Satellite DNAs rising from the transposon graveyards.

Repetitive DNA sequences, satellite DNAs (satDNAs) and transposable elements (TEs) are essential components of the genome landscape, with many different roles in genome function and evolution. Despite significant advances in sequencing technologies and bioinformatics tools, detection and classification of repetitive sequences can still be an obstacle to the analysis of genomic repeats. Here, we summarize how specificities in repetitive DNA organizational patterns can lead to an inability to classify (and study) a significant fraction of bivalve mollusk repetitive sequences. We suggest that the main reasons for this inability are: the predominant association of satDNA arrays with Helitron/Helentron TEs; the existence of many complex loci; and the unusual, highly scattered organization of short satDNA arrays or single monomers across the whole genome. The specificities of bivalve genomes confirm the need for introducing diverse organisms as models in order to understand all aspects of repetitive DNA biology. It is expected that further development of sequencing techniques and synergy among different bioinformatics tools and databases will enable quick and unambiguous characterization and classification of repetitive DNA sequences in assembled genomes.

Transposable elements (TEs) are repetitive DNA sequences which create mutations and generate genetic diversity across the tree of life. In amniote vertebrates, TEs have been mainly studied in mammals and birds, whose genomes generally display low TE diversity. Squamates (Order Squamata; including ∼11,000 extant species of lizards and snakes) show as much variation in TE abundance and activity as they do in species and phenotypes. Despite this high TE activity, squamate genomes are remarkably uniform in size. We hypothesize that novel, lineage-specific genome dynamics have evolved over the course of squamate evolution. To understand the interplay between TEs and host genomes, we analyzed the evolutionary history of the chicken repeat 1 (CR1) retrotransposon, a TE family found in most tetrapod genomes which is the dominant TE in most reptiles. We compared 113 squamate genomes to the genomes of turtles, crocodilians, and birds and used ancestral state reconstruction to identify shifts in the rate of CR1 copy number evolution across reptiles. We analyzed the repeat landscapes of CR1 in squamate genomes and determined that shifts in the rate of CR1 copy number evolution are associated with lineage-specific variation in CR1 activity. We then used phylogenetic reconstruction of CR1 subfamilies across amniotes to reveal both recent and ancient CR1 subclades across the squamate tree of life. The patterns of CR1 evolution in squamates contrast other amniotes, suggesting key differences in how TEs interact with different host genomes and at different points across evolutionary history.

Transposable elements (TEs) are repetitive DNA sequences which create mutations and generate genetic diversity across the tree of life. In amniotic vertebrates, TEs have been mainly studied in mammals and birds, whose genomes generally display low TE diversity. Squamates (Order Squamata; ~11,000 extant species of lizards and snakes) show as much variation in TE abundance and activity as they do in species and phenotypes. Despite this high TE activity, squamate genomes are remarkably uniform in size. We hypothesize that novel, lineage-specific dynamics have evolved over the course of squamate evolution to constrain genome size across the order. Thus, squamates may represent a prime model for investigations into TE diversity and evolution. To understand the interplay between TEs and host genomes, we analyzed the evolutionary history of the CR1 retrotransposon, a TE family found in most tetrapod genomes. We compared 113 squamate genomes to the genomes of turtles, crocodilians, and birds, and used ancestral state reconstruction to identify shifts in the rate of CR1 copy number evolution across reptiles. We analyzed the repeat landscapes of CR1 in squamate genomes and determined that shifts in the rate of CR1 copy number evolution are associated with lineage-specific variation in CR1 activity. We then used phylogenetic reconstruction of CR1 subfamilies across amniotes to reveal both recent and ancient CR1 subclades across the squamate tree of life. The patterns of CR1 evolution in squamates contrast other amniotes, suggesting key differences in how TEs interact with different host genomes and at different points across evolutionary history.

