Effects of recombination rate and gene density on transposable element distributions in Arabidopsis thaliana

Genome Research

Volumn 13, Issue 8, 2003, Pages 1897-1903

  Wright, Stephen I ^a   Agrawal, Newton ^b   Bureau, Thomas E ^b  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

^b MCGILL UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS; CAENORHABDITIS ELEGANS; CENTROMERE; CONTROLLED STUDY; CORRELATION ANALYSIS; DENSITY; EUKARYOTE; FERTILIZATION; GENE DISRUPTION; GENE EXPRESSION; GENE INSERTION; GENE LOCATION; GENE STRUCTURE; GENETIC MODEL; GENETIC RECOMBINATION; GENETIC SELECTION; GENETIC VARIABILITY; GENOME ANALYSIS; INBREEDING; INTRON; NATURAL SELECTION; NONHUMAN; PRIORITY JOURNAL; REVIEW; TRANSPOSON;

ARABIDOPSIS; CENTROMERE; CHROMOSOMES, PLANT; CODON; DNA TRANSPOSABLE ELEMENTS; DNA, INTERGENIC; DNA, PLANT; GENES, PLANT; GENOME, PLANT; MULTIVARIATE ANALYSIS; RECOMBINATION, GENETIC; SELECTION (GENETICS);

ARABIDOPSIS; ARABIDOPSIS THALIANA; CAENORHABDITIS; CAENORHABDITIS ELEGANS; EMBRYOPHYTA; EUKARYOTA; ILEX COOKII; INSERTION SEQUENCES; NEMATODA; TRANSPOSONS;

EID: 0043026711     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Review

References (53)

