Contrasting patterns of transposable-element insertion polymorphism and nucleotide diversity in autotetraploid and allotetraploid Arabidopsis species

Genetics

Volumn 179, Issue 1, 2008, Pages 581-592

  Hazzouri, Khaled M ^a   Mohajer, Arezou ^a   Dejak, Steven I ^b   Otto, Sarah P ^c   Wright, Stephen I ^a  

^a YORK UNIVERSITY   (Canada)

^b UNIVERSITY OF TORONTO   (Canada)

^c UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS; ARTICLE; CONTROLLED STUDY; DNA POLYMORPHISM; DNA TRANSPOSITION; GENE INSERTION; GENETIC VARIABILITY; GENOME; NATURAL SELECTION; NONHUMAN; POLYPLOIDY; POPULATION SIZE; PRIORITY JOURNAL; SEQUENCE ANALYSIS; TETRAPLOIDY; TRANSPOSON; BIOLOGICAL MODEL; COMPARATIVE STUDY; DNA SEQUENCE; GENETICS; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; POPULATION GENETICS; STATISTICAL MODEL;

ARABIDOPSIS; ARABIDOPSIS ARENOSA; ARABIDOPSIS SUECICA; ARABIDOPSIS THALIANA;

PRIMER DNA;

ARABIDOPSIS; BASE SEQUENCE; DNA PRIMERS; DNA TRANSPOSABLE ELEMENTS; GENETICS, POPULATION; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; POLYPLOIDY; SEQUENCE ANALYSIS, DNA; VARIATION (GENETICS);

EID: 52049107891     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.107.085761     Document Type: Article

References (58)

