Distribution of genes and repetitive elements in the Diabrotica virgifera virgifera genome estimated using BAC sequencing

Journal of Biomedicine and Biotechnology

Volumn 2012, Issue , 2012, Pages

  Coates, Brad S ^a,b   Alves, Analiza P ^c   Wang, Haichuan ^c   Walden, Kimberly K O ^d   French, B Wade ^e   Miller, Nicholas J ^c   Abel, Craig A ^a   Robertson, Hugh M ^d   Sappington, Thomas W ^a,b   Siegfried, Blair D ^c  

^a AGRICULTURAL RESEARCH SERVICE   (United States)

^b IOWA STATE UNIVERSITY   (United States)

^c UNIVERSITY OF NEBRASKA LINCOLN   (United States)

^d UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^e NORTH CENTRAL AGRICULTURAL RESEARCH LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BAC PROTEIN; BAC1 PROTEIN; DNA; PROTEIN; UNCLASSIFIED DRUG;

ARTICLE; CLONE; DIABROTICA VIRGIFERA VIRGIFERA; FLOW CYTOMETRY; GENE SEQUENCE; GENOME SIZE; INTERSPERSED REPEAT; INTRON; MAIZE; MOLECULAR GENETICS; NONHUMAN; NUCLEOTIDE SEQUENCE; UNINDEXED SEQUENCE; WORM; AGAR GEL ELECTROPHORESIS; ANIMAL; BACTERIAL ARTIFICIAL CHROMOSOME; BEETLE; DNA SEQUENCE; GENE; GENE LIBRARY; GENETICS; GENOMICS; HAPLOTYPE; METHODOLOGY; NUCLEOTIDE REPEAT; TRANSPOSON;

DIABROTICA VIRGIFERA VIRGIFERA; ZEA MAYS;

ANIMALS; BEETLES; CHROMOSOMES, ARTIFICIAL, BACTERIAL; DNA TRANSPOSABLE ELEMENTS; ELECTROPHORESIS, AGAR GEL; FLOW CYTOMETRY; GENE LIBRARY; GENES, INSECT; GENOME SIZE; GENOMICS; HAPLOTYPES; MOLECULAR SEQUENCE ANNOTATION; REPETITIVE SEQUENCES, NUCLEIC ACID; SEQUENCE ANALYSIS, DNA;

EID: 84866128215     PISSN: 11107243     EISSN: 11107251     Source Type: Journal    
DOI: 10.1155/2012/604076     Document Type: Article

References (60)

