Error-Robust Nature of Genome Profiling Applied for Clustering of Species Demonstrated by Computer Simulation
Genome profiling (GP), a genotype based technology, which exploits random PCR and temperature gradient gel electrophoresis, has been successful in identification/classification of organisms. In this technology, spiddos (Species identification dots) and PaSS (Pattern similarity score) were employed for measuring the closeness (or distance) between genomes. Based on the closeness (PaSS), we can buildup phylogenetic trees of the organisms. We noticed that the topology of the tree is rather robust against the experimental fluctuation conveyed by spiddos. This fact was confirmed quantitatively in this study by computer-simulation, providing the limit of the reliability of this highly powerful methodology. As a result, we could demonstrate the effectiveness of the GP approach for identification/classification of organisms.
[1] Nishigaki K., Naimuddin M., Hamano K., "Genome profiling: a realistic
solution for genotype based identification of species," J Biochem,
128:107-112, 2000.
[2] Amann R. I., Ludwig W., and Schleifer K. H., "Phylogenetic identification
and in situ detection of individual microbial cells without cultivation,"
Microbiological Reviews, vol. 59, no. 1, pp. 143-169, 1995.
[3] Sebat J. L., Colwell F. S., and Crawford R. L., "Metagenomic profiling:
microarray analysis of an environmental genomic library," Applied and
Environmental Microbiology, vol. 69, no. 8, pp. 4927-4934, 2003.
[4] Miner B. G., Sultan S. E., Morgan S. G., Padilla D. K., and Relyea R. A.,
"Ecological consequences of phenotypic plasticity," Trends in Ecology
and Evolution, vol. 20, no. 12, pp. 685-692, 2005.
[5] 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.
[6] Cole J. R., Chai B., Farris R. J., 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.
[7] Maidak B. L., Cole J. R., Parker Jr. C. T., et al., "A new version of the
RDP (Ribosomal Database Project)," Nucleic Acids Research, vol. 27, no.
1, pp. 171-173, 1999.
[8] Woese C.R., Kandler O., and Wheelis M. L., "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.
[9] Urwin R., and Maiden M. C. J., "Multi-locus sequence typing: a tool for
global epidemiology," Trends inMicrobiology, vol. 11, no. 10, pp. 479-
487, 2003.
[10] Sorokin A., Candelon B., Guilloux K., et al., "Multiplelocus 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.
[11] Maiden M. C. J., Bygraves J. A., Feil E., 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.
[12] Kouduka M., Sato D., Komori M., Kikuchi M., Miyamoto K., Kosaku A.,
Naimuddin M., Matsuoka A., and Nishigaki K., "A Solution for Universal
Classification of Species Based on Genomic DNA," International Journal
of Plant Genomics, Vol. 2007, Article ID 27894, 8 pages, 2007.
[13] Naimuddin M., Kurazono T., Zhangc Y., Watanabe T., Yamaguchi M.,
Nishigaki K., "Species-identification dots: a potent tool for developing
genome microbiology," Gene, 261:243-250. 2000.
[14] Futakami M., and Nishigaki K., "Measurement of DNA mutations caused
by seconds-period UV-irradiation," Chemistry Letters, vol. 36, no. 3, p.
358-359, 2007.
[15] Futakami M., Salimullah M., Miura T., Tokita S., and Nishigaki K.,
"Novel mutation assay with high sensitivity based on direct measurement
of genomic DNA alteration: comparable results to the Ames test," J.
Biochem. 141, 675-686, 2007.
[16] Kouduka M., Matsuoka A., and Nishigaki K., "Acquisition of genome
information from single-celled unculturable organisms (radiolaria) by
exploiting genome profiling (GP)," BMC Genomics, vol. 7, p. 135, 2006.
[17] Myers R. M., Fischer S. G., Lerman L. S., and Maniatis T., "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.
[18] Salimullah M., Mori M., Nishigaki K., "High throughput threedimensional
gel electrophoresis for versatile utilities: a stacked slice-gel
system for separation and reactions (4SR)," Genomics Proteomics
Bioinformatics, 4(1): 26-33, Feb 2006.