1. The Arabidopsis Genome Initiative 2000. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815.
2. Barnes, T.M., Kohara, Y., Coulson, A., and Hekimi, S. 1995. Meiotic recombination, noncoding DNA and genomic organization in Caenorhabditis elegans. Genetics 141: 159-179.
3. Bartolome, C., Maside, X., and Charlesworth, B. 2002. On the abundance and distribution of transposable elements in the genome of Drosophila melanogaster. Mol. Biol. Evol. 19: 926-937.
4. Biemont, C., Tsitrone, A., Vieira, C., and Hoogland, C. 1997. Transposable element distribution in Drosophila. Genetics 147: 1997-1999.
5. Boissinot, S., Entezam, A., and Furano, A.V. 2001. Selection against deleterious LINE-1-containing loci in the human lineage. Mol. Biol. Evol. 18: 926-935.
6. The C. elegans Sequencing Consortium 1998. Genome sequence of the nematode C. elegans: A platform for investigating biology. Science 282: 2012-2018.
7. Charlesworth, B. and Langley, C.H. 1986. The evolution of self-regulated transposition of transposable elements. Genetics 112: 359-383.
8. Charlesworth, B. and Langley, C.H. 1989. The population genetics of Drosophila transposable elements. Annu. Rev. Genet. 23: 251-287.
9. Charlesworth, D. and Charlesworth, B. 1995. Transposable elements in inbreeding and outbreeding populations. Genetics 140: 415-417.
10. Charlesworth, D. and Wright, S.I. 2001. Breeding systems and genome evolution. Curr. Opin. Genet. Dev. 11: 685-690.
11. Comeron, J.M., and Kreitman, M. 2000. The correlation between intron length and recombination in Drosophila. Dynamic equilibrium between mutational and selective forces. Genetics 156: 1175-1190.
12. Copenhaver, G.P., Nickel, K., Kuromori, T., Benito, M.I., Kaul, S., Lin, X., Bevan, M., Murphy, G., Harris, B., Parnell, L.D., et al. 1999. Genetic definition and sequence analysis of Arabidopsis centromeres. Science 286: 2468-2474.
13. Daborn, P.J., Yen, J.L., Bogwitz, M.R., Le Goff, G., Feil, E., Jeffers, S., Tijet, N., Perry, T., Heckel, D., Batterham, P., et al. 2002. A single p45O allele associated with insecticide resistance in Drosophila. Science 297: 2253-2256.
14. Devos, K.M., Brown, J.K., and Bennetzen, J.L. 2002. Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis. Genome Res. 12: 1075-1079.
15. Duret, L., Marais, G., and Biemont, C. 2000. Transposons but not retrotransposons are located preferentially in regions of high recombination rate in Caenorhabditis elegans. Genetics 156: 1661-1669.
16. Eickbush, T.H. and Furano, A.V. 2002. Fruit flies and humans respond differently to retrotransposons. Curr. Opin. Genet. Dev. 12: 669-674.
17. Fu, H., Zheng, Z., and Dooner, H.K. 2002. Recombination rates between adjacent genic and retrotransposon regions in maize vary by 2 orders of magnitude. Proc. Natl. Acad. Sci. 99: 1082-1087.
18. Gendrel, A.V., Lippman, Z., Yordan, C., Colot, V., and Martienssen, R.A. 2002. Dependence of heterochromatic histone H3 methylation patterns on the Arabidopsis gene DDM1. Science 297: 1871-1873.
19. Graustein, A., Gaspar, J.M., Walters, J.R., and Palopoli, M.F. 2002. Levels of DNA polymorphism vary with mating system in the nematode genus Caenorhabditis. Genetics 161: 99-107.
20. Harrison, P.M., Echols, N., and Gerstein, M.B. 2001. Digging for dead genes: An analysis of the characteristics of the pseudogene population in the Caenorhabditis elegans genome. Nucleic Acids Res. 29: 818-830.
21. Haupt, W., Fischer, T.C., Winderl, S., Fransz, P., and Torres-Ruiz, R.A. 2001. The CENTROMERE1 (CEN1) region of Arabidopsis thaliana: Architecture and functional impact of chromatin. Plant J. 27: 285-296.
22. Hill, W.G. and Robertson, A. 1966. The effect of linkage on limits to artificial selection. Genet. Res. 8: 269-294.
23. Jakubczak, J.L., Burke, W.D., and Eickbush, T.H. 1991. Retrotransposable elements R1 and R2 interrupt the rRNA genes of most insects. Proc. Natl. Acad. Sci. 88: 3295-3299.
24. Kapitonov, V.V. and Jurka, J. 2001. Rolling-circle transposons in eukaryotes. Proc. Natl. Acad. Sci. 98: 8714-8719.
25. Kliman, R.M. and Hey, J. 1993. Reduced natural selection associated with low recombination in Drosophila melanogaster. Mol. Biol. Evol. 10: 1239-1258.
26. Koch, M., Haubold, M., and Mitchell-Olds, T. 2000. Comparative evolutionary analysis of chalcone synthase and alcohol dehydrogenase loci in Arabidopsis, Arabis, and related genera (Brassicaceae). Mol. Biol. Evol. 17: 1483-1498.
