What is perhaps most surprising about the maize retrotransposon blocks that have been characterized is that they grow quite slowly. The transposition mechanism assures that retrotransposon ends are almost always identical when an element inserts, hence the divergence between the LTRs of a single element reflects the age of the insertion. Bennetzen and his colleagues found that the sequence difference between the LTRs of a given element is almost invariably less than the sequence difference between the LTRs of the element into which it is inserted. Using these differences to order and date the insertions, they inferred that all of the insertions have occurred within roughly the last 5 million years, well after the divergence of maize and sorghum (SanMiguel et al., 1998). Importantly, no retrotransposons have been found in the corresponding Adh1 flanking sequence in sorghum (SanMiguel et al., 1998; Tikhonov et al., 1999). This raises the possibility that retrotransposon activity may differ between closely related lineages.
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. Exceptionally detailed examples of the role of transposition, retrotransposition, amplification, and transposon-mediated rearrangements in the evolution of a contemporary chromosome are provided by recent studies on the human Y chromosome (Saxena et al., 1996; Schwartz et al., 1998; Lahn and Page, 1999a, b). Although the level of resolution is not yet sufficient in many cases to determine the molecular history of each duplication, it is evident that many, if not a majority of plant genes belong to gene families ranging in size from a few members to hundreds (Michelmore and Meyers, 1998; Riechmann and Meyerowitz, 1998; Martienssen and Irish, 1999; Rabinowicz et al., 1999). R genes, for example, comprise a superfamily of similar myc-homologous, helix-loop-helix transcriptional activators of genes in anthocyanin biosynthesis (Ludwig et al., 1989; Perrot and Cone, 1989; Consonni et al., 1993). Detailed analysis of the R-r complex, a well-studied member of the R superfamily, reveals a history of transposon-catalyzed rearrangement and duplication (Walker et al., 1995).
There also may be other genetic mechanisms that drive genome expansion. A recent analysis of the behavior of maize chromosomal knobs reveals that the pattern of segregation under the influence of a “meiotic drive” locus of as yet unknown function results in the preferential transmission of chromosomes with larger knobs over chromosomes with smaller knobs (Buckler et al., 1999). Maize knobs are blocks of similar short tandemly repeated sequences, ranging from as few as 100 copies to as many as 25,000