Mechanisms of Transposable Element Evolution in Plants and Their Effects on Gene Expression

Abstract

Transposable elements (TEs), first described in the 1940s by Barbara McClintock, are DNA elements of variable sequence that can (or were previously able to) move within a genome. TEs account for almost half of the human genome and the majority of the genomes of many economically important plants [1][2][3] There are two major categories of TEs; those than move via a "copy-and-paste" mechanism with an RNA intermediate that is reverse transcribed prior to reintegration (class I retrotransposons), and those that use a "cut-and-paste" mechanism with a DNA intermediate and have terminal inverted repeats (class II transposons; Fig. 8.1). Class II TEs also include helitrons which are thought to replicate by a rolling circle mechanism [15]. The most common family of TEs in plants is the long terminal repeat (LTR) retrotransposons, with the LTRs defining the transcriptional direction and boundaries of the TE [16][17][18]. Other class I retrotransposons include autonomous long interspersed elements (LINEs) and nonautonomous short interspersed elements (SINEs) that are derived from transfer RNAs (tRNAs) [19].

Surviving in a Hostile World: Plant Strategies to Resist Pests and Diseases

“…ARjats.cls July 29, 2019 15:31 retroduplication, reversed ends duplication, and nonallelic homologous recombination (103,116,124). Functional redundancy allows for subsequent diversification of duplicated R genes via nonsynonymous mutations (103).…”

“…Functional redundancy allows for subsequent diversification of duplicated R genes via nonsynonymous mutations (103). Considering that methylated cytosines are subject to higher G:C→A:T mutation rates (102,124), the occurrence of nonsynonymous mutations will be enhanced by the spreading of DNA methylation from nearby TEs. Because exposure to biotic stress is also known to increase homologous recombination frequency (18,64,69,83,94), the R-gene diversification rate will be enhanced further by homologous recombination between highly similar sequences (47,93).…”