Variation and Evolution in Plants and Microorganisms Toward a New Synthesis 50 Years After Stebbins (2000) / Chapter Skim
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10 Transposons and Genome Evolution in Plants
10 Transposons and Genome Evolution in Plants
Pages 167-186
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From page 167... ...
The thesis is developed that the mechanisms that control transposition are a reflection of the more general capacity of eukaryotic organisms to detect, mark, and retain duplicated DNA through repressive chromatin structures. The 50 years that have elapsed since the publication of Stebbins' Variation and Evolution in Plants have seen extraordinary changes in our understanding of how genomes are structured and how they change in evolution.
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From page 168... ...
Today we know that transposons constitute a large fraction even a majority of the DNA in some species of plants and animals, among them mice, humans, and such agriculturally important plants as corn and wheat. Given what we now know about genome organization, it is paradoxical that the discovery of transposable elements lagged so far behind the discovery of the basic laws of genetic transmission.
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From page 169... ...
Because genetic mapping is predicated on the invariance of recombination frequencies, there was plentiful evidence that genes have fixed chromosomal locations. Written at this time, Stebbins' book in general and in particular his third chapter, titled "The Basis of Individual Variation," clearly acknowledges the existence of many chromosomal differences among organisms in a population, including duplications, inversions, translocations, and deletions.
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From page 170... ...
Several prominent geneticists, among them Correns and Goldschmidt, dismissed unstable mutations as a special category of "diseased genes" (Goldschmidt, 1938; Fedoroff, 1998~. It was their view that little could be learned from the study of such mutations that was relevant to the study of conventional genes.
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From page 171... ...
small. Hence the genetic impact of transposable elements was limited.
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From page 172... ...
THE PARADOX One might think that given their abundance, transposable elements would rapidly randomize genome order. Yet the results of a decade of comparative plant genome studies has revealed that gene order is surprisingly conserved between species.
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From page 173... ...
A detailed sequence comparison of the small region around the maize and sorghum Adhl loci reveals a surprising amount of change in a constant framework (Tikhonov et al., 1999~. The sorghum and maize genomes are 750 and 2,500 Mbp, respectively.
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From page 174... ...
Plant transposons generate additional copies of themselves by virtue of excising from only one of two newly replicated sister chromatids and reinserting into as yet unreplicated sites (Fedoroff, 1989~. Absent countering forces, genome expansion is an inevitable consequence of the properties of transposable elements.
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From page 175... ...
AMPLIFICATION AND REARRANGEMENT New copies of transposons and retrotransposons provide new sites of homology for unequal crossing over. Evidence that transposable elements are central to the evolutionary restructuring of genomes has accumulated in every organism for which sufficient sequence data exist.
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From page 176... ...
And indeed, preferential loss of nonredundant sequences early after polyploidization has been detected in wheat (Feldman et al., 1997~. CONTROLLING TRANSCRIPTION, RECOMBINATION, AND TRANSPOSITION Despite our growing awareness of the abundance of plant transposable elements and the role they have played in shaping contemporary chromosome organization, the fact is they eluded discovery for the first half century of intensive genetic analysis.
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From page 177... ...
He suggested that the transcriptional "noise reduction" mechanisms that arose at the prokaryote/eukaryote boundary were the nuclear envelope, chromatin, and separation of the transcriptional and translational machinery, as well as RNA processing, capping, and polyadenylation to discriminate authentic from spurious transcripts. He proposed that genome-wide DNA methylation is the novel "noise reduction" mechanism that has permitted the additional quantal leap in gene numbers characteristic of vertebrates.
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From page 178... ...
Posttranscriptional silencing appears to be caused by RNA destabilization, whereas transcriptional gene silencing involves DNA methylation (Vaucheret et al., 1998; Kooter et al., 1999~. There is also some evidence that posttranscriptional silencing triggers DNA methylation (Wassenegger et al., 1994~.
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From page 179... ...
Thus questions about the origin of certain kinds of transposons may devolve to questions about the association of sequence-specific DNA binding domains with endonuclease domains. Although the majority of methylated sequences in a genome can be transposable elements, the view that DNA methylation evolved to control transposons seems implausible in the light of evidence that duplications of any kind trigger methylation in organisms that methylate DNA (Yoder et al., 1997; Garrick et al., 1998; Selker, 1999~.
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From page 180... ...
This is evidenced in position effect variegation in Drosophila, an organism that does not methylate its DNA, as well as in plant paramutation, which involves DNA methylation (Kermicle et al., 1995; Henikoff, 1998~. What has been learned recently from analyzing gene silencing and paramutation suggests that it does not take many tandem duplications to trigger the formation of a compacted, silenced region.
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From page 181... ...
(1992) Tourist: a large family of small inverted repeat elements frequently associated with maize genes.
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From page 182... ...
(1989) Maize transposable elements.
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From page 183... ...
(1998) Comparative mapping between Arabidopsis thaliana and Brassica nigra indicates that Brassica genomes have evolved through extensive genome replication accompanied by chromosome fusions and frequent rearrangements.
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From page 184... ...
(1987) The Discovery and Characterization of Transposable Elements (Garland Publishing, Inc., New York)
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From page 185... ...
(1985a) Plant transposable elements generate the DNA sequence diversity needed in evolution.
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From page 186... ...
(1989) The splicing of maize transposable elements from pre-mRNA a minireview.
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