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Journal of Biomedicine and Biotechnology
Volume 2012 (2012), Article ID 604076, 9 pages
http://dx.doi.org/10.1155/2012/604076
Research Article

Distribution of Genes and Repetitive Elements in the Diabrotica virgifera virgifera Genome Estimated Using BAC Sequencing

1Corn Insects and Crop Genetics Research Unit, ARS, USDA, Ames, IA 50011, USA
2Department of Entomology, Iowa State University, Ames, IA 50011, USA
3Department of Entomology, University of Nebraska, Lincoln, NE 68583, USA
4University of Illinois, Champaign-Urbana, IL 61801, USA
5North Central Agricultural Research Laboratory, Brookings, ARS, USDA, SD 57006, USA

Received 29 February 2012; Accepted 16 May 2012

Academic Editor: Yong Lim

Copyright © 2012 Brad S. Coates 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.

Linked References

  1. B. Grisart, W. Coppieters, F. Farnir et al., “Positional candidate cloning of a QTL in dairy cattle: identification of a missense mutation in the bovine DGAT1 gene with major effect on milk yield and composition,” Genome Research, vol. 12, no. 2, pp. 222–231, 2002. View at Publisher · View at Google Scholar · View at Scopus
  2. B. S. Coates, D. V. Sumerford, R. L. Hellmich, and L. C. Lewis, “Repetitive genome elements in a European corn borer, Ostrinia nubilalis, bacterial artificial chromosome library were indicated by bacterial artificial chromosome end sequencing and development of sequence tag site markers: implications for lepidopteran genomic research,” Genome, vol. 52, no. 1, pp. 57–67, 2009. View at Publisher · View at Google Scholar · View at Scopus
  3. T. Wicker, E. Schlagenhauf, A. Graner, T. J. Close, B. Keller, and N. Stein, “454 sequencing put to the test using the complex genome of barley,” BMC Genomics, vol. 7, article 275, 2006. View at Publisher · View at Google Scholar · View at Scopus
  4. K. Osoegawa, A. G. Mammoser, C. Wu et al., “A bacterial artificial chromosome library for sequencing the complete human genome,” Genome Research, vol. 11, no. 3, pp. 483–496, 2001. View at Publisher · View at Google Scholar · View at Scopus
  5. J. M. Kelley, C. E. Field, M. B. Craven et al., “High throughput direct end sequencing of BAC clones,” Nucleic Acids Research, vol. 27, no. 6, pp. 1539–1546, 1999. View at Publisher · View at Google Scholar · View at Scopus
  6. J. L. Krysan and T. F. Branson, “Biology, ecology and distribution of Diabrotica,” in Proceedings of the International Maize Virus Disease Colloquium and Workshop, O. H. Wooster, D. T. Gordon, J. K. Knoke, L. R. Nault, and R. M. Ritter, Eds., pp. 144–150, August 1982.
  7. M. E. Gray, T. W. Sappington, N. J. Miller, J. Moeser, and M. O. Bohn, “Adaptation and invasiveness of western corn rootworm: intensifying research on a worsening pest,” Annual Review of Entomology, vol. 54, pp. 303–321, 2009. View at Publisher · View at Google Scholar · View at Scopus
  8. L. J. Meinke, T. W. Sappington, D. W. Onstad et al., “Western corn rootworm (Diabrotica virgifera virgifera LeConte) population dynamics,” Agricultural and Forest Entomology, vol. 11, no. 1, pp. 29–46, 2009. View at Publisher · View at Google Scholar · View at Scopus
  9. F. Baca, “New member of the harmful entomofauna of Yugoslavia Diabrotica virgifera virgifera LeConte (Coleoptera: Chrysomelidae),” Zaštita Bilja, vol. 45, no. 2, pp. 125–131, 1994.
  10. N. Miller, A. Estoup, S. Toepfer et al., “Multiple transatlantic introductions of the western corn rootworm,” Science, vol. 310, no. 5750, p. 992, 2005. View at Publisher · View at Google Scholar · View at Scopus
  11. M. Ciosi, N. J. Miller, K. S. Kim, R. Giordano, A. Estoup, and T. Guillemaud, “Invasion of Europe by the western corn rootworm, Diabrotica virgifera virgifera: multiple transatlantic introductions with various reductions of genetic diversity,” Molecular Ecology, vol. 17, no. 16, pp. 3614–3627, 2008. View at Publisher · View at Google Scholar · View at Scopus