Transposable elements (TEs) are mobile, repetitive DNA sequences that are almost ubiquitous in prokaryotic and eukaryotic genomes. They have a large impact on genome structure, function and evolution. With the recent development of high-throughput sequencing methods, many genome sequences have become available, making possible comparative studies of TE dynamics at an unprecedented scale. Several methods have been proposed for the de novo identification of TEs in sequenced genomes. Most begin with the detection of genomic repeats, but the subsequent steps for defining TE families differ. High-quality TE annotations are available for the Drosophila melanogaster and Arabidopsis thaliana genome sequences, providing a solid basis for the benchmarking of such methods. We compared the performance of specific algorithms for the clustering of interspersed repeats and found that only a particular combination of algorithms detected TE families with good recovery of the reference sequences. We then applied a new procedure for reconciling the different clustering results and classifying TE sequences. The whole approach was implemented in a pipeline using the REPET package. Finally, we show that our combined approach highlights the dynamics of well defined TE families by making it possible to identify structural variations among their copies. This approach makes it possible to annotate TE families and to study their diversification in a single analysis, improving our understanding of TE dynamics at the whole-genome scale and for diverse species.

Eukaryotic genomes contain far more DNA than needed for coding proteins. Some of these additional DNA sequences comprise non-coding repetitive DNA sequences, mostly satellite DNAs and also transposable elements usually located at the heterochromatic regions of chromosomes. Satellite DNAs consist of tandemly repeated DNA sequences inhabiting the mammalian genome, typically organized in long arrays of hundreds or thousands of copies. Different important functions have been ascribed to satellite DNA, from the imperative centromeric function in mitosis and meiosis to the recent discovery of its involvement in regulatory functions via satellite transcripts. Moreover, satellite DNAs, among other repetitive sequences, are believed to be the ‘engine’ triggering mammalian genome evolution. Repetitive DNAs are, most likely, the genetic factors responsible for promoting genomic plasticity and therefore higher rates of chromosome mutation. Furthermore, constitutive heterochromatin regions are thought to be ‘hotspots’ for structural chromosome rearrangements. A considerable collection of evidences places these sequences in the landscape of mammalian evolution. However, the mechanisms that could explain how this alliance between chromosome evolution and satellite DNA is made are still enigmatic and subject of debate. Throughout the mammalian taxa, different patterns of chromosome evolution have been widely registered from heterochromatin additions/eliminations, Robertsonian translocations, whole-arm reciprocal translocations to tandem translocations; the fact is genome’s repetitive fraction is playing a central role in mammalian genome structuring. Throughout this review we will focus on the evidences that associate satellite DNAs and constitutive heterochromatin to the process of chromosome evolution and consequently to domestic species genome’s remodeling.

Transposable elements (TEs) are the most abundant genetic material for almost all eukaryotic genomes. Their effects on the host genomes range from an extensive size variation to the regulation of gene expression, altering gene function and creating new genes. Because of TEs pivotal contribute to the host genome structure and regulation, their identification and characterization provide a wealth of useful data for gaining an in-depth understanding of host genome functioning. The giant reed (Arundo donax) is a perennial rhizomatous C3 grass, octadecaploid, with an estimated nuclear genome size of 2744 Mbp. It is a promising feedstock for second-generation biofuels and biomethane production. To identify and characterize the most repetitive TEs in the genomes of A. donax and its ancestral A. plinii species, we carried out low-coverage whole genome shotgun sequencing for both species. Using a de novo repeat identification approach, 33,041 and 28,237 non-redundant repetitive sequences were identified and characterized in A. donax and A. plinii genomes, representing 37.55 and 31.68% of each genome, respectively. Comparative phylogenetic analyses, including the major TE classes identified in A. donax and A. plinii, together with rice and maize TE paralogs, were carried out to understand the evolutionary relationship of the most abundant TE classes. Highly conserved copies of RIRE1-like Ty1-Copia elements were discovered in two Arundo spp. in which they represented nearly 3% of each genomic sequence. We identified and characterized the medium/highly repetitive TEs in two unexplored polyploid genomes, thus generating useful information for the study of the genomic structure, composition, and functioning of these two non-model species. We provided a valuable resource that could be exploited in any effort aimed at sequencing and assembling these two genomes.

