Research Article | Open Access
Mariko Kouduka, Daisuke Sato, Manabu Komori, Motohiro Kikuchi, Kiyoshi Miyamoto, Akinori Kosaku, Mohammed Naimuddin, Atsushi Matsuoka, Koichi Nishigaki, "A Solution for Universal Classification of Species Based on Genomic DNA", International Journal of Plant Genomics, vol. 2007, Article ID 027894, 8 pages, 2007. https://doi.org/10.1155/2007/27894
A Solution for Universal Classification of Species Based on Genomic DNA
Traditionally, organisms have been classified on the basis of their phenotype. Recently, genotype-based classification has become possible through the development of sequencing technology. However, it is still difficult to apply sequencing approaches to the analysis of a large number of species due to the cost and labor. In most biological fields, the analysis of complex systems comprising various species has become an important theme, demanding an effective method for handling a vast number of species. In this paper, we have demonstrated, using plants, fish, and insects, that genome profiling, a compact technology for genome analysis, can classify organisms universally. Surprisingly, in all three of the domains of organisms tested, the phylogenetic trees generated from the phenotype topologically matched completely those generated from the genotype. Furthermore, a single probe was sufficient for the genome profiling, thereby demonstrating that this methodology is universal and compact.
- R. I. Amann, W. Ludwig, and K.-H. Schleifer, “Phylogenetic identification and in situ detection of individual microbial cells without cultivation,” Microbiological Reviews, vol. 59, no. 1, pp. 143–169, 1995.
- J. L. Sebat, F. S. Colwell, and R. L. Crawford, “Metagenomic profiling: microarray analysis of an environmental genomic library,” Applied and Environmental Microbiology, vol. 69, no. 8, pp. 4927–4934, 2003.
- B. G. Miner, S. E. Sultan, S. G. Morgan, D. K. Padilla, and R. A. Relyea, “Ecological consequences of phenotypic plasticity,” Trends in Ecology and Evolution, vol. 20, no. 12, pp. 685–692, 2005.
- American Museum of Natural History, “The Global Taxonomy Initiative: using systematic inventories to meet country and regional needs,” in DIVERSITAS/Systematics Agenda 2000 International Workshop, New York, NY, USA, 1999.
- C. R. Woese, O. Kandler, and M. L. Wheelis, “Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya,” Proceedings of the National Academy of Sciences of the United States of America, vol. 87, no. 12, pp. 4576–4579, 1990.
- B. L. Maidak, J. R. Cole, and C. T. Parker Jr. et al., “A new version of the RDP (Ribosomal Database Project),” Nucleic Acids Research, vol. 27, no. 1, pp. 171–173, 1999.
- J. R. Cole, B. Chai, and R. J. Farris et al., “The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis,” Nucleic Acids Research, vol. 33, pp. D294–D296, 2005.
- R. Urwin and M. C. J. Maiden, “Multi-locus sequence typing: a tool for global epidemiology,” Trends in Microbiology, vol. 11, no. 10, pp. 479–487, 2003.
- M. C. J. Maiden, J. A. Bygraves, and E. Feil et al., “Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms,” Proceedings of the National Academy of Sciences of the United States of America, vol. 95, no. 6, pp. 3140–3145, 1998.
- A. Sorokin, B. Candelon, and K. Guilloux et al., “Multiple-locus sequence typing analysis of Bacillus cereus and Bacillus thuringiensis reveals separate clustering and a distinct population structure of psychrotrophic strains,” Applied and Environmental Microbiology, vol. 72, no. 2, pp. 1569–1578, 2006.
- M. Kouduka, A. Matsuoka, and K. Nishigaki, “Acquisition of genome information from single-celled unculturable organisms (radiolaria) by exploiting genome profiling (GP),” BMC Genomics, vol. 7, p. 135, 2006.
- T. Watanabe, A. Saito, Y. Takeuchi, M. Naimuddin, and K. Nishigaki, “A database for the provisional identification of species using only genotypes: web-based genome profiling,” Genome Biology, vol. 3, no. 2, pp. 1–8, 2002, research0010.
