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Background. The DNA/H3K9 methylation and Polycomb-group proteins (PcG)-H3K27me3 silencing pathways have long been considered mutually exclusive and specific to transposable elements (TEs) and genes, respectively in mammals, plants, and fungi. However, H3K27me3 can be recruited to many TEs in the absence of DNA/H3K9 methylation machinery and sometimes also co-occur with DNA methylation.Results. In this study, we show that TEs can also be solely targeted and silenced by H3K27me3 in wild-type Arabidopsis plants. These H3K27me3-marked TEs not only comprise degenerate relics but also seemingly intact copies that display the epigenetic features of responsive PcG target genes as well as an active H3K27me3 regulation. We also show that H3K27me3 can be deposited on newly inserted transgenic TE sequences in a TE-specific manner indicating that silencing is determined in cis. Finally, a comparison of Arabidopsis natural accessions reveals the existence of a category of TEs—which we refer to as “bifrons”—that are marked by DNA methylation or H3K27me3 depending on the accession. This variation can be linked to intrinsic TE features and to trans-acting factors and reveals a change in epigenetic status across the TE lifespan.Conclusions Our study sheds light on an alternative mode of TE silencing associated with H3K27me3 instead of DNA methylation in flowering plants. It also suggests dynamic switching between the two epigenetic marks at the species level, a new paradigm that might extend to other multicellular eukaryotes.

Background Transposable element (TE) expansion has long been known to mediate genome evolution and phenotypic diversity in organisms, but its impact on the evolution of post-transcriptional regulation following species divergence remains unclear. Results To address this issue, we perform long-read direct RNA sequencing, polysome profiling sequencing, and small RNA sequencing in the cotton genus Gossypium , the species of which range more than three folds in genome size. We find that TE expansion contributes to the turnover of transcription splicing sites and regulatory sequences, leading to changes in alternative splicing patterns and the expression levels of orthologous genes. We also find that TE-derived upstream open reading frames and microRNAs serve as regulatory elements mediating differences in the translation levels of orthologous genes. We further identify genes that exhibit lineage-specific divergence at the transcriptional, splicing, and translational levels, and showcase the high flexibility of gene expression regulation in the evolutionary process. Conclusions Our work highlights the significant role of TE in driving post-transcriptional regulation divergence in the cotton genus. It offers insights for deciphering the evolutionary mechanisms of cotton species and the formation of biological diversity.

Background Transposable elements (TEs) are DNA sequences that can move within a host genome. Many new TE insertions have deleterious effects on their host and are therefore removed by purifying selection. The genomic distribution of TEs thus reflects a balance between new insertions and purifying selection. However, the inference of purifying selection against deleterious TE insertions from the patterns observed in natural populations is challenged by the confounding effects of demographic events, such as population bottlenecks and migration. Results We use experimental evolution to study the role of purifying selection during the invasion of the P-element, a highly invasive TE, in replicated Drosophila simulans populations under controlled laboratory conditions. Because the change in P-element copy number over time provides information about the transposition rate and the effect of purifying selection, we repeatedly sequence the experimental populations to study the P-element invasion dynamics. Based on the empirical data, we use Gaussian process surrogate models to efficiently explore the parameter space and identify parameter combinations that best reproduce the experimental P-element invasion trajectories. Assuming that beneficial P-element insertions are negligible, and that transposition regulation is well-approximated by our simulation framework, we estimate that, in our experimental populations, 73% (60.9–76.1%) of new P-element insertions are under purifying selection with a mean selection coefficient of − 0.056 (− 0.060 to − 0.042), highlighting the central role of selection in shaping P-element invasion dynamics. Conclusions This study underscores the power of experimental evolution as a tool for studying transposable element invasions and highlights the pivotal role of purifying selection in regulating P-element dynamics.

