Evolutionary Genomics of Miniature Inverted-Repeat Transposable Elements (MITEs) in Plants

Abstract

More and more evidence has accumulated in the past 20 years suggesting that MITEs may have played important roles in plant gene and genome evolution. With a large number of plant genomes sequenced and the development of computational programs for de novo MITE identification, a massive number of MITEs have been identified from plant genomes. The number of MITEs in a genome varied dramatically among different plant species. There is significant correlation between the number of MITEs and genome size, though there are several prominent exceptions. Some MITE families have a high copy number in a genome, probably due to one or several rounds of amplification bursts. Different MITE families in the same genome may have experienced amplification burst at different times, suggesting that their amplifications were triggered by distinct environments (such as stress) or genetic events. However, very few MITEs in plant genomes are currently active. MITEs are often distributed in gene-rich regions, and may be inserted in genes' promoter regions or transcribed regions. They may affect (either upregulate or downregulate) the expression of nearby genes. MITEs may downregulate genes through small RNAs, which may be produced via NAT or double-stranded RNAs formed by transcribed MITE sequences. The presence/ absence of MITEs as well as their potential effects on expression of nearby genes suggests that MITE may provide considerable physiological and phenotypic

A miniature inverted-repeat transposable element, AddIn-MITE, located inside a WD40 gene is conserved in Andropogoneae grasses

“…Here, we identified eight different MITEs within 145 sugarcane methyl-filtered genomic sequences using the MITE-Hunter pipeline and additional steps to select TEs with TSDs sequences. The MITEs’ sequences ranged from 106 to 155 bp with 2 to 4 bp of TSDs sequence, in agreement with characteristics of most of the MITEs, which are usually shorter than 500 bp in length and can have TSDs varying from 2 to more than 10 bp (Chen et al, 2014a). These MITEs were classified into two superfamilies’ previously identified in plant genomes (Bureau & Wessler, 1992; Bureau & Wessler, 1994).…”

High-resolution methylome analysis in the clonalPopulus nigracv. ‘Italica’ reveals environmentally sensitive hotspots and drought-responsive TE superfamilies

“…Both superfamilies are relatively short elements frequently inserted close to and within genes (Kögler et al, 2020; Seibt et al, 2016), likely due to their tendency to integrate in hypomethylated DNA regions (Arnaud et al, 2000). Also, both are preferential targets for de novo methylation, which can then spread into flanking sequences and may affect the expression of nearby genes (Arnaud et al, 2000; Chen et al, 2014). TE proximity to genes may suggest that stress-induced TE hypermethylation could be a by-product of highly expressed nearby genes, as previously suggested by (Secco et al, 2015).…”

Identification and Characterization of PTE-2, a Stowaway-like MITE Activated in Transgenic Chinese Cabbage Lines

“…TEs activation can trigger the generation of tandem repeats [ 45 ], and the genomic structure can be modified by the insertion of MITEs without TPase. Gene expression may be affected by the activation or inactivation of MITEs or by small RNA derived from MITEs [ 46 , 47 ].…”