Abundance and distribution of transposable elements in two drosophila QTL mapping resources

Molecular Biology and Evolution

Volumn 30, Issue 10, 2013, Pages 2311-2327

  Cridland, Julie M ^a   Macdonald, Stuart J ^b   Long, Anthony D ^a   Thornton, Kevin R ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF KANSAS   (United States)

Author keywords

DGRP; DSPR; Genomics; Population genetics; Transposable element

Indexed keywords

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ARTICLE; AUTOSOME; DROSOPHILA MELANOGASTER; EXON; GENE FUNCTION; GENE INSERTION; GENOME; GENOMICS; INBRED STRAIN; INTRON; LONG TERMINAL REPEAT; MULTIGENE FAMILY; NONHUMAN; NUCLEOTIDE SEQUENCE; PARALOGY; PENETRANCE; PHENOTYPE; POPULATION GENETICS; QUANTITATIVE TRAIT LOCUS MAPPING; RETROPOSON; TRANSPOSON; X CHROMOSOME;

DGRP; DSPR; GENOMICS; POPULATION GENETICS; TRANSPOSABLE ELEMENT;

ANIMALS; COMPUTATIONAL BIOLOGY; DNA TRANSPOSABLE ELEMENTS; DROSOPHILA MELANOGASTER; EVOLUTION, MOLECULAR; FEMALE; GENETIC FITNESS; GENOME; MALE; MODELS, GENETIC; MULTIGENE FAMILY; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI; SELECTION, GENETIC; X CHROMOSOME;

EID: 84888588595     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/mst129     Document Type: Article

References (76)