1. ACARKAN, A., M. ROSSBERG, M. KOCH and R. SCHMIDT, 2000 Comparative genome analysis reveals extensive conservation of genome organisation for Arabidopsis thaliana and Capsella rubella. Plant J. 23: 55-62.
2. ALTSCHUL, S. F., T. L. MADDEN, A. A. SCHÄFFER, J. ZHANG, Z. ZHANG et al., 1997 Gapped BLASTand PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25: 3389-3402.
3. ARABIDOPSIS GENOME INITIATIVE, 2000 Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815.
4. BARRINGER, B. C., 2007 Polyploidy and self-fertilization in flowering plants. Am. J. Bot. 94: 1527-1533.
5. BENNETT, J. H., 1968 Mixed self- and cross-fertilization in a tetrasomic species. Biometrics 3: 485-500.
6. BIÉMONT, C., A. TSITRONE, C. VIEIRA and C. HOOGLAND, 1997 Transposable element distribution in Drosophila. Genetics. 147: 1997-1999.
7. BOISSINOT, S., J. DAVIS, A. ENTEZAM, D. PETROV and A. V. FURANO, 2006 Fitness cost of LINE-1 (L1) activity in humans. Proc. Natl. Acad. Sci. USA 103: 9590-9594.
8. CHARLESWORTH, B., and D. CHARLESWORTH, 1983 The population dynamics of transposable elements. Genet. Res. 42: 1-27.
9. CHARLESWORTH, B., and C. H. LANGLEY, 1989 The population genetics of Drosophila transposable elements. Annu. Rev. Genet. 23: 251-287.
10. CHARLESWORTH, B., A. LAPID and D. CANADA, 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.
11. CHARLESWORTH, B., P. D. SNIEGOWSKI and W. STEPHAN, 1994 The evolutionary dynamics of repetitive DNA in eukaryotes. Nature 371: 215-220.
12. CHARLESWORTH, B., C. H. LANGLEY and P. SNIEGOWSKI, 1997 Transposable element distributions in Drosophila. Genetics. 147: 1993-1995.
13. CHARLESWORTH, D., and B. CHARLESWORTH, 1995 Quantitative genetics in plants: the effect of the breeding system on genetic variability. Evolution 49 (5): 911-920.
14. COEN, E. S., and R. CARPENTER, 1986 Transposable elements in Antirrhinum majus: generators of genetic diversity. Trends Genet. 2: 292-296.
15. DELLAPORTA, S. L., J. WOOD and J. B. HICKS, 1983 A plant DNA minipreparation: version II. Plant Mol. Biol. Rep. 1: 19-21.
16. FINGERMAN, E. G., P. G. DOMBROWSKI, C. A. FRANCIS and P. D. SNIEGOWSKI, 2003 Distribution and sequence analysis of a novel Ty3-like element in natural Saccharomyces paradoxus isolates. Yeast 20: 761-770.
17. FOXE, J. P., V. U. DAR, H. ZHENG, M. NORDBORG, B. S. GAUT et al., 2008 Selection on amino acid substitutions in Arabidopsis. Mol. Biol. Evol. (in press).
18. GAUT, B. S., M. LE THIERRY D'ENNEQUIN, A. S. PEEK and M. C. SAWKINS, 2000 Maize as a model for the evolution of plant nuclear genomes. Proc. Natl. Acad. Sci. USA 97: 7008-7015.
19. HANSSON, B., A. KAWABE, S. PREUSS, H. KUITTINEN and D. CHARLESWORTH, 2006 Comparative gene mapping in Arabidopsis lyrata chromosomes 1 and 2 and the corresponding A. thaliana chromosome 1: recombination rates, rearrangements and centromere location. Genet. Res. 87: 75-85.
20. HENK, A. D., R. F. WARREN and R. W. INNES, 1999 A new Ac-like transposon of Arabidopsis is associated with a deletion of the RPS5 disease resistance gene. Genetics 151: 1581-1589.
21. HOOGLAND, C., and C. BIÉMONT, 1996 Chromosomal distribution of transposable elements in Drosophila melanogaster: test of the ectopic recombination model for maintenance of insertion site number. Genetics. 144: 197-204.
22. HUGHES, A. L., and R. FRIEDMAN, 2004 Transposable element distribution in the yeast genome reflects a role in repeated genomic rearrangement events on an evolutionary time scale. Genetica 121: 181-185.
23. HUGHES, A. L., R. FRIEDMAN, V. EKOLLU and J. R. ROSE, 2003 Nonrandom association of transposable elements with duplicated genomic blocks in Arabidopsis thaliana. Mol. Phylogenet. Evol. 29: 410-416.
24. JAKOBSSON, M., J. HAGENBLAD, S. TAVARÉ, T. SÄLL, C. HALLDÉN et al., 2006 A unique recent origin of the allotetraploid species Arabidopsis suecica: evidence from nuclear DNA markers. Mol. Biol. Evol. 23 (6): 1217-1231.
25. KASHKUSH, K., M. FELDMAN and A. A. LEVY, 2003 Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat. Nat. Genet. 33: 102-106.
26. KAWABE, A., B. HANSSON, A. FORREST, J. HAGENBLAD and D. CHARLESWORTH, 2006 Comparative gene mapping in Arabidopsis lyrata chromosomes 6 and 7 and A. thaliana chromosome IV: evolutionary history, rearrangements and local recombination rates. Genet. Res. 88: 45-56.
27. KORSWAGEN, H. C., R. M. DURBIN, M. T. SMITS and R. H. A. PASTERK, 1996 Transposon Tc1-derived, sequence tagged sites in Caenorhabditis elegans as markers for gene mapping. Proc. Natl. Acad. Sci. USA 93: 14680-14685.
28. KUITTINEN, H., A. A. DE HAAN, C. VOGL, S. OIKARINEN, J. LEPPALA et al., 2004 Comparing the linkage maps of the close relatives Arabidopsis lyrata and A. thaliana. Genetics 168: 1575-1584.
29. LABRADOR, M., M. FARRE, F. UTZET and A. FONTDEVILA, 1999 Interspecific hybridization increases transposition rates of Osvaldo. Mol. Biol. Evol. 16: 931-937.
30. LE, Q. H., S. WRIGHT, Z. YU and T. BUREAU, 2000 Transposon diversity in Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA 97: 7376-7381.
