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We thus propose an increase/decrease model for rice genome evolution, in which both amplification and recombination processes drive variations in genome size.

The observation that variation in genome size is not correlated with the biological complexity of higher eukaryotes, referred to as the C-value paradox (Thomas 1971), has been explained in the plant kingdom by the finding that nongenic regions, which make a large proportion of complex plant genomes, are the main source of variation in genome size (Bennetzen et al. In addition, there is now much evidence that the activity of transposable elements (TEs) is at the origin of most of the structural genomic diversity observed in angiosperms (Kidwell and Lisch 1997; Bennetzen 2000).

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The evolutionary mechanisms constraining retrotransposon copy number and chromosomal distribution are still poorly understood.

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Like retroviruses, their (intact) genome consists of two LTRs, which contain the signals for transcription initiation and termination, flanking an internal region (IR) that typically contains genes and other features necessary for autonomous retrotransposition.

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