[19] Wang H., Qin M., Cutler AJ., "A simple method of preparing plant
samples for PCR," Nucleic Acids Res 21:4153-4154, 1993.
[20] Sakuma Y., and Nishigaki K., "Computer prediction of general PCR
products based on dynamical solution structures of DNA," Journal of
Biochemistry, vol. 116, no. 4, pp. 736-741, 1994.
[21] Hamano K., Takasawa T., Kurazono T., Okuyama Y., Nishigaki K.,
"Genome Profiling-Establishment and practical evaluation of its
methodology," Nikkashi 1996:54-61, 1996.
[22] Biyani M., Nishigaki K., "Hundredfold productivity of genome analysis
by introduction of microtemperature-gradient gel electrophoresis,"
Electrophoresis, 22:23-28, 2001.
[23] Nishigaki K., Husimi Y., Masuda M., Kaneko K., Tanaka T., "Strand
dissociation and cooperative melting of double-stranded DNAs detected
by denaturant gradient gel electrophoresis," J Biochem, 95:627-35, 1984.
[24] Watanabe T., Saito A., Takeuchi Y., Naimuddin M., Nishigaki K., "A
database for the provisional identification of species using only genotypes:
web-based genome profiling," Genome Biol, 3:00101.1, 2002.
[25] Nei M., Takezaki N., "Genetic distances and reconstruction of
phylogenetic trees from microsatellite DNA," Genetics, 144, 389-399,
1996.
[26] Jobson J. D., "Applied Multivariate Data Analysis, Categorical and
Multivariate Methods," Springer, New York, NY, USA, vol. 2, 1992.
[27] Ward Jr. J. H., "Hierarchical grouping to optimize an objective function,"
Journal of the American Statistical Association, vol. 58, no. 301, pp. 236-
244, 1963.
[28] On-web GP (http://gp.fms.saitama-u.ac.jp/)
[1] Nishigaki K., Naimuddin M., Hamano K., "Genome profiling: a realistic
solution for genotype based identification of species," J Biochem,
128:107-112, 2000.
[2] Amann R. I., Ludwig W., and Schleifer K. H., "Phylogenetic identification
and in situ detection of individual microbial cells without cultivation,"
Microbiological Reviews, vol. 59, no. 1, pp. 143-169, 1995.
[3] Sebat J. L., Colwell F. S., and Crawford R. L., "Metagenomic profiling:
microarray analysis of an environmental genomic library," Applied and
Environmental Microbiology, vol. 69, no. 8, pp. 4927-4934, 2003.
[4] Miner B. G., Sultan S. E., Morgan S. G., Padilla D. K., and Relyea R. A.,
"Ecological consequences of phenotypic plasticity," Trends in Ecology
and Evolution, vol. 20, no. 12, pp. 685-692, 2005.
[5] 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.
[6] Cole J. R., Chai B., Farris R. J., 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.
[7] Maidak B. L., Cole J. R., Parker Jr. C. T., et al., "A new version of the
RDP (Ribosomal Database Project)," Nucleic Acids Research, vol. 27, no.
1, pp. 171-173, 1999.
[8] Woese C.R., Kandler O., and Wheelis M. L., "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.
[9] Urwin R., and Maiden M. C. J., "Multi-locus sequence typing: a tool for
global epidemiology," Trends inMicrobiology, vol. 11, no. 10, pp. 479-
487, 2003.
[10] Sorokin A., Candelon B., Guilloux K., et al., "Multiplelocus 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.
[11] Maiden M. C. J., Bygraves J. A., Feil E., 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.
[12] Kouduka M., Sato D., Komori M., Kikuchi M., Miyamoto K., Kosaku A.,
Naimuddin M., Matsuoka A., and Nishigaki K., "A Solution for Universal
Classification of Species Based on Genomic DNA," International Journal
of Plant Genomics, Vol. 2007, Article ID 27894, 8 pages, 2007.
[13] Naimuddin M., Kurazono T., Zhangc Y., Watanabe T., Yamaguchi M.,
Nishigaki K., "Species-identification dots: a potent tool for developing
genome microbiology," Gene, 261:243-250. 2000.