1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol. 215:403-410.
2. Aminetzach YT, Macpherson JM, Petrov DA. 2005. Pesticide resistance via transposition-mediated adaptive gene truncation in Drosophila. Science 309:764-767.
3. Bartolome C, Maside X, Charlesworth B. 2002. On the abundance and distribution of transposable elements in the genome of Drosophila melanogaster. Mol Biol Evol. 19:926-937.
4. Bennetzen JL. 2000. Transposable element contributions to plant gene and genome evolution. Plant Mol Biol. 42:251-269.
5. Bergman CM, Bensasson D. 2007. Recent LTR retrotransposon insertion contrasts with waves of non-LTR insertion since speciation in Drosophila melanogaster. Proc Natl Acad Sci U S A. 104: 11340-11345.
6. Biemont C, Vieira C. 2006. Junk DNA as an evolutionary force. Nature 443:521-524.
7. Birchler JA, Hiebert JC. 1989. Interaction of the Enhancer of white-apricot with transposable element alleles at the white locus in Drosophila melanogaster. Genetics 122:129-138.
8. Birchler JA, Hiebert JC, Rabinow L. 1989. Interaction of the mottler of white with transposable element alleles at the white locus in Drosophila melanogaster. Genes Dev. 3:73-84.
9. Bowen NJ, McDonald JF. 2001. Drosophila euchromatic LTR retrotransposons are much younger than the host species in which they reside. Genome Res. 11:1527-1540.
10. Carr M, Soloway JR, Robinson TE, Brookfield JF. 2002. Mechanisms regulating copy numbers of six LTR retrotransposons in the genome of Drosophila melanogaster. Chromosoma 110:511-518.
11. Charlesworth B. 1994. The effect of background selection against deleterious mutations on weakly selected linked variants. Genet Res. 63: 213-227.
12. Charlesworth B, Jarne P, Assimacopoulos S. 1994. The distribution of transposable elements within and between chromosomes in a population of Drosophila melanogaster. III. Element abundances in heterochromatin. Genet Res. 64:183-197.
13. Charlesworth B, Langley CH. 1989. The population genetics of Drosophila transposable elements. Annu Rev Genet. 23:251-287.
14. Charlesworth B, Lapid A. 1989. A study of ten families of transposable elements on X chromosomes from a population of Drosophila melanogaster. Genet Res. 54:113-125.
15. Charlesworth B, Lapid A, Canada D. 1992. The distribution of transposable elements within and between chromosomes in a population of Drosophila melanogaster. I. Element frequencies and distribution. Genet Res. 60:103-114.
16. Chen GK, Marjoram P, Wall JD. 2009. Fast and flexible simulation of DNA sequence data. Genome Res. 19:136-142.
17. Chung H, Bogwitz MR, McCart C, Andrianopoulos A, Ffrench-Constant RH, Batterham P, Daborn PJ. 2007. Cis-regulatory elements in the accord retrotransposon result in tissue-specific expression of the Drosophila melanogaster insecticide resistance gene Cyp6g1. Genetics 175:1071-1077.
18. Cutter AD, Good JM, Pappas CT, SaundersMA, Starrett DM, Wheeler TJ. 2005. Transposable element orientation bias in the Drosophila melanogaster genome. J Mol Evol. 6:733-741.
19. Daborn P, Boundy S, Yen J, Pittendrigh B, Ffrench-Constant R. 2001. DDT resistance in Drosophila correlates with Cyp6g1 over-expression and confers cross-resistance to the neonicotinoid imidacloprid. Mol Genet Genomics. 266:556-563.
20. Deloger M, Cavalli FMG, Lerat E, Biemont C, Sagot M-F, Vieira C. 2009. Identification of expressed transposable element insertions in the sequenced genome of Drosophila melanogaster. Gene 439: 55-62.
21. Dworkin I, Palsson A, Gibson G. 2005. Replication of an Egfr-wing shape association in a wild-caught cohort of Drosophila melanogaster. Genetics 169:2115-2125.
22. Ewing B, Green P. 1998. Base-calling of automated sequencer traces using Phred. II. Error probabilities. Genome Res. 8:186-194.
23. Gruber JD, Genissel A, Macdonald SJ, Long AD. 2007. How repeatable are associations between polymorphisms in achaete-scute and bristle number variation in Drosophila. Genetics 175:1987-1997.
24. Haddrill PR, Charlesworth B, Halligan DL, Andolfatto P. 2005. Patterns of intron sequence evolution in Drosophila are dependent upon length and GC content. Genome Biol. 6:R67.
