The use of next generation sequencing and junction sequence analysis bioinformatics to achieve molecular characterization of crops improved through modern biotechnology

Plant Genome

Volumn 5, Issue 3, 2012, Pages 149-163

  Kovalic, David ^a   Garnaat, Carl ^a   Guo, Liang ^a   Yan, Yongpan ^a   Groat, Jeanna ^a   Silvanovich, Andre ^a   Ralston, Lyle ^a   Huang, Mingya ^a   Tian, Qing ^a   Christian, Allen ^a   Cheikh, Nordine ^a   Hjelle, Jerry ^a   Padgette, Stephen ^a   Bannon, Gary ^a  

^a MONSANTO COMPANY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84882455681     PISSN: None     EISSN: 19403372     Source Type: Journal    
DOI: 10.3835/plantgenome2012.10.0026     Document Type: Article

References (22)

1. Ajay, S.S., S.C. Parker, H.O. Abaan, K.F. Fajardo, and E.H. Margulies. 2011. Accurate and comprehensive sequencing of personal genomes. Genome Res. 21(9):1498-1505. doi:10.1101/gr.123638.111
2. Altschul, S.F., W. Gish, W. Miller, E.W. Myers, and D.J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215(3):403-410.
3. Altschul, S.F., T.L. Madden, A.A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D.J. Lipman. 1997. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25(17):3389-3402. doi:10.1093/nar/25.17.3389
4. Cerny, R.E., J.T. Bookout, C.A. CaJacob, J.R. Groat, J.L. Hart, G.R. Heck, et al. 2010. Development and characterization of a cotton (Gossypium hirsutum L.) event with enhanced reproductive resistance to glyphosate. Crop Sci. 50(4):1375-1384. doi:10.2135/cropsci2009.06.0286
5. Clarke, L., and J. Carbon. 1976. A colony bank containing synthetic Col El hybrid plasmids representative of the entire E. coli genome. Cell 9(1):91-99. doi:10.1016/0092-8674(76)90055-6
6. CLC bio. 2012. CLC main workbench v. 6.6.6, assemble sequences. CLC bio, Cambridge, MA.
7. Codex Alimentarius. 2003. Guideline for the conduct of food safety assessment of foods derived from recombinant-DNA plants. Codex Alimentarius Commission, Joint FAO/WHO Food Standards Programme, Food and Agriculture Organization of the United Nations, Rome, Italy.
8. Codex Alimentarius. 2009. Foods derived from modern biotechnology. 2nd ed. Codex Alimentarius Commission, Joint FAO/WHO Food Standards Programme, Food and Agriculture Organization of the United Nations, Rome, Italy.
9. Ewing, B., and P. Green. 1998. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8(3):186-194.
10. Ewing, B., L. Hillier, M.C. Wendl, and P. Green. 1998. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8(3):175-185.
11. Heck, G.R., C.L. Armstrong, J.D. Astwood, C.F. Behr, J.T. Bookout, S.M. Brown, et al. 2005. Development and characterization of a CP4 EPSPS-based, glyphosate-tolerant corn event. Crop Sci. 45(1):329-339. doi:10.2135/cropsci2005.0329
12. Langmead, B., C. Trapnell, M. Pop, and S.L. Salzberg. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10(3):R25. doi:10.1186/gb-2009-10-3-r25
13. Miller, J.R., S. Koren, and G. Sutton. 2010. Assembly algorithms for nextgeneration sequencing data. Genomics 95(6):315-327. doi:10.1016/j. ygeno.2010.03.001
14. Ming, R., S. Hou, Y. Feng, Q. Yu, A. Dionne-Laporte, J.H. Saw, et al. 2008. Th e draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature 452(7190):991-996. doi:10.1038/nature06856
15. Minoche, A.E., J.C. Dohm, and H. Himmelbauer. 2011. Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and genome analyzer systems. Genome Biol. 12(11):R112. doi:10.1186/gb-2011-12-11-r112
16. Novocraft Technologies. 2008. Novoalign version 2.06.09. Novocraft Technologies, Selangor, Malaysia.
17. Rogers, S.O., and A.J. Bendich. 1985. Extraction of DNA from milligram amounts of fresh, herbarium and mummified plant tissues. Plant Mol. Biol. 5(2):69-76. doi:10.1007/BF00020088
18. Schmutz, J., S.B. Cannon, J. Schlueter, J. Ma, T. Mitros, W. Nelson, et al. 2010. Genome sequence of the palaeopolyploid soybean. Nature 463(7278):178-183. doi:10.1038/nature08670
19. Southern, E.M. 1975. Detection of specific sequences among DNA fragments separated by gel electrophoresis. J. Mol. Biol. 98(3):503-517. doi:10.1016/S0022-2836(75)80083-0
20. Vaughn, T., T. Cavato, G. Brar, T. Coombe, T. DeGooyer, S. Ford, et al. 2005. A method of controlling corn rootworm feeding using a Bacillus thuringiensis protein expressed in transgenic maize. Crop Sci. 45(3):931-938. doi:10.2135/cropsci2004.0304
21. Wang, J., W. Wang, R. Li, Y. Li, G. Tian, L. Goodman, et al. 2008. Th e diploid genome sequence of an Asian individual. Nature 456(7218):60-65. doi:10.1038/nature07484
22. Wei, H., C. Th errien, A. Blanchard, S. Guan, and Z. Zhu. 2008. Th e Fidelity Index provides a systematic quantitation of star activity of DNA restriction endonucleases. Nucleic Acids Res. 36(9):E50. doi:10.1093/nar/gkn182