. "10 Transposons and Genome Evolution in Plants." Variation and Evolution in Plants and Microorganisms: Toward a New Synthesis 50 Years after Stebbins. Washington, DC: The National Academies Press, 2000.
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Variation and Evolution in Plants and Microorganisms: TOWARD A NEW SYNTHESIS 50 YEARS AFTER STEBBINS
crantz, 1998). The synteny among the genomes of economically important cereal grasses is so extensive that they are now represented by concentric circular maps (Gale and Devos, 1998). There are rearrangements, but a relatively small number of major inversions and transpositions is required to harmonize the present day maps. Such maps, of course, are crude representations of the genome, and rearrangements can emerge as the level of resolution increases (Tanksley et al., 1988, 1992; Tikhonov et al., 1999). The frequency of rearrangements also can differ markedly and there is evidence that rearrangements are more prevalent just after polyploidization (Song et al., 1995; Gale and Devos, 1998). Even within a conservative lineage, however, some gene families are more heterogeneous in composition and map distribution than others (Leister et al., 1998).
SYNTENY AND DIVERGENCE
What are the useful generalizations? First, synteny can extend down to a very fine level, but it is far from perfect. A detailed sequence comparison of the small region around the maize and sorghum Adh1 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. The Adh1 gene sequences are highly conserved, and complete sequencing revealed that there were seven and 10 additional genes in the homologous regions of maize and sorghum, respectively. The region of homology extends over about 65 kb of the sorghum genome, but occupies more than 200 kb in the maize genome. The gene order and orientation are conserved, although three of the genes found in the sorghum Adh1 region are not in the maize Adh1 region. The genes are located elsewhere in the maize genome, suggesting that they transposed away from the Adh1 region (Tikhonov et al., 1999). Although homology is confined largely to genes, there are also homologous intergenic regions. There are simple sequence repeats and small transposons, called MITES as a group, scattered throughout this region in both sorghum and maize. MITES are found primarily between genes, but several are in introns. The small MITE transposons are found neither in exons nor in retrotransposons. There are three non-LTR retrotransposons in the maize Adh1 region and none in the sorghum Adh1 region (Tikhonov et al., 1999).
The major difference between the maize and sorghum Adh regions is the presence of very large continuous blocks of retrotransposons in maize that are not present in sorghum. Although most blocks are between genes, one appears to be inside a gene sequence. They are present in many, but not all intergenic regions. There is a relatively long stretch of almost 40 kb containing four genes in maize and seven genes in sorghum, which contains no retrotransposon blocks in maize and in which there is about 10 kb