27. Kumekawa, N., Hosouchi, T., Tsuruoka, H., and Kotani, H. 2000. The size and sequence organization of the centromeric region of Arabidopsis thaliana chromosome 5. DNA Res. 7: 315-321.
28. Lander, E.S., Linton, L.M., Birren, B., Nusbaum, C., Zody, M.C., Baldwin, J., Devon, K., Dewar, K., Doyle, M., Fitzhugh, W., et al. 2001. Initial sequencing and analysis of the human genome. Nature 409: 860-921.
29. Langley, C.H., Montgomery, E., Hudson, R., Kaplan, N., and Charlesworth, B. 1988. On the role of unequal exchange in the containment of transposable element copy number. Genet. Res. 52: 223-235.
30. Le, Q.H., Wright, S., Yu, Z., and Bureau, T. 2000. Transposon diversity in Arabidopsis thaliana. Proc. Natl. Acad. Sci. 97: 7376-7381.
31. Lichten, M. and Goldman, A.S. 1995. Meiotic recombination hotspots. Annu. Rev. Genet. 29: 423-444.
32. Long, A.D., Lyman, R.F., Morgan, A.H., Langley, C.H., and Mackay, T.F. 2000. Both naturally occurring insertions of transposable elements and intermediate frequency polymorphisms at the achaete-scute complex are associated with variation in bristle number in Drosophila melanogaster. Genetics 154: 1255-1269.
33. Malik, H.S. and Henikoff, S. 2002. Conflict begets complexity: The evolution of centromeres. Curr. Opin. Gene. Dev. 12: 711-718.
34. Matzke, M.A., Scheid, O.M., and Matzke, A.J. 1999. Rapid structural and epigenetic changes in polyploid and aneuploid genomes. BioEssays 21: 761-767.
35. McVean, G.A. and Charlesworth, B. 2000. The effects of Hill-Robertson interference between weakly selected mutations on patterns of molecular evolution and variation. Genetics 155: 929-944.
36. Medstrand, P., Van De Lagemaat, L.N., and Mager, D.L. 2002. Retroelement distributions in the human genome: Variations associated with age and proximity to genes. Genome Res. 12: 1483-1495.
37. Morgan, M.T. 2001. Transposable element number in mixed mating populations. Genet. Res. 77: 261-275.
38. Nekrutenko, A. and Li, W.H. 2001. Transposable elements are found in a large number of human protein-coding genes. Trends Genet. 17: 619-621.
39. Nuzhdin, S.V., Pasyukova, E.G., and Mackay, T.F. 1996. Positive association between copia transposition rate and copy number in Drosophila melanogaster. Proc. R. Soc. Lond. B. Biol. Sci. 263: 823-831.
40. Nuzhdin, S.V., Pasyukova, E.G., and Mackay, T.F. 1997. Accumulation of transposable elements in laboratory lines of Drosophila melanogaster. Genetica 100: 167-175.
41. Pavlicek, A., Clay, O., and Bernardi, G. 2002. Transposable elements encoding functional proteins: Pitfalls in unprocessed genomic data? FEBS Lett. 523: 252-253.
42. Pelissier, T., Tutois, S., Deragon, J.M., Tourmente, S., Genestier, S., and Picard, G. 1995. Athila, a new retroelement from Arabidopsis thaliana. Plant Mol. Biol. 29: 441-452.
43. Petrov, D.A., Aminetzach, Y.T., Davis, J.C., Bensasson, D., and Hirsh, A.E. 2003. Size matters: Non-LTR retrotransposable elements and ectopic recombination in Drosophila. Mol. Biol. Evol. 20: 880-892.
44. SanMiguel, P., Gaut, B.S., Tikhonov, A., Nakajima, Y., and Bennetzen, J.L. 1998. The paleontology of intergene retrotransposons of maize. Nat. Genet. 20: 43-45.
45. Schnable, P.S., Hsia, A.P., and Nikolau, B.J. 1998. Genetic recombination in plants. Curr. Opin. Plant. Biol. 1: 123-129.
46. Singer, T., Yordan, C., and Martienssen, R.A. 2001. Robertson's Mutator transposons in A. thaliana are regulated by the chromatin-remodeling gene Decrease in DNA Methylation (DDM1). Genes & Dev. 15: 591-602.
47. Surzycki, S.A. and Belknap, W.R. 1999. Characterization of repetitive DNA elements in Arabidopsis. J. Mol. Evol. 48: 684-691.
48. Virgin, J. B. and Bailey, J.P. 1998. The M26 hotspot of Schizosaccharomyces pombe stimulates meiotic ectopic recombination and chromosomal rearrangements. Genetics 149: 1191-1204.
49. Wilson, R.K. 1999. How the worm was won. The C. elegans genome sequencing project. Trends Genet. 15: 51-58.
50. Wright, S.I. and Finnegan, D. 2001. Genome evolution: Sex and the transposable element. Curr. Biol. 11: R296-R299.
51. Wright, S.I. and Schoen, D.J. 1999. Transposon dynamics and the breeding system. Genetica 107: 139-148.
52. Wright, S.I., Le, Q.H., Schoen, D.J., and Bureau, T.E. 2001. Population dynamics of an ac-like transposable element in self- and cross-pollinating Arabidopsis. Genetics 158: 1279-1288.
53. Yu, Z., Wright, S.I., and Bureau, T.E. 2000. Mutator-like elements in Arabidopsis thaliana. Structure, diversity and evolution. Genetics 156: 2019-2031.