6 nature genetics volume 20 september 1998 The sizes of plant genomes vary re- markably — the well-studied Arabidopsis genome is 10 8 base pairs while those of some lilies are over one thousand times this size 1,2 . 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 fluc- tuations in genome size occur over relatively short periods of evo- lutionary 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 col- leagues document the rapidity by which transposons can restructure genomes; by analysing retrotrans- poson end-sequences, they have determined that an eruption of trans- poson activity over the past six mil- lion years has led to the plethora of transposons that currently litter the maize genome 3 . The most abundant transposable elements in maize are retrotrans- posons — mobile genetic elements that replicate by reverse transcrip- tion. They proliferate by making copies of themselves; parental elements are tran- scribed, 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 ‘pop- ulation’ 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 retro- transposons are flanked by two long ter- minal repeats (LTRs). These repeats are reverse transcribed from an mRNA tem- plate that has only one copy of the LTR sequence, so both LTRs are typically iden- tical after DNA synthesis. Time since inte- gration 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 rel- ative to sequence divergence among orth- ologous 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 retro- transposons have integrated within the past 3 million years. A genome riddled with retrotrans- posons would seem to pose serious chal- lenges to an organism’s well-being. From a mechanistic standpoint, the replication machinery would have to process more DNA. Chromosome pairing may be chal- lenged by the asymmetric accumulation of elements. Finally, and perhaps most importantly, the cell must have an effi- cient means of recognizing vital cod- ing sequences against a changing background of inserted elements. How do so many elements get incorporated so quickly, and why are they tolerated? These two questions may be interrelated: tolerance may promote amplification and amplifi- cation may, in turn, foster tolerance. Assume, for example, that there is just one target site on a chromosome into which an element can insert. When an element occupies this site, its sequence may, in turn, provide multiple new targets for further insertion. As the percentage of ele- ments increases in the genome, there is an exponential increase in the number of potential sites for integra- tion. This may explain both the rapid amplification and the nested organi- zation of the maize retrotransposons. Ploidy and proliferation Plants are known to adapt to other large- scale genome perturbations. Changes in ploidy, for example, are commonplace, and over 50% of all plant species are poly- ploid or have undergone periods of poly- ploidy in their evolutionary history 5 . Although modern maize behaves as a strict diploid, there are relics of a past polyploidization event, including large duplicated segments of the genome 6 and a chromosome number that is twice that of many of its relatives 7 . The increased avail- ability of maize genome sequence has Rapid flux in plant genomes Daniel F. Voytas & Gavin J.P. Naylor Department of Zoology & Genetics and the Iowa Computational Biology Laboratory at Iowa State University, Ames, Iowa 50011, USA. e-mail: voytas@iastate.edu & gnaylor@iastate.edu Plotting and ploiding—genome dynamics in the evolutionary history of maize. n=chromosome number onset of retrotransposon amplification B (n = 5) formation of the allotetraploid and onset of disomy millions of years ago present divergence of diploid progenitors of A & B A (n=5) © 1998 Nature America Inc. • http://genetics.nature.com