  12. H. C. Chiang, “Bionomics of the northern and western corn rootworms,” Annual Review of Entomology, vol. 18, pp. 47–72, 1973. View at Publisher · View at Google Scholar
  13. A. L. Kahler, A. E. Olness, O. R. Sutter, C. D. Dybing, and O. J. Devine, “Root damage by western corn rootworm and nutrient content in maize,” Agronomy Journal, vol. 77, pp. 769–774, 1985. View at Publisher · View at Google Scholar
  14. S. G. Jensen, “Laboratory transmission of maize chlorotic mottle virus by three species of corn rootworms,” Plant Disease, vol. 69, no. 10, pp. 864–868, 1985. View at Publisher · View at Google Scholar
  15. R. L. Gilbertson, W. M. Brown, E. G. Ruppel, and J. L. Capinera, “Association of corn stalk rot Fusarium spp. and western com rootworm beetles in Colorado,” Phytopathology, vol. 76, no. 12, pp. 1309–1314, 1986. View at Publisher · View at Google Scholar
  16. S. A. Lefko, T. M. Nowatzki, S. D. Thompson et al., “Characterizing laboratory colonies of western corn rootworm (Coleoptera: Chrysomelidae) selected for survival on maize containing event DAS-59122-7,” Journal of Applied Entomology, vol. 132, no. 3, pp. 189–204, 2008. View at Publisher · View at Google Scholar · View at Scopus
  17. L. N. Meihls, M. L. Higdon, B. D. Siegfried et al., “Increased survival of western corn rootworm on transgenic corn within three generations of on-plant greenhouse selection,” Proceedings of the National Academy of Sciences of the United States of America, vol. 105, no. 49, pp. 19177–19182, 2008. View at Publisher · View at Google Scholar · View at Scopus
  18. K. J. Oswald, B. W. French, C. Nielson, and M. Bagley, “Selection for Cry3Bb1 resistance in a genetically diverse population of nondiapausing western corn rootworm (Coleoptera: Chrysomelidae),” Journal of Economic Entomology, vol. 104, no. 3, pp. 1038–1044, 2011. View at Publisher · View at Google Scholar · View at Scopus
  19. A. J. Gassmann, J. L. Petzold-Maxwell, R. S. Keweshan, and M. W. Dunbar, “Field-evolved resistance to Bt maize by Western corn rootworm,” PLoS ONE, vol. 6, no. 7, Article ID e22629, 2011. View at Publisher · View at Google Scholar · View at Scopus
  20. J. L. Krysan, D. E. Foster, T. F. Branson, K. R. Ostlie, and W. S. Cranshaw, “Two years before the hatch: rootworms adapt to crop rotation,” Bulletin of the Entomological Society of America, vol. 32, no. 4, pp. 250–253, 1986.
  21. J. T. Shaw, J. H. Paullus, and W. H. Luckmann, “Corn rootworm oviposition in soybeans,” Journal of Economic Entomology, vol. 71, no. 2, pp. 189–191, 1978.
  22. A. E. Sammons, C. R. Edwards, L. W. Bledsoe, P. J. Boeve, and J. J. Stuart, “Behavioral and feeding assays reveal a western corn rootworm (Coleoptera: Chrysomelidae) variant that is attracted to soybean,” Environmental Entomology, vol. 26, no. 6, pp. 1336–1342, 1997. View at Scopus
  23. M. E. O'Neal, C. D. DiFonzo, and D. A. Landis, “Western corn rootworm (Coleoptera: Chrysomelidae) feeding on corn and soybean leaves affected by corn phenology,” Environmental Entomology, vol. 31, no. 2, pp. 285–292, 2002. View at Scopus
  24. T. W. Sappington, B. D. Siegfried, and T. Guillemaud, “Coordinated Diabrotica genetics research: accelerating progress on an urgent insect pest problem,” American Entomologist, vol. 52, no. 2, pp. 90–97, 2006.
  25. N. J. Miller, S. Richards, and T. W. Sappington, “The prospects for sequencing the western corn rootworm genome,” Journal of Applied Entomology, vol. 134, no. 5, pp. 420–428, 2010. View at Publisher · View at Google Scholar · View at Scopus
  26. T. F. Branson, “The selection of a non-diapause strain of Diabrotica virgifera (Coleoptera: Chrysomelidae),” Entomologia Experimentalis et Applicata, vol. 19, no. 2, pp. 148–154, 1976. View at Publisher · View at Google Scholar · View at Scopus