Transposable elements (TEs) are repetitive DNA sequences that can make new copies of themselves that are inserted elsewhere in a host genome. The abundance and distributions of TEs vary considerably among phylogenetically diverse hosts. With the aim of exploring the basis of this variation, we evaluated correlations between several genomic variables and the presence of TEs and non-TE repeats in the complete genome sequence of the Western clawed frog (Silurana tropicalis). This analysis reveals patterns of TE insertion consistent with gene disruption but not with the insertional preference model. Analysis of non-TE repeats recovered unique features of their genome-wide distribution when compared with TE repeats, including no strong correlation with exons and a particularly strong negative correlation with GC content. We also collected polymorphism data from 25 TE insertion sites in 19 wild-caught S. tropicalis individuals. DNA transposon insertions were fixed at eight of nine sites and at a high frequency at one of nine, whereas insertions of long terminal repeat (LTR) and non-LTR retrotransposons were fixed at only 4 of 16 sites and at low frequency at 12 of 16. A maximum likelihood model failed to attribute these differences in insertion frequencies to variation in selection pressure on different classes of TE, opening the possibility that other phenomena such as variation in rates of replication or duration of residence in the genome could play a role. Taken together, these results identify factors that sculpt heterogeneity in TE distribution in S. tropicalis and illustrate that genomic dynamics differ markedly among TE classes and between TE and non-TE repeats.

The arrangement of repetitive and single-copy DNA sequences has been studied in DNA of some species of Echinodermata--sea urchin, starfishes and sea-cucumber. Comparison of the reassociation kinetics of short and long DNA fragments indicates that the pattern of DNA sequence organization of all these species is similar to the so-called "Xenopus pattern" characteristic of the genomes of most animals and plants. However, substantional variations have been found in the amount of repetitive nucleotide sequences in DNA of different species and in the length of DNA regions containing adjacent single-copy and repetitive sequences. Measurements of the size of S1-nuclease resistant reassociated repetitive DNA sequences show a variability of ratios between long and short repetitive DNA sequences of different species.--The degree of divergence of short and long repetitive DNA sequences and single-copy DNA was studied by molecular hybridization of the sea urchin Strongylocentrotus intermedius 3H-DNA with the DNA of other species and by determination of the thermostability of the hybridized molecules so obtained. All three fractions of S. intermedius DNA contain sequences homologous to DNA of the other echinoderm species studied. The results obtained suggest that short repetitive DNA sequences are those which have been most highly conserved throughout the evolution of Echinodermata. A new hypothesis is proposed to explain the nature of the evolutionary changes in DNA sequence interspersion patterns.

'Satellite DNA transcripts have diverse biological roles in Drosophila'.

Transposable elements (TEs) are ubiquitous genetic components that play critical roles in shaping plant genome structure, function, and evolution. Their ability to move within genomes through mechanisms such as “copy-and-paste” and “cut-and-paste” transposition contributes to genome size variation, structural diversity, and regulatory innovation. Research in the last twenty years has convincingly demonstrated that alterations in TEs may not be only the consequences of the disease, but are among those that are involved in the pathogenesis. Further knowledge that environmental stressors can affect TEs has allowed a connection to be drawn between environmental exposures, TEs, and disease development. TEs are classified into two major classes: Class I (retrotransposons) and Class II (DNA transposons), each with distinct transposition mechanisms. Retrotransposons, particularly LTR elements, are major contributors to genome expansion in species such as maize (Zea mays) and wheat (Triticum aestivum), while DNA transposons drive structural rearrangements and gene modification. TE activity is often triggered by environmental stresses, leading to increased genetic diversity and adaptability. TEs also influence gene expression by providing regulatory elements, modifying transcriptional and post-transcriptional processes, and participating in epigenetic regulation. Host genomes have evolved sophisticated mechanisms, including DNA methylation, histone modifications, and small RNA-mediated silencing, to control TE activity and maintain genome integrity. Recent advances in genome editing tools, such as transposon-based vectors and CRISPR-Cas technologies, offer novel opportunities for exploiting TEs in functional genomics and crop improvement. The use of TEs for enhancing genetic diversity, stress tolerance, and adaptability has significant implications for breeding resilient crops. Future research integrating multi-omics approaches, high-resolution sequencing, and predictive models will further elucidate TE dynamics and their contributions to plant evolution. Harnessing the potential of TEs for crop improvement will require precise manipulation of their activity and an understanding of their complex interactions with host genomes. The ongoing exploration of TEs as drivers of genome evolution and tools for biotechnology promises to enhance agricultural productivity and resilience in response to global challenges, including climate change and food security. The interplay between TEs, epigenetic mechanisms, and phytohormones highlights the intricate molecular networks that control plant stress resistance and adaptation. Understanding the role and regulatory mechanisms of TEs in response to abiotic stress could pave the way for developing stress-tolerant crops and improving agricultural sustainability in the face of global environmental challenges.