25. Hahn MW, Han MV, Han S-G. 2007. Gene family evolution across 12 Drosophila genomes. PLoS Genet. 3:e197.
26. Hirschhorn JN, Daly MJ. 2005. Genome-wide association studies for common diseases and complex traits. Nat Rev Genet. 6: 95-108.
27. Hudson RR, Kaplan NL. 1995. Deleterious background selection with recombination. Genetics 141:1605-1617.
28. Hufford MB, Xu X, van Heerwaarden J, et al. (25 co-authors). 2012. Comparative population genomics of maize domestication and improvement. Nat Genet. 44:808-811.
29. Kaminker JS, Bergman CM, Kronmiller B, et al. (12 co-authors). 2002. The transposable elements of the Drosophila melanogaster euchromatin: A genomics perspective. Genome Biol. 3:RESEARCH0084.
30. Kapitonov VV, Jurka J. 2003. Molecular paleontology of transposable elements in the Drosophila melanogaster genome. Proc Natl Acad Sci U S A. 100:6569-6574.
31. Kazazian HH. 2004. Mobile elements: drivers of genome evolution. Science 303:1626-1632.
32. Kidwell MG. 2002. Transposable elements and the evolution of genome size in eukaryotes. Genetica 115:49-63.
33. King EG, Macdonald SJ, Long AD. 2012a. Properties and power of the Drosophila synthetic population resource for the routine dissection of complex traits. Genetics 191:935-949.
34. King EG, Merkes CM, McNeil CL, Hoofer SR, Sen S, Broman KW, Long AD, Macdonald SJ. 2012b. Genetic dissection of a model complex trait using the Drosophila synthetic population resource. Genome Res. 22:1558-1566.
35. Kofler R, Betancourt AJ, Schlotterer C. 2012. Sequencing of pooled DNA samples (Pool-Seq) uncovers complex dynamics of transposable element insertions in Drosophila melanogaster. PLoS Genet. 8: e1002487.
36. Langley CH, Montgomery E, Hudson R, Kaplan N, Charlesworth B. 1988. On the role of unequal exchange in the containment of transposable element copy number. Genet Res. 52:223-235.
37. Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760.
38. Linheiro RS, Bergman CM. 2012. Whole genome resequencing reveals natural target site preferences of transposable elements in Drosophila melanogaster. PLoS One 7:e30008.
39. Lipatov M, Lenkov L, Petrov DA, Bergman CM. 2005. Paucity of chimeric gene-transposable elements in the Drosophila melanogaster genome. BMC Biol. 3:24.
40. Long AD, Lyman RF, Morgan AH, Langley CH, Mackay TFC. 2000. Both naturally occurring insertions of transposable elements and intermediate frequency polymorphisms at the achaete-scute complex are associated with bristle number in Drosophila melanogaster. Genetics 154:1255-1269.
41. Lonnig W-E, Saedler H. 2002. Chromosome rearrangements and transposable elements. Annu Rev Genet. 36:389-410.
42. Macdonald SJ, Long AD. 2007. Joint estimates of quantitative trait locus effect and frequency using synthetic recombinant populations of Drosophila melanogaster. Genetics 176: 1261-1281.
43. Macdonald SJ, Pastinen T, Long AD. 2005. The effect of polymorphisms in the Enhancer of split gene complex on bristle number variation in a large wild-caught cohort of Drosophila melanogaster. Genetics 171: 1741-1756.
44. Mackay TFC. 1984. Jumping genes meet abdominal bristles: hybrid dysgenesis- induced quantitative variation in Drosophila melanogaster. Genet Res. 44:231-237.
45. Mackay TFC. 1989. Transposable elements and fitness in Drosophila melanogaster. Genome 31:284-295.
46. Mackay TFC. 2010. Mutations and quantitative genetic variation: lessons from Drosophila. Philos Trans R Soc Lond B Biol Sci. 365: 1229-1239.
47. Mackay TFC, Langley CH. 1990. Molecular and phenotypic variation in the achaete-scute region of Drosophila melanogaster. Nature 348: 64-66.
48. Mackay TFC, Lyman RF, Jackson MS. 1992. Effects of P element insertions on quantitative traits in Drosophila melanogaster. Genetics 130: 315-332.
49. Mackay TFC, Richards S, Stone EA, et al. (52 co-authors). 2012. The Drosophila melanogaster genetic reference panel. Nature 482: 173-178.
50. Meyer LR, Zweig AS, Hinrichs AS, et al. (32 co-authors). 2013. The UCSC genome browser database: extensions and updates 2013. Nucleic Acids Res. 41:D64-D69.
51. Montgomery E, Charlesworth B, Langley CH. 1987. A test for the role of natural selection in the stabilization of transposable element copy number in a population of Drosophila melanogaster. Genet Res. 49: 31-41.
