The story began years earlier, when the research team, then working on the rice transposable element mPing, discovered that hydrostatic pressurization could mobilize mPing and its autonomous partner Pong in living plants. From that same experimental system, a single lineage was isolated and propagated by continuous self-pollination. By the ninth generation, designated HPM, the plants were unmistakably different from their wild-type ancestor, the japonica cultivar JL307. They were shorter, produced fewer tillers, and set seed far less reliably, a suite of agronomic changes that had remained stable through every selfed generation in between.

The phenotypic measurements were striking in their magnitude. Average plant height in the HPM lineage was 90.93 centimeters compared with 97.91 centimeters in the wild type, a difference the authors report with a probability value of 1.90 times ten to the minus seventeenth. Tiller number dropped from 29.79 per plant to 20.27, and the seed-setting rate, the proportion of spikelets that develop into filled grains, fell from 97.05 percent to 61.63 percent on average. Notably, the seed-setting distribution in HPM was bimodal: 44 percent of the measured plants showed severe reduction below 50 percent, while the remainder were largely comparable to the wild type, hinting at heterogeneity within the lineage that may itself reflect the mosaic nature of transposon activity.

To understand what was happening inside the genome, the team deployed a battery of molecular techniques. Transposon display, a polymerase chain reaction based method that maps insertion sites of a specific element, targeted mPing across roughly 1100 amplified fragments in four independent ninth-generation plants. Both novel bands and missing bands appeared in every HPM plant relative to the wild type, with polymorphism rates between 0.82 and 0.91 percent. This confirmed that the miniature inverted-repeat transposable element, famously responsive to environmental and genomic perturbation in rice, remained mobile generations after the pressure treatment, its excisions and reinsertions still churning through the genome.

Whole-genome resequencing then widened the lens beyond mPing. Using a paired-end mapping strategy on an Illumina platform, with sequencing depths of roughly 13.2-fold for the wild type and 21.7-fold for HPM, the researchers identified 255 candidate transposable element insertion sites specific to the pressure-derived lineage. The insertions were far from randomly distributed among element families. The LTR retrotransposons Dasheng and Hopi dominated, contributing 73 and 44 candidate insertions respectively, followed by Osr29 with 17 and Echidne with 16. This pattern makes biological sense: LTR retrotransposons are the most abundant class in the rice genome and propagate through a copy-and-paste mechanism, so even a modest number of activation events can seed many new insertions and amplify genomic diversity without requiring excision.

The epigenetic layer told a complementary story. Methylation-sensitive amplified polymorphism analysis, which uses the restriction enzymes HpaII and MspI to probe cytosine methylation at CCGG sites, generated 1189 reproducible fragments per sample. Across all four HPM plants, between 4.63 and 5.72 percent of scored fragments showed methylation polymorphisms, and hypomethylation consistently outnumbered hypermethylation in both CG and CHG sequence contexts. In other words, the pressure-derived lineage had undergone a general loosening of DNA methylation, the very epigenetic mark that normally keeps transposable elements locked in a silent state. The concordance between reduced methylation and ongoing transposon activity is exactly what models of stress-induced genome destabilization would predict.

To connect methylation to gene function, the team selected four genes that the microarray analysis showed to be strongly upregulated in HPM and sequenced bisulfite-converted promoter DNA at each locus. Three of the four promoters showed statistically supported methylation losses at individual cytosine positions. The most dramatic case was LOC_Os02g48770, whose promoter methylation collapsed from 23.01 percent in the wild type to 2.81 percent in HPM, accompanied by a 9.71-fold increase in transcript abundance. LOC_Os06g48870 dropped from 38.85 to 23.48 percent methylation alongside a 23.12-fold expression increase, and LOC_Os03g08320 fell from 65.98 to 54.64 percent with an 11.51-fold increase. The fourth gene showed only a small, statistically unsupported change. Although four loci cannot settle a genome-wide question, the pattern is consistent with the classical inverse relationship between promoter methylation and transcriptional activity.