1. Grisart B., Coppieters W., Farnir F., Karim L., Ford C., Berzi P., Cambisano N., Mni M., Reid S., Simon P., Spelman R., Georges M., Snell R., 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 2002 12 2 222 231 2-s2.0-0036175484 10.1101/gr.224202 (Pubitemid 34162989)
2. Coates B. S., Sumerford D. V., Hellmich R. L., Lewis L. C., 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 2009 52 1 57 67 2-s2.0-65349175865 10.1139/G08-104
3. Wicker T., Schlagenhauf E., Graner A., Close T. J., Keller B., Stein N., 454 sequencing put to the test using the complex genome of barley. BMC Genomics 2006 7, article 275 2-s2.0-33750688196 10.1186/1471-2164-7-275 (Pubitemid 44697663)
4. Osoegawa K., Mammoser A. G., Wu C., Frengen E., Zeng C., Catanese J. J., De Jong P. J., A bacterial artificial chromosome library for sequencing the complete human genome. Genome Research 2001 11 3 483 496 2-s2.0-0035080952 10.1101/gr.169601 (Pubitemid 32243858)
5. Kelley J. M., Field C. E., Craven M. B., Bocskai D., Kim U. J., Rounsley S. D., Adams M. D., High throughput direct end sequencing of BAC clones. Nucleic Acids Research 1999 27 6 1539 1546 2-s2.0-0033559110 10.1093/nar/27.6.1539 (Pubitemid 29206298)
6. Krysan J. L., Branson T. F., Wooster O. H., Gordon D. T., Knoke J. K., Nault L. R., Ritter R. M., Biology, ecology and distribution of Diabrotica. Proceedings of the International Maize Virus Disease Colloquium and Workshop August 1982 144 150
7. Gray M. E., Sappington T. W., Miller N. J., Moeser J., Bohn M. O., Adaptation and invasiveness of western corn rootworm: intensifying research on a worsening pest. Annual Review of Entomology 2009 54 303 321 2-s2.0-60549083851 10.1146/annurev.ento.54.110807.090434
8. Meinke L. J., Sappington T. W., Onstad D. W., Guillemaud T., Miller N. J., Komáromi J., Levay N., Furlan L., Kiss J., Toth F., Western corn rootworm (Diabrotica virgifera virgifera LeConte) population dynamics. Agricultural and Forest Entomology 2009 11 1 29 46 2-s2.0-58549117739 10.1111/j.1461-9563.2008.00419.x
9. Baca F., New member of the harmful entomofauna of Yugoslavia Diabrotica virgifera virgifera LeConte (Coleoptera: Chrysomelidae). Zaštita Bilja 1994 45 2 125 131
10. Miller N., Estoup A., Toepfer S., Bourguet D., Lapchin L., Derridj S., Kim K. S., Reynaud P., Furlan L., Guillemaud T., Multiple transatlantic introductions of the western corn rootworm. Science 2005 310 5750 992 2-s2.0-27744569906 10.1126/science.1115871 (Pubitemid 41611905)
11. Ciosi M., Miller N. J., Kim K. S., Giordano R., Estoup A., Guillemaud T., Invasion of Europe by the western corn rootworm, Diabrotica virgifera virgifera: multiple transatlantic introductions with various reductions of genetic diversity. Molecular Ecology 2008 17 16 3614 3627 2-s2.0-49249097860 10.1111/j.1365-294X.2008.03866.x
12. Chiang H. C., Bionomics of the northern and western corn rootworms. Annual Review of Entomology 1973 18 47 72 10.1146/annurev.en.18.010173.000403
13. Kahler A. L., Olness A. E., Sutter O. R., Dybing C. D., Devine O. J., Root damage by western corn rootworm and nutrient content in maize. Agronomy Journal 1985 77 769 774 10.2134/agronj1985.00021962007700050023x
14. Jensen S. G., Laboratory transmission of maize chlorotic mottle virus by three species of corn rootworms. Plant Disease 1985 69 10 864 868 10.1094/PD-69-864
15. Gilbertson R. L., Brown W. M., Ruppel E. G., Capinera J. L., Association of corn stalk rot Fusarium spp. and western com rootworm beetles in Colorado. Phytopathology 1986 76 12 1309 1314 10.1094/Phyto-76-1309
16. Lefko S. A., Nowatzki T. M., Thompson S. D., Binning R. R., Pascual M. A., Peters M. L., Simbro E. J., Stanley B. H., Characterizing laboratory colonies of western corn rootworm (Coleoptera: Chrysomelidae) selected for survival on maize containing event DAS-59122-7. Journal of Applied Entomology 2008 132 3 189 204 2-s2.0-40849092779 10.1111/j.1439-0418.2008.01279.x (Pubitemid 351392976)
17. Meihls L. N., Higdon M. L., Siegfried B. D., Miller N. J., Sappington T. W., Ellersieck M. R., Spencer T. A., Hibbard B. E., 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 2008 105 49 19177 19182 2-s2.0-58049220275 10.1073/pnas.0805565105
18. Oswald K. J., French B. W., Nielson C., Bagley M., Selection for Cry3Bb1 resistance in a genetically diverse population of nondiapausing western corn rootworm (Coleoptera: Chrysomelidae). Journal of Economic Entomology 2011 104 3 1038 1044 2-s2.0-79960380963 10.1603/EC10312
