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of extensive homology, some genic and some intergenic. Thus synteny extends down to a relatively fine level and includes both genic and intergenic sequences.


A second generalization is that plant genomes grow. Genome sizes among flowering plants vary dramatically over almost 3 orders of magnitude, from the roughly 130 Mbp Arabidopsis genome to the 110,000 Mbp Fritillaria assyriaca genome (Bennett et al., 1982). Genome size variation greatly exceeds estimates of differences in gene numbers (Bennetzen and Freeling, 1997). This, of course, is the celebrated C-value paradox (Thomas, 1971). Plant genomes expand by several mechanisms, including polyploidization, transposition, and duplication. Thus, for example, a fine-scale comparison of the Arabidopsis thaliana and Brassica nigra genomes reveals that the Brassica genome contains a triplication of the much smaller Arabidopsis genome, as well as chromosome fusions and rearrangements (Lagercrantz, 1998). There is evidence that the maize genome is a segmental allotetraploid (White and Doebley, 1998). It is estimated that up to 70% of flowering plants have polyploidy in their lineages (Leitch and Bennett, 1997). Thus replication of whole genomes or parts of genomes is a common and important theme in plant genome evolution.


Transposition is also a major cause of plant genome expansion. To begin with, transposition generates DNA. Retrotransposition results from transcription of genomic retrotransposons, followed by insertion of reverse transcripts into the genome at new sites (Howe and Berg, 1989). 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. The accumulation of retrotransposon blocks between genes is a major factor in the size difference between the maize genome and those of its smaller relatives (SanMiguel et al., 1996, 1998). Retrotransposon blocks occupy 74% of the recently sequenced 240-kb maize Adh region (Tikhonov et al., 1999). These blocks contain 23 members of 11 different retrotransposon families, primarily as complete retrotransposons, but also occasionally as solo LTRs (Tikhonov et al., 1999). Within these blocks, retrotransposons are commonly nested by insertion of retrotransposons into each other (SanMiguel et al., 1996, 1998).

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