Background Because transposable elements (TEs) can cause heritable genetic changes, past work on TE mobility in Arabidopsis thaliana has mostly focused on new TE insertions in the germline of hypomethylated plants. It is, however, well-known that TEs can also be active in the soma, although the high-confidence detection of somatic events has been challenging. Results Here, we leverage the high accuracy of PacBio HiFi long reads to evaluate the somatic mobility of TEs in individuals of an A. thaliana non-reference strain lacking activity of METHYLTRANSFERASE1 (MET1), a major component of the DNA methylation maintenance machinery. Most somatically mobile families coincide with those found in germline studies of hypomethylated genotypes, although the exact TE copies differ. We also discover mobile elements that had been missed by standard TE annotation methods. Somatic TE activity is variable among individual plants, but also within TE families. Finally, our approach points to the possible involvement of alternative transposition as a cause for somatic hypermutability in a region that contains two closely spaced VANDAL21 elements. Conclusions Long-read sequencing reveals widespread TE transposition in the soma of A. thaliana hypomethylated mutants. Assessing somatic instead of germline mobilization is a fast and reliable method to investigate different aspects of TE mobility at the single plant level.

Background Self-incompatibility is controlled by a highly polymorphic supergene complex, the S -locus, which is structurally complex, rich in repetitive sequences, and varies in length from hundreds of kilobases to tens of megabases across different plant families. Due to these challenges, the S -locus has been fully reconstructed in only a few species, limiting our understanding of its evolutionary dynamics. Results This study systematically explores the evolutionary mechanisms and structural characteristics of the self-incompatibility system mediated by S-RNase in the Aurantioideae (orange subfamily) of Rutaceae. We construct a pan- S -locus framework spanning 11 genera within the orange subfamily from 14 newly assembled genomes from representative accessions and the analysis of 41 published citrus genomes. Our analyses reveal significant structural variations and transposable element (TE)-driven pseudogenization of SLF genes. By constructing a comprehensive library of S-RNases and developing a novel genotyping pipeline, we reveal divergent frequencies of S-RNases between self-incompatible and self-compatible populations. Comparative analyses demonstrate a unique evolutionary trajectory marked by asynchronous core nonS -genes duplication and TE-mediated structural diversification, distinct from other families. Innovatively, we identified TE-induced self-incompatibility loss as the primary driver of self-compatibility transition, which implies the uniqueness of the origin and evolution of self-incompatibility in the orange subfamily. Conclusions Through the construction and characterization of the pan- S -locus, this study provides profound insight into the origin and evolution of the S -locus in the orange subfamily. These findings not only advance our understanding of self-incompatibility mechanisms, but also establish a foundational framework for investigating the evolution of the gametophytic self-incompatibility systems in other families.

Background Many metazoan genomes are characterized by highly conserved chromosomal homologies that predate the ancient origin of this clade. This conservation has been tested by expansions of selfish DNA elements, in particular transposable elements (TEs). While comparative genomics studies have highlighted their diversity across animal genomes, common principles underlying their evolution along deeply conserved chromosomes have been elusive. A detailed mechanistic understanding from phylogenetically key and early branching animal species has been lacking. Results We present a comprehensive stem-cell resolved genomic and transcriptomic study of the freshwater cnidarian Hydra , an animal characterized by its high regenerative capacity, the ability to propagate clonally, and an apparent lack of aging. Using single-haplotype telomere-to-telomere genome assemblies of two recently diverged strains and utilizing unique features of hydra biology allowed us to sequence and compare the individual genomes of hydra’s three stem cell lineages. We show that distinct TE families are active at both transcriptional and genomic levels via non-random insertions in each of these lineages. We show that the core set of these active TE families, primarily composed of DNA elements, is evolutionarily deeply conserved and contributes to consistent genomic expansions in metazoan lineages. These anciently active TEs differentially contribute to structural variants around loci associated with cell proliferation and long-range topological contacts. This is in strong contrast to the frequently observed and highly varied substantial genome expansions that often happen via retroelements. Conclusions Our study suggests an ancient and conserved role for these core TEs as self-renewing components of animal chromosomes.