  27. J. Doležel and J. Bartoš, “Plant DNA flow cytometry and estimation of nuclear genome size,” Annals of Botany, vol. 95, no. 1, pp. 99–110, 2005. View at Publisher · View at Google Scholar · View at Scopus
  28. J. Doležel, J. Bartoš, H. Voglmayr, J. Greilhuber, and R. A. Thomas, “Nuclear DNA content and genome size of trout and human,” Cytometry Part A, vol. 51, no. 2, pp. 127–129, 2003. View at Scopus
  29. L. Clarke and J. Carbon, “A colony bank containing synthetic Col El hybrid plasmids representative of the entire E. coli genome,” Cell, vol. 9, no. 1, pp. 91–99, 1976. View at Scopus
  30. Y. S. Yim, P. Moak, H. Sanchez-Villeda et al., “A BAC pooling strategy combined with PCR-based screenings in a large, highly repetitive genome enables integration of the maize genetic and physical maps,” BMC Genomics, vol. 8, article 47, 2007. View at Publisher · View at Google Scholar · View at Scopus
  31. B. S. Coates, D. V. Sumerford, N. J. Miller et al., “Comparative performance of single nucleotide polymorphism and microsatellite markers for population genetic analysis,” Journal of Heredity, vol. 100, no. 5, pp. 556–564, 2009. View at Publisher · View at Google Scholar · View at Scopus
  32. 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. View at Scopus
  33. B. L. Cantarel, I. Korf, S. M. C. Robb et al., “MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes,” Genome Research, vol. 18, no. 1, pp. 188–196, 2008. View at Publisher · View at Google Scholar · View at Scopus
  34. L. M. Knolhoff, K. K. O. Walden, S. T. Ratcliffe, D. W. Onstad, and H. M. Robertson, “Microarray analysis yields candidate markers for rotation resistance in the western corn rootworm beetle, Diabrotica virgifera virgifera,” Evolutionary Applications, vol. 3, no. 1, pp. 17–27, 2010. View at Publisher · View at Google Scholar · View at Scopus
  35. B. D. Siegfried, N. Waterfield, and R. H. Ffrench-Constant, “Expressed sequence tags from Diabrotica virgifera virgifera midgut identify a coleopteran cadherin and a diversity of cathepsins,” Insect Molecular Biology, vol. 14, no. 2, pp. 137–143, 2005. View at Publisher · View at Google Scholar · View at Scopus
  36. M. Stanke, R. Steinkamp, S. Waack, and B. Morgenstern, “AUGUSTUS: a web server for gene finding in eukaryotes,” Nucleic Acids Research, vol. 32, pp. W309–W312, 2004. View at Publisher · View at Google Scholar · View at Scopus
  37. S. E. Lewis, S. M. J. Searle, N. Harris, et al., “Apollo: a sequence annotation editor,” Genome Biology, vol. 3, no. 12, Article ID R0082, 2002.
  38. X. Huang and A. Madan, “CAP3: a DNA sequence assembly program,” Genome Research, vol. 9, no. 9, pp. 868–877, 1999. View at Publisher · View at Google Scholar · View at Scopus
  39. R. S. Harris, Improved pairwise alignment of genomic DNA [Ph.D. thesis], The Pennsylvania State University, 2007.
  40. H. Li, B. Handsaker, A. Wysoker et al., “The sequence alignment/map format and SAMtools,” Bioinformatics, vol. 25, no. 16, pp. 2078–2079, 2009. View at Publisher · View at Google Scholar · View at Scopus
  41. K. Rutherford, J. Parkhill, J. Crook et al., “Artemis: sequence visualization and annotation,” Bioinformatics, vol. 16, no. 10, pp. 944–945, 2000. View at Scopus
  42. Y. Kapustin, A. Souvorov, T. Tatusova, and D. Lipman, “Splign: algorithms for computing spliced alignments with identification of paralogs,” Biology Direct, vol. 3, article 20, 2008. View at Publisher · View at Google Scholar · View at Scopus
  43. Y. Chen, F. Zhou, G. Li, and Y. Xu, “A recently active miniature inverted-repeat transposable element, Chunjie, inserted into an operon without disturbing the operon structure in Geobacter uraniireducens Rf4,” Genetics, vol. 179, no. 4, pp. 2291–2297, 2008. View at Publisher · View at Google Scholar · View at Scopus
  44. M. Zuker, “Mfold web server for nucleic acid folding and hybridization prediction,” Nucleic Acids Research, vol. 31, no. 13, pp. 3406–3415, 2003. View at Publisher · View at Google Scholar · View at Scopus
