Grande retrotransposons contain an accessory gene in the unusually long 3'-internal region that encodes a nuclear protein transcribed from its own promoter

Retand LTR-retrotransposons in plants: a long way from pol to 3'LTR

BACKGROUND

Plant Gypsy LTR-retrotransposons are classified into lineages according to the phylogenetic relationships of the reverse transcriptase. Retand is a lineage of non-chromovirus elements characterized by the presence of a long internal region compared to other lineages.

RESULTS

This work focuses on the identification and characterization of Potentially Recently Active Retand Elements (PRAREs) in 617 genomic sequence assemblies of Viridiplantae species. The Retand elements were considered PRAREs if their LTRs and insertion sequences were identical, and the sizes of their internal regions and LTRs did not differ by more than 2% from the consensus. A total of 2,735 PRAREs were identified, distributed in 122 clusters corresponding to 34 species, with copy numbers per cluster varying between 1 and 180. They are present in Eudicotyledons and Liliopsida but not in other groups of plants. Some PRAREs are non-autonomous elements, lacking some of the typical LTR retrotransposon coding domains. The size of the POL-3'LTR regions varies between 2,933 and 6,566 bp, and in all cases, includes potential coding regions oriented antisense to the gag and pol genes. 97% of the clusters contain antisense ORFs encoding the TRP28 protein domain of unknown function. The analysis of the consensus TRP28 domain indicates that it probably can bind DNA. About half of the PRAREs contain arrays of tandem repeats in the POL-3'LTR region.

CONCLUSIONS

The large internal region of the Retand elements is due to the presence of a long POL-3'LTR region. This region frequently contains arrays of tandem repeats that contribute to the expansion of this area. The presence of antisense ORFs in the POL-3'LTR region is also a common feature in these elements, many of which encode proteins with conserved domains, especially the TRP28 domain. The possible function of these TRP28-containing proteins is unknown, but their potential DNA binding capacity and the comparison with similar genes in some retroviruses suggest that they may play a regulatory role in the Retand transposition process.

Comparative Analysis of Active LTR Retrotransposons in Sunflower (Helianthus annuus L.): From Extrachromosomal Circular DNA Detection to Protein Structure Prediction

Plant genomes possess numerous transposable element (TE) insertions that have occurred during evolution. Most TEs are silenced or diverged; therefore, they lose their ability to encode proteins and are transposed in the genome. Knowledge of active plant TEs and TE-encoded proteins essential for transposition and evasion of plant cell transposon silencing mechanisms remains limited. This study investigated active long terminal repeat (LTR) retrotransposons (RTEs) in sunflowers (Helianthus annuus), revealing heterogeneous and phylogenetically distinct RTEs triggered by epigenetic changes and heat stress. Many of these RTEs belong to three distinct groups within the Tekay clade, showing significant variations in chromosomal insertion distribution. Through protein analysis of these active RTEs, it was found that Athila RTEs and Tekay group 2 elements possess additional open reading frames (aORFs). The aORF-encoded proteins feature a transposase domain, a transmembrane domain, and nuclear localization signals. The aORF proteins of the Tekay subgroup exhibited remarkable conservation among over 500 Tekay members, suggesting their functional importance in RTE mobility. The predicted 3D structure of the sunflower Tekay aORF protein showed significant homology with Tekay proteins in rice, maize, and sorghum. Additionally, the structural features of aORF proteins resemble those of plant DRBM-containing proteins, suggesting their potential role in RNA-silencing modulation. These findings offer insights into the diversity and activity of sunflower RTEs, emphasizing the conservation and structural characteristics of aORF-encoded proteins.

The Genomic Shock Hypothesis: Genetic and Epigenetic Alterations of Transposable Elements after Interspecific Hybridization in Plants

Transposable elements (TEs) are major components of plant genomes with the ability to change their position in the genome or to create new copies of themselves in other positions in the genome. These can cause gene disruption and large-scale genomic alterations, including inversions, deletions, and duplications. Host organisms have evolved a set of mechanisms to suppress TE activity and counter the threat that they pose to genome integrity. These includes the epigenetic silencing of TEs mediated by a process of RNA-directed DNA methylation (RdDM). In most cases, the silencing machinery is very efficient for the vast majority of TEs. However, there are specific circumstances in which TEs can evade such silencing mechanisms, for example, a variety of biotic and abiotic stresses or in vitro culture. Hybridization is also proposed as an inductor of TE proliferation. In fact, the discoverer of the transposons, Barbara McClintock, first hypothesized that interspecific hybridization provides a "genomic shock" that inhibits the TE control mechanisms leading to the mobilization of TEs. However, the studies carried out on this topic have yielded diverse results, showing in some cases a total absence of mobilization or being limited to only some TE families. Here, we review the current knowledge about the impact of interspecific hybridization on TEs in plants and the possible implications of changes in the epigenetic mechanisms.