[14] Futakami M., and Nishigaki K., "Measurement of DNA mutations caused
by seconds-period UV-irradiation," Chemistry Letters, vol. 36, no. 3, p.
358-359, 2007.
[15] Futakami M., Salimullah M., Miura T., Tokita S., and Nishigaki K.,
"Novel mutation assay with high sensitivity based on direct measurement
of genomic DNA alteration: comparable results to the Ames test," J.
Biochem. 141, 675-686, 2007.
[16] Kouduka M., Matsuoka A., and Nishigaki K., "Acquisition of genome
information from single-celled unculturable organisms (radiolaria) by
exploiting genome profiling (GP)," BMC Genomics, vol. 7, p. 135, 2006.
[17] Myers R. M., Fischer S. G., Lerman L. S., and Maniatis T., "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.
[18] Salimullah M., Mori M., Nishigaki K., "High throughput threedimensional
gel electrophoresis for versatile utilities: a stacked slice-gel
system for separation and reactions (4SR)," Genomics Proteomics
Bioinformatics, 4(1): 26-33, Feb 2006.
[19] Wang H., Qin M., Cutler AJ., "A simple method of preparing plant
samples for PCR," Nucleic Acids Res 21:4153-4154, 1993.
[20] Sakuma Y., and Nishigaki K., "Computer prediction of general PCR
products based on dynamical solution structures of DNA," Journal of
Biochemistry, vol. 116, no. 4, pp. 736-741, 1994.
[21] Hamano K., Takasawa T., Kurazono T., Okuyama Y., Nishigaki K.,
"Genome Profiling-Establishment and practical evaluation of its
methodology," Nikkashi 1996:54-61, 1996.
[22] Biyani M., Nishigaki K., "Hundredfold productivity of genome analysis
by introduction of microtemperature-gradient gel electrophoresis,"
Electrophoresis, 22:23-28, 2001.
[23] Nishigaki K., Husimi Y., Masuda M., Kaneko K., Tanaka T., "Strand
dissociation and cooperative melting of double-stranded DNAs detected
by denaturant gradient gel electrophoresis," J Biochem, 95:627-35, 1984.
[24] Watanabe T., Saito A., Takeuchi Y., Naimuddin M., Nishigaki K., "A
database for the provisional identification of species using only genotypes:
web-based genome profiling," Genome Biol, 3:00101.1, 2002.
[25] Nei M., Takezaki N., "Genetic distances and reconstruction of
phylogenetic trees from microsatellite DNA," Genetics, 144, 389-399,
1996.
[26] Jobson J. D., "Applied Multivariate Data Analysis, Categorical and
Multivariate Methods," Springer, New York, NY, USA, vol. 2, 1992.
[27] Ward Jr. J. H., "Hierarchical grouping to optimize an objective function,"
Journal of the American Statistical Association, vol. 58, no. 301, pp. 236-
244, 1963.
[28] On-web GP (http://gp.fms.saitama-u.ac.jp/)
@article{"International Journal of Biological, Life and Agricultural Sciences:63712", author = "Shamim Ahmed Koichi Nishigaki", title = "Error-Robust Nature of Genome Profiling Applied for Clustering of Species Demonstrated by Computer Simulation", abstract = "Genome profiling (GP), a genotype based technology, which exploits random PCR and temperature gradient gel electrophoresis, has been successful in identification/classification of organisms. In this technology, spiddos (Species identification dots) and PaSS (Pattern similarity score) were employed for measuring the closeness (or distance) between genomes. Based on the closeness (PaSS), we can buildup phylogenetic trees of the organisms. We noticed that the topology of the tree is rather robust against the experimental fluctuation conveyed by spiddos. This fact was confirmed quantitatively in this study by computer-simulation, providing the limit of the reliability of this highly powerful methodology. As a result, we could demonstrate the effectiveness of the GP approach for identification/classification of organisms.
", keywords = "Fluctuation, Genome profiling (GP), Pattern similarity score (PaSS), Robustness, Spiddos-shift.", volume = "1", number = "5", pages = "67-7", }
