 반면 핵에서는 G와 C가 더 선호성을 나타내었다(G+C 함량은 63.2-64.2%).

Keywords

References

  1. Alvarez, I. and J. F. Wendel. 2003. Ribosomal ITS sequences and plant phylogenetic inference. Mol. Phylogen. Evol. 29, 417-434. https://doi.org/10.1016/S1055-7903(03)00208-2
  2. Arnheim, N. 1983. Concerted evolution of multigene families, pp. 38-61, In Nei, M. and P. K. Koehn (eds.), Evolution and Proteins, Sinauer, Sunderland, MA.
  3. Bailey, C. D., T. G. Carr, S. A. Harris, and C. E. Hughes. 2003. Characterization of angiosperm nrDNA polymorphism, paralogy, and psudogenes. Mol. Phylogen. Evol. 29, 435-455. https://doi.org/10.1016/j.ympev.2003.08.021
  4. Baldwin, B. G., M.J. Sanderson, J. M. Porter, M. F. Wojciechowski, C. S. Campbell, and M. G. Donoghue. 1995. The ITS region of nuclear ribosomal DNA: a valuable source of evidence on angiosperm phylogeny. Ann. Missouri Bot. Gard. 82, 247-277. https://doi.org/10.2307/2399880
  5. Campbell, C. S., M. J. Donoghue, B. G. Baldwin, and M. F. Wojciechowski. 1995. Phylogenetic relationships in Maloideae (Rosaceae): evidence from sequences of the internal transcribed spacers of nuclear ribosomal DNA and its congruence with morphology. Am. J. Bot. 82, 903-918. https://doi.org/10.2307/2445977
  6. Duret, L. 2000. tRNA gene number and codon usage in the C. elegans genome are co-adapted for optimal translation of highly expressed genes. Trends in Genetics 16, 287-289. https://doi.org/10.1016/S0168-9525(00)02041-2
  7. Gaut, B. S. 1997. Molecular clocks and nucleotide substitution rates in higher plants, pp. 93-116, In Hecht, M. K., R. J. MacIntyre, and M. T. Clegg (eds.), Evolutionary Biology, Vol 30, Plenum Press, New York.
  8. Huh, M. K., S. H. Kim, and S. H. Park. 2007. Phylogenetic study of genus Sorbus in Korea by internal transcribed spacer sequence (ITS). J. Life Sci. 17, 1610-1615. https://doi.org/10.5352/JLS.2007.17.12.1610
  9. Ino, Y. 1995. New methods for estimating the numbers of synonymous and nonsynonymous substitutions. J. Mol. Evol. 40, 190-226. https://doi.org/10.1007/BF00167113
  10. Li, W. H. 1993. Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J. Mol. Evol. 36, 96-99. https://doi.org/10.1007/BF02407308
  11. Li, W. H., C. I. Wu, and C. C. Luo. 1985. A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes. Mol. Biol. Evol. 2, 150-174.
  12. Lloyd, A. T. and P. M. Sharp. 1992. CODONS: a microcomputer program for codon usage analysis. J. Hered. 83, 239-240.
  13. Kuzoff, R. K., J. A. Sweere, D. E. Soltis, and E. A. Zimmer. 1998. The phylogenetic potential of entire 26S rDNA sequences in plants. Mol. Biol. Evol. 15, 251-263. https://doi.org/10.1093/oxfordjournals.molbev.a025922
  14. Moore, M. J., A. Dhingra, P. S. Soltis, R. Shaw, W. G. Farmerie, K. M. Folta, and D. E. Soltis. 2006. Rapid and accurate pyrosequencing of angiosperm plastid genomes. BMC Plant Biol. 6, 17-30. https://doi.org/10.1186/1471-2229-6-17
  15. Moriyama, E. N. and J. R. Powell. 1997. Synonymous substitution rates in Drosophila: mitochondrial versus nuclear genes. J. Mol. Evol. 45, 378-391. https://doi.org/10.1007/PL00006243
  16. Palmer, J. D., K. L. Adams, Y. Cho, C. L. Parkinsonv, Y. L. Qiu, and K. Song. 2000. Dynamic evolution of plant mitochondrial genomes: mobile genes and introns and highly variable mutation rates. Proc. Natl. Acad. Sci. USA. 97,6960-6966. https://doi.org/10.1073/pnas.97.13.6960
  17. Raspe, O., P. Saumitou-Laprade, J. Cuguen, and A. L. Jacquemart. 2000. Chloroplast DNA haplotype variation and population differentiation in Sorbus aucuparia L. (Rosaceae: Maloideae). Mol. Ecol. 9, 1113-1122. https://doi.org/10.1046/j.1365-294x.2000.00977.x
  18. Robertson, K. R., J. B. Phipps, J. R. Rohrer, and P. G. Smith. 1991. A synopsis of genera in Maloideae (Rosaceae). Syst. Bot. 16, 376-394. https://doi.org/10.2307/2419287
  19. Sharp, P. M., D. C. Sields, K. H. Wolfe, and W. H. Li. 1989. Chromosomal location and evolutionary rate variation in enterobacterial genes. Science 246, 808-810. https://doi.org/10.1126/science.2683084
  20. Shields, D. C., P. M. Sharp, D. G. Higgins, and F. Wright. 1988. "Silent" sites in Drosophila genes are not neutral: evidence of selection among synonymous codons. Mol. Biol. Evol. 5, 704-716.
  21. Small, R. L., R. C. Cronn, and J. F. Wendel. 2004. Use of nuclear genes for phylogeny reconstruction in plants. Aust. J. Bot. 17, 145-170. https://doi.org/10.1071/SB03015
  22. Soltis, D. E., C. D. Bell, S. Kim, and P. S. Soltis. 2008. Origin and early evolution of angiosperms. Ann. N.Y. Acad. Sci. 1133, 3-25. https://doi.org/10.1196/annals.1438.005
  23. Sorhannus, U. and M. Fox. 1999. Synonymous and nonsynonymous substitution rates in diatons: a comparison between chloroplast and nuclear genes. J. Mol. Evol. 48, 209-212. https://doi.org/10.1007/PL00006459
  24. Tamura, K., J. Dudley, M. Nei, and S. Kumar. 2007. MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24, 1596-1599. https://doi.org/10.1093/molbev/msm092
  25. Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. CLUSTAL W: improving the sensitivity of procreative multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673-4680. https://doi.org/10.1093/nar/22.22.4673
  26. White, T. J., T. Bruns, S. Lee, and J. Taylor. 1999. Amplification and direct sequencing of fungal ribosomal genes for phylogenetics, pp. 315-322, In Innis, M. A., D. H. Gelfand, J. J. Sninsky, and T. J. White (eds.), PCR Protocols: A Guide to Methods and Applications, New York Academic Press.
  27. Wolfe, K. H., W. H. Li, and P. M. Sharp. 1987. Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. Proc. Natl. Acad. Sci. USA. 84, 9054-9058. https://doi.org/10.1073/pnas.84.24.9054
  28. Wright, F. 1990. The "effective number of codons" used in a gene. Gene 87, 23-29. https://doi.org/10.1016/0378-1119(90)90491-9
  29. Zimmer, E. A., S. L. Martin, S. M. Beverly, W. Kan, and A. C. Wilson. 1980. Rapid duplication and loss of genes coding for the $\alpha$ chains of hemoglobin. Proc. Natl. Acad. Sci. USA. 77, 2158-2162. https://doi.org/10.1073/pnas.77.4.2158