19. Gassmann A. J., Petzold-Maxwell J. L., Keweshan R. S., Dunbar M. W., Field-evolved resistance to Bt maize by Western corn rootworm. PLoS ONE 2011 6 7 2-s2.0-79960900035 10.1371/journal.pone.0022629 e22629
20. Krysan J. L., Foster D. E., Branson T. F., Ostlie K. R., Cranshaw W. S., Two years before the hatch: rootworms adapt to crop rotation. Bulletin of the Entomological Society of America 1986 32 4 250 253
21. Shaw J. T., Paullus J. H., Luckmann W. H., Corn rootworm oviposition in soybeans. Journal of Economic Entomology 1978 71 2 189 191
22. Sammons A. E., Edwards C. R., Bledsoe L. W., Boeve P. J., Stuart J. J., Behavioral and feeding assays reveal a western corn rootworm (Coleoptera: Chrysomelidae) variant that is attracted to soybean. Environmental Entomology 1997 26 6 1336 1342 2-s2.0-0000446839 (Pubitemid 127493603)
23. O'Neal M. E., DiFonzo C. D., Landis D. A., Western corn rootworm (Coleoptera: Chrysomelidae) feeding on corn and soybean leaves affected by corn phenology. Environmental Entomology 2002 31 2 285 292 2-s2.0-0036557214 (Pubitemid 36178130)
24. Sappington T. W., Siegfried B. D., Guillemaud T., Coordinated Diabrotica genetics research: accelerating progress on an urgent insect pest problem. American Entomologist 2006 52 2 90 97
25. Miller N. J., Richards S., Sappington T. W., The prospects for sequencing the western corn rootworm genome. Journal of Applied Entomology 2010 134 5 420 428 2-s2.0-77954064749 10.1111/j.1439-0418.2009.01448.x
26. Branson T. F., The selection of a non-diapause strain of Diabrotica virgifera (Coleoptera: Chrysomelidae). Entomologia Experimentalis et Applicata 1976 19 2 148 154 2-s2.0-0008969023 10.1007/BF00345776
27. Doležel J., Bartoš J., Plant DNA flow cytometry and estimation of nuclear genome size. Annals of Botany 2005 95 1 99 110 2-s2.0-21644446318 10.1093/aob/mci005 (Pubitemid 41214452)
28. Doležel J., Bartoš J., Voglmayr H., Greilhuber J., Thomas R. A., Nuclear DNA content and genome size of trout and human. Cytometry Part A 2003 51 2 127 129 2-s2.0-0347275780 (Pubitemid 37521519)
29. Clarke L., Carbon J., A colony bank containing synthetic Col El hybrid plasmids representative of the entire E. coli genome. Cell 1976 9 1 91 99 2-s2.0-0017085802
30. Yim Y. S., Moak P., Sanchez-Villeda H., Musket T. A., Close P., Klein P. E., Mullet J. E., McMullen M. D., Fang Z., Schaeffer M. L., Gardiner J. M., Coe E. H., Davis G. L., 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 2007 8, article 47 2-s2.0-33947361960 10.1186/1471-2164-8-47 (Pubitemid 46443323)
31. Coates B. S., Sumerford D. V., Miller N. J., Kim K. S., Sappington T. W., Siegfried B. D., Lewis L. C., Comparative performance of single nucleotide polymorphism and microsatellite markers for population genetic analysis. Journal of Heredity 2009 100 5 556 564 2-s2.0-69249216496 10.1093/jhered/esp028
32. Rice P., Longden L., Bleasby A., EMBOSS: the European molecular biology open software suite. Trends in Genetics 2000 16 6 276 277 2-s2.0-0034201441
33. Cantarel B. L., Korf I., Robb S. M. C., Parra G., Ross E., Moore B., Holt C., Alvarado A. S., Yandell M., MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Research 2008 18 1 188 196 2-s2.0-38049057159 10.1101/gr.6743907
34. Knolhoff L. M., Walden K. K. O., Ratcliffe S. T., Onstad D. W., Robertson H. M., Microarray analysis yields candidate markers for rotation resistance in the western corn rootworm beetle, Diabrotica virgifera virgifera. Evolutionary Applications 2010 3 1 17 27 2-s2.0-77954271352 10.1111/j.1752-4571.2009.00094.x
35. Siegfried B. D., Waterfield N., Ffrench-Constant R. H., Expressed sequence tags from Diabrotica virgifera virgifera midgut identify a coleopteran cadherin and a diversity of cathepsins. Insect Molecular Biology 2005 14 2 137 143 2-s2.0-17444424279 10.1111/j.1365-2583.2004.00538.x (Pubitemid 40534279)
36. Stanke M., Steinkamp R., Waack S., Morgenstern B., AUGUSTUS: a web server for gene finding in eukaryotes. Nucleic Acids Research 2004 32 W309 W312 2-s2.0-3242889577 10.1093/nar/gkh379 (Pubitemid 38997349)
37. Lewis S. E., Searle S. M. J., Harris N., Apollo: a sequence annotation editor. Genome Biology 2002 3 12 R0082
38. Huang X., Madan A., CAP3: a DNA sequence assembly program. Genome Research 1999 9 9 868 877 2-s2.0-0032849859 10.1101/gr.9.9.868 (Pubitemid 29488446)
39. Harris R. S., Improved pairwise alignment of genomic DNA [Ph.D. thesis] 2007 The Pennsylvania State University
40. Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R., The sequence alignment/map format and SAMtools. Bioinformatics 2009 25 16 2078 2079 2-s2.0-68549104404 10.1093/bioinformatics/ btp352