52. Montgomery EA, Huang S-M, Langley CH, Judd BH. 1991. Chromosome rearrangement by ectopic recombination in Drosophila melanogaster: genome structure and evolution. Genetics 129: 1085-1098.
53. NCI-NHGRI Working Group on Replication in Association Studies. 2007. Replicating genotype-phenotype associations. Nature 447: 655-660.
54. Nuzhdin SV, Mackay TFC. 1994. The genomic rate of transposable element movement in Drosophila melanogaster. Mol Biol Evol. 12: 180-181.
55. Nuzhdin SV, Pasyukova EG, Mackay TFC. 1997. Accumulation of transposable elements in laboratory lines of Drosophila melanogaster. Genetica 100:167-175.
56. Ometto L, Stephan W, Lorenzo DD. 2005. Insertion/deletion and nucleotide polymorphism data reveal constraints in Drosophila melanogaster introns and intergenic regions. Genetics 169: 1521-1527.
57. Palsson A, Gibson G. 2004. Association between nucleotide variation in Egfr and wing shape in Drosophila melanogaster. Genetics 167: 1187-1198.
58. Petrov DA, Fiston-Lavier A-S, Lipatov M, Lenkov K, Gonzalez J. 2011. Population genomics of transposable elements in Drosophila melanogaster. Mol Biol Evol. 28:1633-1644.
59. Presgraves DC. 2006. Intron length evolution in Drosophila.Mol Biol Evol. 13:2203-2213.
60. Quinian AR, Hall IM. 2010. BEDTools: A flexible suite of utilities for comparing genomic features. Bioinformatics 26:841-842.
61. R Development Core Team. 2008. R: A language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing. [cited 2013 May 1] Available from: http://www.R-project.org.
62. Rizzon C, Marais G, Gouy M, Biemont C. 2002. Recombination rate and the distribution of transposable elements in the Drosophila melanogaster genome. Genome Res. 12:400-407.
63. ackton TB, Kulathinal RJ, Bergman CM, Quinlan AR, Dopman EB, Carneiro M, Marth GT, Hartl DL, Clark AG. 2009. Population genomic inferences from sparse high-throughput sequencing of two populations of Drosophila melanogaster. Genome Biol Evol. 1: 449-465.
64. Sakurai M, Aoki T, Yoshikawa S, et al. (11 co-authors). 2009. Differentially expressed Drl and Drl-2 play opposing roles in Wnt5 signaling during Drosophila olfactory system development. J Neurosci. 29: 4972-4980.
65. Schmidt JM, Good RT, Appleton B, et al. (11 co-authors). 2010. Copy number variation and transposable elements feature in recent, ongoing adaptation at the Cyp6g1 locus. PLoS Genet. 6: e1000998.
66. Shrimpton AE, Mackay TFC, Brown AJL. 1990. Transposable element-induced response to artificial selection in Drosophila melanogaster: molecular analysis of selection lines. Genetics 125:803-811.
67. Slotkin RK, Martienssen R. 2007. Transposable elements and the epigenetic regulation of the genome. Nat Rev Genet. 8:272-285.
68. Smith PA, Corces VG. 1991. Drosophila transposable elements: mechanisms of mutagenesis and interactions with the host genome. Adv Genet. 29:229-300.
69. Thornton K. 2003. Libsequence; a C++ class library for evolutionary genetic analysis. Bioinformatics 19:2325-2327.
70. Vazquez JF, Albornoz J, Dominguez A. 2007. Direct determination of the effects of genotype and extreme temperature on the transposition of roo in long-term mutation accumulation lines of Drosophila melanogaster. Mol Genet Genomics. 278:653-664.
71. Voight BF, Pritchard JK. 2005. Confounding from cryptic relatedness in case-control association studies. PLoS Genet. 1:e32.
72. Wakeley J. 2009. Coalescent theory: An introduction. Greenwood Village: Roberts and Company Publishers.
73. Wicker T, Sabot F, Hua-Van A, et al. (13 co-authors). 2007. A unified classification system for eukaryotic transposable elements. Nat Rev Genet. 8:973-982.
74. Xing J, Witherspoon DJ, Jorde LB. 2013. Mobile element biology: new possibilities with high-throughput sequencing. Trends Genet. 29: 280-289.
75. Yoshikawa S, McKinnon RD, Kokel M, Thomas JB. 2003. Wntmediated axon guidance via Drosophila derailed receptor. Nature 422:583-588.
76. Zachar Z, Bingham PM. 1982. Regulation of white locus expression: The structure of mutant alleles at the white locus of Drosophila melanogaster. Cell 30:529-541.