Transposable elements (TEs) are repetitive DNA sequences capable of changing position in host genomes, thereby causing mutations. TE insertions typically have deleterious effects but they can also be beneficial. Increasing evidence of the contribution of TEs to adaptive evolution further raises interest in understanding what factors impact TE activity. Based on previous studies associating the bacterial endosymbiont Wolbachia with changes in the abundance of piRNAs, a mechanism for TE repression, and to transposition of specific TEs, we hypothesized that Wolbachia infection would interfere with TE activity. We tested this hypothesis by studying the expression of 14 TEs in a panel of 25 Drosophila melanogaster host genotypes, naturally infected with Wolbachia and annotated for TE insertions. The host genotypes differed significantly in Wolbachia titers inside individual flies, with broad-sense heritability around 20%, and in the number of TE insertions, which depended greatly on TE identity. By removing Wolbachia from the target host genotypes, we generated a panel of 25 pairs of Wolbachia-positive and Wolbachia-negative lines in which we quantified transcription levels for our target TEs. We found variation in TE expression that was dependent on Wolbachia status, TE identity, and host genotype. Comparing between pairs of Wolbachia-positive and Wolbachia-negative flies, we found that Wolbachia removal affected TE expression in 21.1% of the TE-genotype combinations tested, with up to 2.3 times differences in the median level of transcript. Our data show that Wolbachia can impact TE activity in host genomes, underscoring the importance this endosymbiont can have in the generation of genetic novelty in hosts.

The methylation of cytosines shapes the epigenetic landscape of plant genomes, coordinates transgenerational epigenetic inheritance, represses the activity of transposable elements (TEs), affects gene expression and, hence, can influence the phenotype. Sugar beet (Beta vulgaris ssp. vulgaris), an important crop that accounts for 30% of worldwide sugar needs, has a relatively small genome size (758Mbp) consisting of approximately 485Mbp repetitive DNA (64%), in particular satellite DNA, retrotransposons and DNA transposons. Genome-wide cytosine methylation in the sugar beet genome was studied in leaves and leaf-derived callus with a focus on repetitive sequences, including retrotransposons and DNA transposons, the major groups of repetitive DNA sequences, and compared with gene methylation. Genes showed a specific methylation pattern for CG, CHG (H=A, C, and T) and CHH sites, whereas the TE pattern differed, depending on the TE class (class 1, retrotransposons and class 2, DNA transposons). Along genes and TEs, CG and CHG methylation was higher than that of adjacent genomic regions. In contrast to the relatively low CHH methylation in retrotransposons and genes, the level of CHH methylation in DNA transposons was strongly increased, pointing to a functional role of asymmetric methylation in DNA transposon silencing. Comparison of genome-wide DNA methylation between sugar beet leaves and callus revealed a differential methylation upon tissue culture. Potential epialleles were hypomethylated (lower methylation) at CG and CHG sites in retrotransposons and genes and hypermethylated (higher methylation) at CHH sites in DNA transposons of callus when compared with leaves.

Extensive and complex links exist between transposable elements (TEs) and satellite DNA (satDNA), which are the two largest fractions of eukaryotic genome. These relationships have a crucial effect on genome structure, function and evolution. Here, we report a novel case of mutual relationships between TEs and satDNA. In the genomes of Chenopodium s. str. species, the deletion derivatives of tnp2 conserved domain of the newly discovered CACTA-like TE Jozin are involved in generating monomers of the most abundant satDNA family of the Chenopodium satellitome. The analysis of the relative positions of satDNA and different TEs utilizing assembled Illumina reads revealed several associations between satDNA arrays and the transposases of putative CACTA-like elements when an ~ 40 bp fragment of tnp2 served as the start monomer of the satDNA array. The high degree of identity of the consensus satDNA monomers of the investigated species and the tnp2 fragment (from 82.1 to 94.9%) provides evidence of the genesis of CficCl-61-40 satDNA family monomers from analogous regions of their respective parental elements. The results were confirmed via molecular genetic methods and Oxford Nanopore sequencing. The discovered phenomenon leads to the continuous replenishment of species genomes with new identical satDNA monomers, which in turn may increase species satellitomes similarity.