Background Mobilization of transposable elements (TEs) can generate large effect mutations. However, due to the difficulty of detecting new TE insertions in genomes and the typically rare occurrence of transposition, the actual rate, distribution, and population dynamics of new insertions remain largely unexplored. Results We present a TE display sequencing approach that leverages target amplification of TE extremities to detect non-reference TE insertions with high specificity and sensitivity, enabling the detection of insertions at frequencies as low as 1 in 250,000 within a DNA sample. Moreover, this method allows the simultaneous detection of insertions for distinct TE families, including both retrotransposons and DNA transposons, enhancing its versatility and cost-effectiveness for investigating complex “mobilomes.” When combined with nanopore sequencing, this approach enables the identification of insertions using long-read information and achieves a turnaround time from DNA extraction to insertion identification of less than 24 h, significantly reducing the time-to-answer. By analyzing a population of Arabidopsis thaliana plants undergoing a transposition burst, we demonstrate the power of the multiplex TE display sequencing to analyze “evolve and resequence” experiments. Notably, we find that 3–4% of de novo TE insertions exhibit recurrent allele frequency changes indicative of either positive or negative selection. Conclusions TE display sequencing is an ultra-sensitive, specific, simple, and cost-effective approach for investigating the rate and landscape of new TE insertions across multiple families in large-scale population experiments. We provide a step-by-step experimental protocol and ready-to-use bioinformatic pipelines to facilitate its straightforward implementation.

Transposable elements (TEs) are often epigenetically repressed in eukaryotic cells, but still affect the molecular state of the cell in certain contexts. A flurry of recent studies have elucidated new effects of TE sequences in eukaryotic cells. We review these emerging molecular effects of TEs, including a variety of new mechanisms by which TE sequences affect the cell, including pre- and post-transcriptional regulation of gene expression; cell-to-cell transmission of genes within a multicellular organism through virus-like activity; and RNA-guided DNA insertion. Recent demonstration of TE-guided genome editing underscores the importance of these investigations for both basic and translational research. Future work is needed to continue to unravel the molecular effects of TE sequences across developmental stages, across cell types, and in various diseases.

Background Comprising up to 90% of eukaryotic genomes, transposable elements (TEs) are mobile genetic units that play fundamental roles in evolution. Brown algae, one of the most complex multicellular eukaryotic groups that evolved independently from plants, fungi, and animals, are particularly underexplored in their transposon biology, especially when studied in a developmental context. Results Here, we explore the TE landscape of the model brown alga Ectocarpus , using a high-quality genome assembly complemented by extensive manual curation. TEs account for 28% of the genome, with a predominance of evolutionarily young elements. DNA transposons represent the most abundant and diverse TE subclass. Notably, TEs are significantly enriched along the sex chromosomes, a pattern potentially driven by local transposition events from the non-recombining sex-determining region into the pseudoautosomal regions. The genome harbors a high density of intronic TEs, which show minimal impact on host gene expression; however, intronic TEs tend to be shorter and more degraded than intergenic copies, suggesting selective pressures on their retention in the genome. Intact and potentially active TEs are preferentially associated with small RNAs and the histone modification H3K79me2, with over 70% of H3K79me2-marked intact TEs also enriched in small RNAs. This stable association indicates tight and sustained silencing of intact TEs throughout the life cycle of Ectocarpus. Conclusions Our study highlights the genetic diversity of the Ectocarpus mobilome and presents a complex, multilayered landscape of TE regulation mechanisms which involves small RNAs and chromatin modifications in the absence of an epigenetic silencing machinery that would be comparable to animals or plants.

We present GenomeDelta, a novel tool for identifying sample-specific sequences, such as recent transposable element (TE) invasions, without requiring a repeat library. GenomeDelta compares high-quality assemblies with short-read data to detect sequences absent from the short reads. It is applicable to both model and non-model organisms and can identify recent TE invasions, spatially heterogeneous sequences, viral insertions, and hotizontal gene transfers. GenomeDelta was validated with simulated and real data and used to discover three recent TE invasions in Drosophila melanogaster and a novel TE with geographic variation in Zymoseptoria tritici .