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Advances in Bioinformatics
Volume 2010 (2010), Article ID 976792, 7 pages
Applying Small-Scale DNA Signatures as an Aid in Assembling Soybean Chromosome Sequences
USDA-ARS-CICGR Unit and Department of Agronomy, Iowa State University, Ames, IA 50011, USA
Received 19 November 2009; Accepted 28 June 2010
Academic Editor: Izabela Makalowska
Copyright © 2010 Myron Peto 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.
- J. Schmutz, S. B. Cannon, J. Schlueter et al., “Genome sequence of the palaeopolyploid soybean,” Nature, vol. 463, no. 7278, pp. 178–183, 2010.
- S. A. Jackson, D. Rokhsar, G. Stacey, R. C. Shoemaker, J. Schmutz, and J. Grimwood, “Toward a reference sequence of the soybean genome: a multiagency effort,” Crop Science, vol. 46, no. 1, pp. 55–61, 2006.
- D. L. Hyten, S. B. Cannon, Q. Song et al., “High-throughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence,” BMC Genomics, vol. 11, no. 1, article 38, 2010.
- D. L. Hyten, I.-Y. Choi, Q. Song et al., “A high density integrated genetic linkage map of soybean and the development of a 1536 universal soy linkage panel for quantitative trait locus mapping,” Crop Science, vol. 50, no. 3, pp. 960–968, 2010.
- L. K. Anderson, N. Salameh, H. W. Bass et al., “Integrating genetic linkage maps with pachytene chromosome structure in maize,” Genetics, vol. 166, no. 4, pp. 1923–1933, 2004.
- M. I. Tenaillon, M. C. Sawkins, L. K. Anderson, S. M. Stack, J. Doebley, and B. S. Gaut, “Patterns of diversity and recombination along chromosome 1 of maize (Zea mays ssp. mays L.),” Genetics, vol. 162, no. 3, pp. 1401–1413, 2002.
- W. Nelson and C. Soderlund, “Integrating sequence with FPC fingerprint maps,” Nucleic Acids Research, vol. 37, no. 5, article e36, 2009.
- P. Rice, L. Longden, and A. Bleasby, “EMBOSS: the European molecular biology open software suite,” Trends in Genetics, vol. 16, no. 6, pp. 276–277, 2000.
- N. Gill, S. Findley, J. G. Walling et al., “Molecular and chromosomal evidence for allopolyploidy in soybean,” Plant Physiology, vol. 151, no. 3, pp. 1167–1174, 2009.
- S. Batzoglou, D. B. Jaffe, K. Stanley et al., “ARACHNE: a whole-genome shotgun assembler,” Genome Research, vol. 12, no. 1, pp. 177–189, 2002.
- S. Kaul, H. L. Koo, J. Jenkins et al., “Analysis of the genome sequence of the flowering plant Arabidopsis thaliana,” Nature, vol. 408, no. 6814, pp. 796–815, 2000.
- International Rice Genome Sequencing Project, “The map-based sequence of the rice genome,” Nature, vol. 436, no. 7052, pp. 793–800, 2005.
- G. A. Tuskan, S. DiFazio, S. Jansson et al., “The genome of black cottonwood, Populus trichocarpa (Torr. & Gray),” Science, vol. 313, no. 5793, pp. 1596–1604, 2006.
- S. Karlin and C. Burge, “Dinucleotide relative abundance extremes: a genomic signature,” Trends in Genetics, vol. 11, no. 7, pp. 283–290, 1995.
- C. Burge, A. M. Campbell, and S. Karlin, “Over- and under-representation of short oligonucleotides in DNA sequences,” Proceedings of the National Academy of Sciences of the United States of America, vol. 89, no. 4, pp. 1358–1362, 1992.
- A. J. Gentles and S. Karlin, “Genome-scale compositional comparisons in Eukaryotes,” Genome Research, vol. 11, no. 4, pp. 540–546, 2001.
- S. Karlin, L. Brocchieri, J. Trent, B. E. Blaisdell, and J. Mrázek, “Heterogeneity of genome and proteome content in bacteria, archaea, and eukaryotes,” Theoretical Population Biology, vol. 61, no. 4, pp. 367–390, 2002.
- J. Josse, A. D. Kaiser, and A. Kornberg, “Enzymatic synthesis of deoxyribonucleic acid. VIII. Frequencies of nearest neighbor base sequences in deoxyribonucleic acid,” Journal of Biological Chemistry, vol. 236, pp. 864–875, 1961.
