What makes up plant genomes: The vanishing line between transposable elements and genes

•Transposable elements influence gene expressions both in cis and in trans.•Transposable elements duplicate genes sequences and modify gene structures.•Many normal genes may have derived from transposable elements.•Interaction among transposable elements determines proliferation.•New transposition activity arises from horizontal transfer and swapping of existing elements.

The ultimate source of evolution is mutation. As the largest component in plant genomes, transposable elements (TEs) create numerous types of mutations that cannot be mimicked by other genetic mechanisms. When TEs insert into genomic sequences, they influence the expression of nearby genes as well as genes unlinked to the insertion. TEs can duplicate, mobilize, and recombine normal genes or gene fragments, with the potential to generate new genes or modify the structure of existing genes. TEs also donate their transposase coding regions for cellular functions in a process called TE domestication. Despite the host defense against TE activity, a subset of TEs survived and thrived through discreet selection of transposition activity, target site, element size, and the internal sequence. Finally, TEs have established strategies to reduce the efficacy of host defense system by increasing the cost of silencing TEs. This review discusses the recent progress in the area of plant TEs with a focus on the interaction between TEs and genes.