BackgroundMycosphaerella fijiensis is a ascomycete that causes Black Sigatoka in bananas. Recently, the M. fijiensis genome was sequenced. Repetitive sequences are ubiquitous components of fungal genomes. In most genomic analyses, repetitive sequences are associated with transposable elements (TEs). TEs are dispersed repetitive DNA sequences found in a host genome. These elements have the ability to move from one location to another within the genome, and their insertion can cause a wide spectrum of mutations in their hosts. Some of the deleterious effects of TEs may be due to ectopic recombination among TEs of the same family. In addition, some transposons are physically linked to genes and can control their expression. To prevent possible damage caused by the presence of TEs in the genome, some fungi possess TE-silencing mechanisms, such as RIP (Repeat Induced Point mutation). In this study, the abundance, distribution and potential impact of TEs in the genome of M. fijiensis were investigated.ResultsA total of 613 LTR-Gypsy and 27 LTR-Copia complete elements of the class I were detected. Among the class II elements, a total of 28 Mariner, five Mutator and one Harbinger complete elements were identified. The results of this study indicate that transposons were and are important ectopic recombination sites. A distribution analysis of a transposable element from each class of the M. fijiensis isolates revealed variable hybridization profiles, indicating the activity of these elements. Several genes encoding proteins involved in important metabolic pathways and with potential correlation to pathogenicity systems were identified upstream and downstream of transposable elements. A comparison of the sequences from different transposon groups suggested the action of the RIP silencing mechanism in the genome of this microorganism.ConclusionsThe analysis of TEs in M. fijiensis suggests that TEs play an important role in the evolution of this organism because the activity of these elements, as well as the rearrangements caused by ectopic recombination, can result in deletion, duplication, inversion and translocation. Some of these changes can potentially modify gene structure or expression and, thus, facilitate the emergence of new strains of this pathogen.

Transposable elements (TEs) are selfish fragments of DNA able to reproduce themselves into the host genomes. TEs typically occupy ∼40–50% of the mammalian genomes. In our studies, we focus on evolutionary recent TE inserts that appeared in the DNA of human ancestor lineage after divergence with the chimpanzee ancestry, i.e. less than ∼6 million years ago. These human specific elements (hsTEs) represent only a minor fraction of the whole TE cargo of the human genome. hsTEs are represented by the four families called HERV-K(HML-2), L1, Alu and SVA. The number of human specific copies for HERV-K(HML-2), L1, Alu and SVA families is approx. 150, 1,200, 5,500 and 860 copies per genome, respectively. Taken together, hsTEs shape ∼6.4 megabases of human DNA, which is about 6-times lower than what is occupied by the human specific simple nucleotide polymorphisms, and 23-times smaller than the overall length of human specific deletions and duplications. However, although modest in terms of genomic proportion, hsTEs should be regarded as the perspective candidates for being molecular genetic agents of human speciation. Unlike most of random mutations and duplications, each novel insert of hsTE has provided to the recipient genomic locus a set of functional transcriptional factor binding sites positively selected during the TE evolution. For example, clusters of novel inserts of Alu elements may serve as CpG islets, SVA elements provide functional splice sites and polyadenylation signals, whereas L1 and HERV-K(HML-2) elements donate enhancers, promoters, splice sites and polyadenylation signals. Significant proportion of the human-specific genomic deletions, duplications and translocations has been also generated due to ectopic recombinations between the different individual TE inserts. Among the other, we report for the first time a detailed functional characteristics of the HERV-K(HML-2) hsTEs done at the genome-wide level. We have identified 65 active in vivo human specific promoters contributed by these elements. We also identified three cases of the hsTE-mediated human specific transcriptional regulation of functional protein-coding genes taking part in brain development during embryogenesis. We found ∼180 human specific polyadenylation signals transferred by the SVA elements into the introns of known functional genes. Scaling of these data to the total number of the hsTEs predicts that hundreds of human genes are regulated by these elements. Finally, we discovered the first exclusively human specific TE family, represented by ∼80 members formed by a combination of a part of a CpG islet of human gene MAST2 ansd of the 3′-terminal part of an SVA retrotransposon. According to our estimates, this family, termed CpG-SVA, was far more active than the ancestral SVA family. Our data indicate that MAST2 regulatory sequence was recruited during the evolution to provide effective CpG-SVA transcription in human testicular germ-line cells.