- K. Nishigaki, M. Naimuddin, and K. Hamano, “Genome profiling: a realistic solution for genotype-based identification of species,” Journal of Biochemistry, vol. 128, no. 1, pp. 107–112, 2000.
- M. Naimuddin and K. Nishigaki, “Genome analysis technologies: towards species identification by genotype,” Briefings in Functional Genomics and Proteomics, vol. 1, no. 4, pp. 356–371, 2003.
- R. Yasugi, O. Koseki, M. Hurutani, and T. Hidaka, Iwanami Biology Encyclopedia, Iwanami Press, Tokyo, Japan, 4th edition, 1996.
- H. Wang, M. Qi, and A. J. Cutler, “A simple method of preparing plant samples for PCR,” Nucleic Acids Research, vol. 21, no. 17, pp. 4153–4154, 1993.
- A. Shinomiya, M. Matsuda, S. Hamaguchi, and M. Sakaizumi, “Identification of genetic sex of the medaka by PCR,” The Fish Biology Journal Medaka, vol. 10, pp. 31–32, 1999.
- M. Naimuddin, T. Kurazono, Y. Zhang, T. Watanabe, M. Yamaguchi, and K. Nishigaki, “Species-identification dots: a potent tool for developing genome microbiology,” Gene, vol. 261, no. 2, pp. 243–250, 2000.
- R. M. Myers, S. G. Fischer, L. S. Lerman, and T. Maniatis, “Nearly all single base substitutions in DNA fragments joined to a GC-clamp can be detected by denaturing gradient gel electrophoresis,” Nucleic Acids Research, vol. 13, no. 9, pp. 3131–3145, 1985.
- K. Nishigaki, Y. Husimi, M. Masuda, K. Kaneko, and T. Tanaka, “Strand dissociation and cooperative melting of double-stranded DNAs detected by denaturant gradient gel electrophoresis,” Journal of Biochemistry, vol. 95, no. 3, pp. 627–635, 1984.
- M. Biyani and K. Nishigaki, “Hundredfold productivity of genome analysis by introduction of microtemperature-gradient gel electrophoresis,” Electrophoresis, vol. 22, no. 1, pp. 23–28, 2001.
- J. H. Ward Jr., “Hierarchical grouping to optimize an objective function,” Journal of the American Statistical Association, vol. 58, no. 301, pp. 236–244, 1963.
- J. D. Jobson, Applied Multivariate Data Analysis, vol. 2 of Categorical and Multivariate Methods, Springer, New York, NY, USA, 1992.
- Y. Sakuma and K. Nishigaki, “Computer prediction of general PCR products based on dynamical solution structures of DNA,” Journal of Biochemistry, vol. 116, no. 4, pp. 736–741, 1994.
- D. Riesner, G. Steger, U. Wiese, M. Wulfert, M. Heibey, and K. Henco, “Temperature-gradient gel electrophoresis for the detection of polymorphic DNA and for quantitative polymerase chain reaction,” Electrophoresis, vol. 13, no. 9-10, pp. 632–636, 1992.
- M. Naimuddin, T. Kurazono, and K. Nishigaki, “Commonly conserved genetic fragments revealed by genome profiling can serve as tracers of evolution,” Nucleic Acids Research, vol. 30, no. 10, p. e42, 2002.
- T. M. Cover and P. E. Hart, “Nearest neighbor pattern classification,” IEEE Transactions on Information Theory, vol. 13, no. 1, pp. 21–27, 1967.
- K. Nishigaki, N. Amano, and T. Takasawa, “DNA profiling. An approach of systemic characterization, classification and comparison of genomic DNAs,” Chemistry Letters, vol. 20, no. 7, pp. 1097–1100, 1991.
- H. Shimodaira, “An approximately unbiased test of phylogenetic tree selection,” Systematic Biology, vol. 51, no. 3, pp. 492–508, 2002.
- K. Nishigaki, A. Saito, T. Hasegawa, and M. Naimuddin, “Whole genome sequence-enabled prediction of sequences performed for random PCR products of Escherichia coli,” Nucleic Acids Research, vol. 28, no. 9, pp. 1879–1884, 2000.
Copyright © 2007 Mariko Kouduka 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.