31. MABLE, B. K., M. H. SCHIERUP and D. CHARLESWORTH, 2003 Estimating the number, frequency, and dominance of S-alleles in a natural population of Arabidopsis lyrata (Brassicaceae) with sporophytic control of self-incompatibility. Heredity 90: 422-431.
32. MADLUNG, A., R. W. MASUELLI, B. WATSON, S. H. REYNOLDS and J. DAVISON, 2002 Remodeling of DNA methylation and phenotypic and transcriptional changes in synthetic Arabidopsis allotetraploids. Plant Physiol. 129: 733-746.
33. MADLUNG, A., R. W. MASUELLI, B. WATSON, S. H. REYNOLDS, J. DAVISON et al., 2005 Remodeling of DNA methylation and phenotypic and transcriptional changes in synthetic Arabidopsis allotetraploids. Plant Physiol. 129: 733-746.
34. MATZKE, M. A., and A. J. M. MATZKE, 1998 Polyploidy and transposons. Trends Ecol. Evol. 13: 241.
35. MONTGOMERY, E. A., S.-M. HUANG, C. H. LANGLEY and B. H. JUDD, 1991 Chromosome rearrangement by ectopic recombination in Drosophila melanogaster: genome structure and evolution. Genetics 129: 1085-1098.
36. MORGAN, M. T., 2001 Transposable element number in mixed mating populations. Genet. Res. 77: 261-275.
37. O'NEILL, R. J., M. J. O'NEILL and J. A. GRAVES, 1998 Undermethylation associated with retroelement activation and chromosome remodelling in an interspecific mammalian hybrid. Nature 393: 68-72.
38. PETROV, D. A., Y. T. AMINETZACH, J. C. DAVIS, D. BENSASSON and A. E. HIRSH, 2003 Size matters: non-LTR retrotransposable elements and ectopic recombination in Drosophila. Mol. Biol. Evol. 20: 880-892.
39. SÄLL, T., C. LIND-HALLDÉN, M. JAKOBSSON and C. HALLDÉN, 2004 Mode of reproduction in Arabidopsis suecica. Hereditas 141: 313-317.
40. SCHRANZ, M. E., A. J. WINDSOR, B. H. SONG, A. LAWTON-RAUH and T. MITCHELL-OLDS, 2007 Comparative genetic mapping in Boechera stricta, a close relative of Arabidopsis. Plant Physiol. 144: 286-298.
41. SCHWARZBACH, A. E., and L. H. RIESEBERG, 2002 Likely multiple origins of diploid hybrid subflower species. Mol. Ecol. 11: 1703-1715.
42. SHALEV, G., and A. A. LEVY, 1997 The maize transposable element Ac induces recombination between the donor site and a homologous ectopic sequence. Genetics 146: 1143-1151.
43. TAJIMA, F., 1989 Statistical methods to test for nucleotide mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
44. TENAILLON, M. I., M. C. SAWKINS, L. K. ANDERSON, S. M. STACK, J. DOEBLEY et al., 2002 Patterns of diversity and recombination along chromosome 1 of maize (Zea mays L. ssp. mays). Genetics 162: 1401-1413.
45. THON, M. R., H. PAN, S. DIENER, J. PEPALAS, A. TARO et al., 2006 The role of transposable element clusters in genome evolution and loss of synteny in the rice blast fungus Magnaporthe oryzae. Genome Biol. 7: R16.
46. TIKHONOV, A. P., P. J. SAN MIGUEL, Y. NAKAJIMA, N. M. GORENSTEIN, J. L. BENNETZEN et al., 1999 Colinearity and its exceptions in orthologous Adh regions of maize and sorghum. Proc. Natl. Acad. Sci. USA 96 (13): 7409-7414.
47. UNGERER, M. C., S. C. STRAKOSH and Y. ZHEN, 2006 Genome expansion in three hybrid sunflower species is associated with retrotransposon proliferation. Curr. Biol. 16: R872-R873.
48. VAN DEN BROECK, D., T. MAES, M. SAUER, J. ZETHO, P. DE KEUKELEIRE et al., 1998 Transposon display identifies individual transposable elements in high copy number lines. Plant J. 13: 121-129.
49. VOS, P., R. HOGERS, M. BLEEKER, M. REIJANS, T. VAN DE LEE et al., 1995 AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res. 23: 4407-4414.
50. WATTERSON, G., 1975 On the number of segregation sites in genetical models without recombination. Theor. Popul. Biol. 7: 256-276.
51. WAUGH, R., K. MCLEAN, A. J. FLAVELL, S. R. PEARCE, A. KUMAR et al., 1997 Genetic distribution of BARE-1 retrotransposable elements in the barley genome revealed by sequence-specific amplification polymorphisms. Mol. Gen. Genet. 253: 687-694.
52. WRIGHT, S. I., and D. J. SCHOEN, 1999 Transposon dynamics and the breeding system. Genetica 107 (1-3): 139-148.
53. WRIGHT, S. I., Q. H. LE, D. J. SCHOEN and T. E. BUREAU, 2001 Population dynamics of an Ac-like transposable element in self- and cross-pollinating Arabidopsis. Genetics 158: 1279-1288.
54. WRIGHT, S. I, N. AGRAWAL and T. E. BUREAU, 2003 Effects of recombination rate and gene density on transposable element distributions in Arabidopsis thaliana. Genome Res. 13 (8): 1897-1903.
55. WRIGHT, S. I., J. P. FOXE, L. DE ROSE-WILSON, A. KAWABE, M. LOOSELEY et al., 2006 Testing for effects of recombination rate on nucleotide diversity in natural populations of Arabidopsis lyrata. Genetics 174: 1421-1430.
56. ZHANG, J., and T. PETERSON, 1999 Genome rearrangements by nonlinear transposons in maize. Genetics 153: 1403-1410.
57. ZHANG, X., and S. WESSLER, 2004 Genome-wide comparative analysis of the transposable elements in related species Arabidopsis thaliana and Brassica oleracea. Proc. Natl. Acad. Sci. USA 101: 5589-5594.
58. ZIOLKOWSKI, P. A., M. KACZMAREK, D. BABULA and J. SADOWSKI, 2006 Genome evolution in Arabidopsis/Brassica: conservation and divergence of ancient rearranged segments and their breakpoints. Plant J. 47: 63-74.