Roles of transposable elements on plant genome evolution, epigenetics and adaptation

Transposable elements (TEs) are mobile DNA sequences within the genome. and their structure and transposition mechanism are highly diverse. TEs can be divided into retrotransposons (RTs; Class I) and DNA transposons (Class II), depending on whether their transposition intermediate is RNA or DNA. RTs transpose in a "copy-and-paste" manner and are therefore considered to be an essential contributor during genome expansion. RTs can be further divided into long terminal repeat retrotransposons (LTR-RTs) and non-long terminal repeat retrotransposons (non-LTR-RTs). Copia and Gypsy are two superfamilies of LTR-RTs commonly found in plant genomes, and their structural differences lie in the INT positions in the internal sequence of the poi open reading frame (ORF). Non-LTR-RTs include long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs), which lack LTRs and usually have poly(A) or simple repeats at their 3' end. DNA transposons directly cut the DNA sequence at the original site by transposase and insert a new site, similar to "cut-and-paste". Insertion of DNA transposons into new sites results in target site duplications (TSDs), and DNA strand breaks due to transposition are repaired by DNA repair mechanisms. DNA transposons in plants can be further divided into "cut-and-paste" transposons and Helitrons with the "rolling circle" transposition pattern. TEs play an important role in genome evolution. In the process of their insertion, deletion. and amplification. the host may alter its genome size, gene expression, and gene function Additionally. TEs may mediate chromosomal rearrangements through homologous recombination or alternative transposition. Overall, TEs are very powerful mutagens that can affect the stability of their host genomes. In order to defend against the transposition of TEs, the host has evolved various silencing mechanisms. In plants. the silencing of TEs is mainly established through RNA-directed DNA methylation (RdDM). which can stably repress the activity of TEs across generations. Methylation not only silences TEs but may also result in DNA methylation of nearby genes and affect expression and function of host genes. Interestingly, the phenotypic differences caused by the insertion of TEs play an important role in crop domestication. Methylation does not always keep TEs silent. such as burst events in some TE families. The evidence for the interaction between TEs and the host is growing, especially under environmental stress conditions, and TEs can be re-activated to help the host survive under stressful conditions. Furthermore. the insertion of TEs is preferred in many cases. and their insertion can be tolerated. Thus, TEs may not be completely inhibited, and they and their hosts may develop a cooperative relationship under environmental stress. This review summarizes some relevant research on TEs in plant genome evolution, introduces commonly occurring TEs found in plants, and examines how TEs are involved in plant genome evolution, epigenetic regulation, and the symbiotic relationship with the host under cooperative stress.