- A. Campbell, J. Mrázek, and S. Karlin, “Genome signature comparisons among prokaryote, plasmid, and mitochondrial DNA,” Proceedings of the National Academy of Sciences of the United States of America, vol. 96, no. 16, pp. 9184–9189, 1999.
- S. Karlin and I. Ladunga, “Comparisons of eukaryotic genomic sequences,” Proceedings of the National Academy of Sciences of the United States of America, vol. 91, no. 26, pp. 12832–12836, 1994.
- S. Karlin and J. Mrázek, “Compositional differences within and between eukaryotic genomes,” Proceedings of the National Academy of Sciences of the United States of America, vol. 94, no. 19, pp. 10227–10232, 1997.
- M. W. J. van Passel, E. E. Kuramae, A. C. M. Luyf, A. Bart, and T. Boekhout, “The reach of the genome signature in prokaryotes,” BMC Evolutionary Biology, vol. 6, article 84, 2006.
- F. Collyn, L. Guy, M. Marceau, M. Simonet, and C.-A. H. Roten, “Describing ancient horizontal gene transfers at the nucleotide and gene levels by comparative pathogenicity island genometrics,” Bioinformatics, vol. 22, no. 9, pp. 1072–1079, 2006.
- B. Fertil, M. Massin, S. Lespinats, C. Devic, P. Dumee, and A. Giron, “GENSTYLE: exploration and analysis of DNA sequences with genomic signature,” Nucleic Acids Research, vol. 33, no. 2, pp. W512–W515, 2005.
- S. Karlin, “Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial genomes,” Trends in Microbiology, vol. 9, no. 7, pp. 335–343, 2001.
- A. Paz, V. Kirzhner, E. Nevo, and A. Korol, “Coevolution of DNA-interacting proteins and genome "dialect",” Molecular Biology and Evolution, vol. 23, no. 1, pp. 56–64, 2006.
- S. Karlin, J. Mrázek, and A. M. Campbell, “Compositional biases of bacterial genomes and evolutionary implications,” Journal of Bacteriology, vol. 179, no. 12, pp. 3899–3913, 1997.
- J. Du, Z. Tian, C. S. Hans, et al., “Evolutionary conservation, diversity and specificity of LTR retrotransposons in flowering plants: new insights from genome-wide analysis and multi-specific comparison,” The Plant Journal, vol. 63, no. 4, pp. 584–598, 2010.
- W. Li and P. Miramontes, “Large-scale oscillation of structure-related DNA sequence features in human chromosome 21,” Physical Review E, vol. 74, no. 2, part 1, Article ID 021912, 2006.
- O. Jaillon, J.-M. Aury, B. Noel et al., “The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla,” Nature, vol. 449, no. 7161, pp. 463–467, 2007.
- S. Karlin and L. R. Cardon, “Computational DNA sequence analysis,” Annual Review of Microbiology, vol. 48, pp. 619–654, 1994.
- C. J. Benham and C. Bi, “The analysis of stress-induced duplex destabilization in long genomic DNA sequences,” Journal of Computational Biology, vol. 11, no. 4, pp. 519–543, 2004.
- E. Yeramian, S. Bonnefoy, and G. Langsley, “Physics-based gene identification: proof of concept for plasmodium falciparum,” Bioinformatics, vol. 18, no. 1, pp. 190–193, 2002.
- E. Yeramian and L. Jones, “GeneFizz: a web tool to compare genetic (coding/non-coding) and physical (helix/coil) segmentations of DNA sequences. Gene discovery and evolutionary perspectives,” Nucleic Acids Research, vol. 31, no. 13, pp. 3843–3849, 2003.
- K. J. Breslauer, R. Frank, H. Blocker, and L. A. Marky, “Predicting DNA duplex stability from the base sequence,” Proceedings of the National Academy of Sciences of the United States of America, vol. 83, no. 11, pp. 3746–3750, 1986.
- R. Gonzalez, Y. Zeng, V. Ivanov, and G. Zocchi, “Bubbles in DNA melting,” Journal of Physics Condensed Matter, vol. 21, no. 3, Article ID 034102, 9 pages, 2009.
- W. A. Kibbe, “OligoCalc: an online oligonucleotide properties calculator,” Nucleic Acids Research, vol. 35, pp. W43–W46, 2007.
- J. SantaLucia Jr., “A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics,” Proceedings of the National Academy of Sciences of the United States of America, vol. 95, no. 4, pp. 1460–1465, 1998.