Genome-wide characterization of LTR retrotransposons in the non-model deep-sea annelid Lamellibrachia luymesi

Background

Long Terminal Repeat retrotransposons (LTR retrotransposons) are mobile genetic elements composed of a few genes between terminal repeats and, in some cases, can comprise over half of a genome’s content. Available data on LTR retrotransposons have facilitated comparative studies and provided insight on genome evolution. However, data are biased to model systems and marine organisms, including annelids, have been underrepresented in transposable elements studies. Here, we focus on genome of Lamellibrachia luymesi, a vestimentiferan tubeworm from deep-sea hydrocarbon seeps, to gain knowledge of LTR retrotransposons in a deep-sea annelid.

Results

We characterized LTR retrotransposons present in the genome of L. luymesi using bioinformatic approaches and found that intact LTR retrotransposons makes up about 0.1% of L. luymesi genome. Previous characterization of the genome has shown that this tubeworm hosts several known LTR-retrotransposons. Here we describe and classify LTR retrotransposons in L. luymesi as within the Gypsy, Copia and Bel-pao superfamilies. Although, many elements fell within already recognized families (e.g., Mag, CSRN1), others formed clades distinct from previously recognized families within these superfamilies. However, approximately 19% (41) of recovered elements could not be classified. Gypsy elements were the most abundant while only 2 Copia and 2 Bel-pao elements were present. In addition, analysis of insertion times indicated that several LTR-retrotransposons were recently transposed into the genome of L. luymesi, these elements had identical LTR’s raising possibility of recent or ongoing retrotransposon activity.

Conclusions

Our analysis contributes to knowledge on diversity of LTR-retrotransposons in marine settings and also serves as an important step to assist our understanding of the potential role of retroelements in marine organisms. We find that many LTR retrotransposons, which have been inserted in the last few million years, are similar to those found in terrestrial model species. However, several new groups of LTR retrotransposons were discovered suggesting that the representation of LTR retrotransposons may be different in marine settings. Further study would improve understanding of the diversity of retrotransposons across animal groups and environments.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07749-1.

Additional ORFs in Plant LTR-Retrotransposons

LTR-retrotransposons share a common genomic organization in which the 5' long terminal repeat (LTR) is followed by the gag and pol genes and terminates with the 3' LTR. Although GAG-POL-encoded proteins are considered sufficient to accomplish the LTR-retrotransposon transposition, a number of elements carrying additional open reading frames (aORF) have been described. In some cases, the presence of an aORF can be explained by a phenomenon similar to retrovirus gene transduction, but in these cases the aORFs are present in only one or a few copies. On the contrary, many elements contain aORFs, or derivatives, in all or most of their copies. These aORFs are more frequently located between pol and 3' LTR, and they could be in sense or antisense orientation with respect to gag-pol. Sense aORFs include those encoding for ENV-like proteins, so called because they have some structural and functional similarities with retroviral ENV proteins. Antisense aORFs between pol and 3' LTR are also relatively frequent and, for example, are present in some characterized LTR-retrotransposon families like maize Grande, rice RIRE2, or Silene Retand, although their possible roles have been not yet determined. Here, we discuss the current knowledge about these sense and antisense aORFs in plant LTR-retrotransposons, suggesting their possible origins, evolutionary relevance, and function.

Impact of transposable elements on polyploid plant genomes

BACKGROUND

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.

SCOPE

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.

CONCLUSIONS

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.

Genetic diversity of maize germplasm assessed by retrotransposon-based markers

Maize is one of the most important crops and also a model for grass genome research. Transposable elements comprise over 78% of the maize genome and their ability to generate new copies makes them good potential markers. Interretrotransposon-amplified polymorphism (IRAP) and retrotransposon microsatellite amplified polymorphism (REMAP) protocols were used for the first time in maize to study the genetic variability between maize cultivars. Ten PCR primers were selected based on a systematic analysis of the sequence conservation in the extremities of different high copy number transposable elements, whereas one primer was chosen based on a microsatellite sequence. Of the 16 primer combinations tested, 14 produced polymorphic bands. These markers were used to identify genetic similarity among 20 maize cultivars selected by their different kernel oil content. Genetic similarity analysis was performed based on the polymorphic band profiles and dendrograms were developed by the unweighted pair-group method with arithmetic averages. Clustering technique revealed that samples were grouped into three clusters that differed in their kernel oil content and size, and in their relative embryo size. In the current investigation, there is evidence that IRAP/REMAP may be useful as markers in maize.

Retrotransposon replication in plants

Retrotransposons comprise the bulk of large plant genomes, replicating via an RNA intermediate whereby the original, integrated element remains in place. Of the two main orders, the LTR retrotransposons considerably outnumber the LINEs. LINEs integrate into target sites simultaneously with the RNA transcript being copied into cDNA by target-primed reverse transcription. LTR retrotransposon replication is basically equivalent to the intracellular phase of retroviral life cycles. The envelope gene giving extracellular mobility to retroviruses is in fact widespread in plants and their retrotransposons. Evolutionary analyses of the retrotransposons and retroviruses suggest that both form an ancient monophyletic group. The particular adaptations of LTR retrotransposons to plant life cycles enabling their success remain to be clarified.