Vicient Carlos M, Casacuberta Josep M
Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Cerdanyola del Vallès, 08193 Barcelona, Spain.
Ann Bot. 2017 Aug 1;120(2):195-207. doi: 10.1093/aob/mcx078.
The growing wealth of knowledge on whole-plant genome sequences is highlighting the key role of transposable elements (TEs) in plant evolution, as a driver of drastic changes in genome size and as a source of an important number of new coding and regulatory sequences. Together with polyploidization events, TEs should thus be considered the major players in evolution of plants.
This review outlines the major mechanisms by which TEs impact plant genome evolution and how polyploidy events can affect these impacts, and vice versa. These include direct effects on genes, by providing them with new coding or regulatory sequences, an effect on the epigenetic status of the chromatin close to genes, and more subtle effects by imposing diverse evolutionary constraints to different chromosomal regions. These effects are particularly relevant after polyploidization events. Polyploidization often induces bursts of transposition probably due to a relaxation in their epigenetic control, and, in the short term, this can increase the rate of gene mutations and changes in gene regulation due to the insertion of TEs next to or into genes. Over longer times, TE bursts may induce global changes in genome structure due to inter-element recombination including losses of large genome regions and chromosomal rearrangements that reduce the genome size and the chromosome number as part of a process called diploidization.
TEs play an essential role in genome and gene evolution, in particular after polyploidization events. Polyploidization can induce TE activity that may explain part of the new phenotypes observed. TEs may also play a role in the diploidization that follows polyploidization events. However, the extent to which TEs contribute to diploidization and fractionation bias remains unclear. Investigating the multiple factors controlling TE dynamics and the nature of ancient and recent polyploid genomes may shed light on these processes.
关于植物全基因组序列的知识日益丰富，这凸显了转座元件（TEs）在植物进化中的关键作用，它是基因组大小急剧变化的驱动因素，也是大量新编码和调控序列的来源。因此，与多倍体化事件一起，TEs应被视为植物进化的主要参与者。
本综述概述了TEs影响植物基因组进化的主要机制，以及多倍体化事件如何影响这些影响，反之亦然。这些包括对基因的直接影响，为它们提供新的编码或调控序列，对基因附近染色质的表观遗传状态的影响，以及通过对不同染色体区域施加各种进化限制而产生的更微妙的影响。这些影响在多倍体化事件后尤为重要。多倍体化通常会导致转座爆发，这可能是由于其表观遗传控制的放松，并且在短期内，这会由于TEs插入基因旁边或基因内部而增加基因突变率和基因调控的变化。在更长的时间内，TE爆发可能会由于元件间重组而导致基因组结构的全局变化，包括大基因组区域的丢失和染色体重排，这些变化会减少基因组大小和染色体数量，这是一个称为二倍体化过程的一部分。
TEs在基因组和基因进化中起着至关重要的作用，特别是在多倍体化事件之后。多倍体化可以诱导TE活性，这可能解释了观察到的部分新表型。TEs也可能在多倍体化事件后的二倍体化中发挥作用。然而，TEs对二倍体化和分馏偏差的贡献程度仍不清楚。研究控制TE动态的多种因素以及古代和近期多倍体基因组的性质可能会揭示这些过程。
