Transposable element contributions to plant gene and genome evolution

Transposable elements were first discovered in plants because they can have tremendous effects on genome structure and gene function. Although only a few or no elements may be active within a genome at any time in any individual, the genomic alterations they cause can have major outcomes for a species. All major element types appear to be present in all plant species, but their quantitative and qualitative contributions are enormously variable even between closely related lineages. In some large-genome plants, mobile DNAs make up the majority of the nuclear genome. They can rearrange genomes and alter individual gene structure and regulation through any of the activities they promote: transposition, insertion, excision, chromosome breakage, and ectopic recombination. Many genes may have been assembled or amplified through the action of transposable elements, and it is likely that most plant genes contain legacies of multiple transposable element insertions into promoters. Because chromosomal rearrangements can lead to speciating infertility in heterozygous progeny, transposable elements may be responsible for the rate at which such incompatibility is generated in separated populations. For these reasons, understanding plant gene and genome evolution is only possible if we comprehend the contributions of transposable elements.