  45. E. Petitpierre, C. Segarra, and C. Juan, “Genome size and chromosomal evolution in leaf beetles (Coleoptera, Chrysomelidae),” Hereditas, vol. 119, no. 1, pp. 1–6, 1993. View at Publisher · View at Google Scholar · View at Scopus
  46. K. Sharaf, L. Horová, T. Pavlíček, E. Nevo, and P. Bureš, “Genome size and base composition in Oryzaephilus surinamensis (Coleoptera: Sylvanidae) and differences between native (feral) and silo pest populations in Israel,” Journal of Stored Products Research, vol. 46, no. 1, pp. 34–37, 2010. View at Publisher · View at Google Scholar · View at Scopus
  47. C. A. Thomas Jr., “The genetic organization of chromosomes,” Annual Review of Genetics, vol. 5, pp. 237–256, 1971. View at Scopus
  48. R. Hinegardner, “Evolution of genome size,” in Molecular Evolution, F. Ayala, Ed., pp. 179–199, Sinauer, Sunderland, Mass, USA, 1976.
  49. Tribolium Genome Sequencing Consortium, “The genome of the model beetle and pest Tribolium castaneum,” Nature, vol. 452, no. 6782, pp. 949–955, 2008.
  50. S. Wang, M. D. Lorenzen, R. W. Beeman, and S. J. Brown, “Analysis of repetitive DNA distribution patterns in the Tribolium castaneum genome,” Genome Biology, vol. 9, no. 3, article R61, 2008. View at Publisher · View at Google Scholar · View at Scopus
  51. L. Mao, T. C. Wood, Y. Yu et al., “Rice Transposable elements: a survey of 73,000 sequence-tagged-connectors,” Genome Research, vol. 10, no. 7, pp. 982–990, 2000. View at Publisher · View at Google Scholar · View at Scopus
  52. S. R. Cornman, M. C. Schatz, S. J. Johnston et al., “Genomic survey of the ectoparasitic mite Varroa destructor, a major pest of the honey bee Apis mellifera,” BMC Genomics, vol. 11, no. 1, article 602, 2010. View at Publisher · View at Google Scholar · View at Scopus
  53. M. D. Lorenzen, Z. Doyungan, J. Savard et al., “Genetic linkage maps of the red flour beetle, Tribolium castaneum, based on bacterial artificial chromosomes and expressed sequence tags,” Genetics, vol. 170, no. 2, pp. 741–747, 2005. View at Publisher · View at Google Scholar · View at Scopus
  54. Y. Pauchet, P. Wilkinson, H. Vogel et al., “Pyrosequencing the Manduca sexta larval midgut transcriptome: messages for digestion, detoxification and defence,” Insect Molecular Biology, vol. 19, no. 1, pp. 61–75, 2010. View at Publisher · View at Google Scholar · View at Scopus
  55. D. A. Rasmussen and M. A. F. Noor, “What can you do with 0.1× genome coverage? A case study based on a genome survey of the scuttle fly Megaselia scalaris (Phoridae),” BMC Genomics, vol. 10, article 382, 2009. View at Publisher · View at Google Scholar · View at Scopus
  56. K. S. Kim, B. W. French, D. V. Sumerford, and T. W. Sappington, “Genetic diversity in laboratory colonies of western corn rootworm (Coleoptera: Chrysomelidae), including a nondiapause colony,” Environmental Entomology, vol. 36, no. 3, pp. 637–645, 2007. View at Publisher · View at Google Scholar · View at Scopus
  57. M. B. Davis, J. Dietz, D. M. Standiford, and C. P. Emerson, “Transposable element insertions respecify alternative exon splicing in three Drosophila myosin heavy chain mutants,” Genetics, vol. 150, no. 3, pp. 1105–1114, 1998. View at Scopus
  58. M. G. Kidwell, “Transposable elements and the evolution of genome size in eukaryotes,” Genetica, vol. 115, no. 1, pp. 49–63, 2002. View at Publisher · View at Google Scholar · View at Scopus
  59. J. González, T. L. Karasov, P. W. Messer, and D. A. Petrov, “Genome-wide patterns of adaptation to temperate environments associated with transposable elements in Drosophila,” PLoS Genetics, vol. 6, no. 4, 2010. View at Publisher · View at Google Scholar · View at Scopus
  60. M. A. F. Noor and A. S. Chang, “Evolutionary Genetics: jumping into a New Species,” Current Biology, vol. 16, no. 20, pp. R890–R892, 2006. View at Publisher · View at Google Scholar · View at Scopus