41. Rutherford K., Parkhill J., Crook J., Horsnell T., Rice P., Rajandream M. A., Barrell B., Artemis: sequence visualization and annotation. Bioinformatics 2000 16 10 944 945 2-s2.0-0033635022
42. Kapustin Y., Souvorov A., Tatusova T., Lipman D., Splign: algorithms for computing spliced alignments with identification of paralogs. Biology Direct 2008 3, article 20 2-s2.0-46649115430 10.1186/1745-6150-3-20 (Pubitemid 351943441)
43. Chen Y., Zhou F., Li G., Xu Y., A recently active miniature inverted-repeat transposable element, Chunjie, inserted into an operon without disturbing the operon structure in Geobacter uraniireducens Rf4. Genetics 2008 179 4 2291 2297 2-s2.0-55749115436 10.1534/genetics.108.089995
44. Zuker M., Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Research 2003 31 13 3406 3415 2-s2.0-0042121256 10.1093/nar/gkg595 (Pubitemid 37442169)
45. Petitpierre E., Segarra C., Juan C., Genome size and chromosomal evolution in leaf beetles (Coleoptera, Chrysomelidae). Hereditas 1993 119 1 1 6 2-s2.0-0027442093 10.1111/j.1601-5223.1993.00001.x (Pubitemid 23349153)
46. Sharaf K., Horová L., Pavlíček T., Nevo E., Bureš P., 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 2010 46 1 34 37 2-s2.0-76549136480 10.1016/j.jspr.2009.08.001
47. Thomas C. A. Jr., The genetic organization of chromosomes. Annual Review of Genetics 1971 5 237 256 2-s2.0-0000822856
48. Hinegardner R., Ayala F., Evolution of genome size. Molecular Evolution 1976 Sunderland, Mass, USA Sinauer 179 199
49. Tribolium Genome Sequencing Consortium, The genome of the model beetle and pest Tribolium castaneum. Nature 2008 452 6782 949 955
50. Wang S., Lorenzen M. D., Beeman R. W., Brown S. J., Analysis of repetitive DNA distribution patterns in the Tribolium castaneum genome. Genome Biology 2008 9 3, article R61 2-s2.0-45549103936 10.1186/gb-2008-9-3-r61 (Pubitemid 351959554)
51. Mao L., Wood T. C., Yu Y., Budiman M. A., Tomkins J., Woo S. S., Sasinowski M., Presting G., Frisch D., Goff S., Dean R. A., Wing R. A., Rice Transposable elements: a survey of 73,000 sequence-tagged-connectors. Genome Research 2000 10 7 982 990 2-s2.0-0033854088 10.1101/gr.10.7.982 (Pubitemid 30608633)
52. Cornman S. R., Schatz M. C., Johnston S. J., Chen Y. P., Pettis J., Hunt G., Bourgeois L., Elsik C., Anderson D., Grozinger C. M., Evans J. D., Genomic survey of the ectoparasitic mite Varroa destructor, a major pest of the honey bee Apis mellifera. BMC Genomics 2010 11 1, article 602 2-s2.0-77958129830 10.1186/1471-2164-11-602
53. Lorenzen M. D., Doyungan Z., Savard J., Snow K., Crumly L. R., Shippy T. D., Stuart J. J., Brown S. J., Beeman R. W., Genetic linkage maps of the red flour beetle, Tribolium castaneum, based on bacterial artificial chromosomes and expressed sequence tags. Genetics 2005 170 2 741 747 2-s2.0-22144457440 10.1534/genetics.104.032227 (Pubitemid 40980675)
54. Pauchet Y., Wilkinson P., Vogel H., Nelson D. R., Reynolds S. E., Heckel D. G., Ffrench-Constant R. H., Pyrosequencing the Manduca sexta larval midgut transcriptome: messages for digestion, detoxification and defence. Insect Molecular Biology 2010 19 1 61 75 2-s2.0-73649120985 10.1111/j.1365-2583.2009. 00936.x
55. Rasmussen D. A., Noor M. A. F., 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 2009 10, article 382 2-s2.0-69549112948 10.1186/1471-2164-10-382
56. Kim K. S., French B. W., Sumerford D. V., Sappington T. W., Genetic diversity in laboratory colonies of western corn rootworm (Coleoptera: Chrysomelidae), including a nondiapause colony. Environmental Entomology 2007 36 3 637 645 2-s2.0-34250758230 10.1603/0046-225X(2007)36[637:GDILCO]2.0.CO;2 (Pubitemid 46954971)
57. Davis M. B., Dietz J., Standiford D. M., Emerson C. P., Transposable element insertions respecify alternative exon splicing in three Drosophila myosin heavy chain mutants. Genetics 1998 150 3 1105 1114 2-s2.0-0031770676 (Pubitemid 28510038)
58. Kidwell M. G., Transposable elements and the evolution of genome size in eukaryotes. Genetica 2002 115 1 49 63 2-s2.0-0036021699 10.1023/A:1016072014259 (Pubitemid 34842170)
59. González J., Karasov T. L., Messer P. W., Petrov D. A., Genome-wide patterns of adaptation to temperate environments associated with transposable elements in Drosophila. PLoS Genetics 2010 6 4 2-s2.0-77952410170 10.1371/journal.pgen.1000905
60. Noor M. A. F., Chang A. S., Evolutionary Genetics: jumping into a New Species. Current Biology 2006 16 20 R890 R892 2-s2.0-33750005972 10.1016/j.cub.2006.09.022 (Pubitemid 44573829)