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Rapid flux in plant genomes

Nature Genetics volume 20, page 6 (1998)Cite this article

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The sizes of plant genomes vary remarkably — the well-studied Arabidopsis genome is 108 base pairs while those of some lilies are over one thousand times this size1,2. Genome sizes vary even among closely related plants. The plum genome, for example, is three times larger than that of peaches (both are members of the genus Prunus ), suggesting that fluctuations in genome size occur over relatively short periods of evolutionary time. While transposon insertion is recognized as a force underlying genome fluidity, the pace at which it contributes to genome evolution has remained obscure. On page 43, Phillip SanMiguel and colleagues document the rapidity by which transposons can restructure genomes; by analysing retrotransposon end-sequences, they have determined that an eruption of transposon activity over the past six million years has led to the plethora of transposons that currently litter the maize genome3.

The most abundant transposable elements in maize are retrotransposons — mobile genetic elements that replicate by reverse transcription. They proliferate by making copies of themselves; parental elements are transcribed, reverse transcribed, and the resulting progeny are `seeded' to new genomic sites. Maize retrotransposons have amplified to such an extent that they are densely packed in intergenic regions and, in total, occupy over 50% of the nuclear DNA (ref. 4). To explore the `population' dynamics of retrotransposon activity, SanMiguel et al. took advantage of the fact that the retrotransposon can be used to gauge evolutionary time; it can be thought of as a molecular clock that is set to zero when it integrates into a genome. Like retroviral proviruses, the maize retrotransposons are flanked by two long terminal repeats (LTRs). These repeats are reverse transcribed from an mRNA template that has only one copy of the LTR sequence, so both LTRs are typically identical after DNA synthesis. Time since integration is measured by the extent of nucleotide sequence divergence that has occurred between the two LTRs of a single element. This `clock' can be calibrated relative to sequence divergence among orthologous genes between species, whose rates of change, in turn, are set by fossil data. By this method, SanMiguel et al. have calculated that most maize retrotransposons have integrated within the past 3 million years.

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  1. Department of Zoology & Genetics and the Iowa Computational Biology Laboratory at Iowa State University, Ames, 50011, Iowa, USA

    Daniel F Voytas & Gavin J P Naylor

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  1. Daniel F Voytas
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  2. Gavin J P Naylor
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Voytas, D., Naylor, G. Rapid flux in plant genomes. Nat Genet 20, 6 (1998). https://doi.org/10.1038/1652

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