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FIGURE 3. The estimated insertion times of retrotransposons in the Adh1 region (SanMiguel et al., 1998). Each gray box represents a retrotransposon. The horizontal line through the box is the estimate of insertion time, and the height of the box represents the standard deviation of the estimate. Arrows between boxes indicate the order of insertion. For example, Huck-2 inserted into Fourf ≈1 mya.

present in the Adh1 region (although it should be noted that the sample of repetitive DNAs from other regions was small and thus this estimate may not be robust). Finally, a more recent study suggests that retrotransposons hybridize fairly uniformly to maize bacterial artificial chromosome clones, suggesting that the distribution of retrotransposons is reasonably homogeneous throughout the genome (B. Meyers, personal communication).

The Timing of Retrotransposon Multiplication

Maize repetitive DNA seems to be primarily retrotransposons, but the second question remains: when did these retroelements multiply? To answer this question, SanMiguel et al. (1998) sequenced the long terminal repeat (LTR) of retrotransposons in the Adh1 region. The rationale was as follows: when a single retrotransposon inserts into genomic DNA, both copies of the LTR are identical. Over time, the LTRs accumulate nucleotide substitutions and diverge in sequence. If the accumulation of nucleotide substitutions occurs at a regular pace, the number of nucleotide differences between the two LTRs provide insight into the date of LTR divergence and hence the date of retrotransposon insertion.

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