The transcriptomic survey itself was sweeping. Of 1079 candidate differentially expressed probes identified on the Affymetrix Rice Genome Array with a fold change of at least two, 305 remained significant after Benjamini-Hochberg correction at a false discovery rate below 0.05. Among the affected genes, transcription factor families prominent in plant stress signaling stood out: twelve WRKY genes, nine ERF/AP2 genes, eight MYB genes, and five VQ-associated genes showed altered expression, alongside members of the NAC, bHLH, Dof, and homeobox families. Stress-responsive genes were also dramatically induced, including WRKY71 with a 25.98-fold increase and the glutathione S-transferase gene GST42 with a 79.34-fold increase, together with chitinases and genes involved in reactive oxygen species detoxification and cell wall processes. Quantitative RT-PCR on twelve selected genes confirmed the direction of the microarray results.

The authors are careful about what these correlations do and do not prove. Because the analyzed material descends from a single lineage maintained by selfing, contributions from spontaneous mutation or cumulative selection during propagation cannot be formally excluded. The study is descriptive: transposon mobilization, methylation change, and transcriptional reprogramming co-occur, but causal chains linking the pressure treatment to each molecular alteration, or linking any single insertion to a specific trait, remain unestablished. Individual insertion events were not validated by locus-specific polymerase chain reaction, zygosity was not determined, the phenotypic evaluation covered a single growing season, and segregation analysis through reciprocal crosses, which would be needed to demonstrate Mendelian inheritance, was not performed. The persistence of the phenotype across nine generations, while remarkable, is not by itself proof of classical heritability.

Even with those caveats, the implications are considerable. Hydrostatic pressure is an exotic stimulus in plant biology, and this study is, to the authors’ knowledge, the first to document such multi-level molecular variation persisting in a selfed lineage derived from pressure-treated seeds. The findings echo Barbara McClintock’s long-standing proposal that genomes respond to challenge by reorganizing themselves, and they align with modern evidence that drought, salinity, temperature stress, and tissue culture can all awaken dormant transposable elements and reshape methylomes. Practically, the work suggests that hydrostatic pressure could complement conventional mutagens in rice breeding, either as a physical mutagen for generating novel germplasm or as a platform for transposon-based gene tagging. As genome-wide methylome profiling and functional validation of candidate genes mature, the pressure-squeezed rice of Jilin may prove to be more than a curiosity: it could become a standard system for dissecting how environmental shocks become written into the heritable fabric of a crop genome.

Subject of Research: Transgenerational molecular and phenotypic variation induced by hydrostatic pressure in rice

Article Title: Hydrostatic pressure-induced heritable variation in rice is associated with transposon mobilization, DNA methylation changes, and transcriptional reprogramming

Article References: Hu, L., Wang, Q., Li, Y., Jiang, W., Zhong, Y., Huang, S., Feng, Z., Xing, X., Guo, B., Peng, J., Du, X., & Ma, Z. (2026). Hydrostatic pressure-induced heritable variation in rice is associated with transposon mobilization, DNA methylation changes, and transcriptional reprogramming. Plant Cell Reports, 45(11), Article 322. https://doi.org/10.1007/s00299-026-04009-y

Image Credits: AI Generated

DOI: 10.1007/s00299-026-04009-y

Keywords: rice, hydrostatic pressure, transposable elements, mPing, DNA methylation, epigenetics, transcriptional reprogramming, LTR retrotransposons, plant breeding, stress response, heritable variation, WRKY transcription factors

The Copia superfamily belongs to the long terminal repeat, or LTR, retrotransposons. These elements replicate through an RNA intermediate, in a manner reminiscent of retroviruses, using a reverse transcriptase enzyme to copy their RNA back into DNA that is then inserted at a new genomic location. Genome-based surveys had previously identified roughly 25 distinct Copia clades, which are deep evolutionary lineages within the superfamily, each defined by characteristic sequences in the reverse transcriptase and RNase H domains of the pol region. Importantly, the earlier work revealed a striking pattern: Copia clades appeared to be strongly partitioned between marine and terrestrial animals, as though a boundary drawn at the water’s edge also ran through the repetitive DNA content of animal genomes.

That earlier picture, however, came with a caveat. It was built largely from whole-genome sequences, and genomes are expensive to produce. As a result, the taxonomic sampling was uneven, dominated by a handful of well-studied model organisms and major phyla while many minor lineages of the animal kingdom remained unexamined. Whether the marine-terrestrial dichotomy held across the full breadth of metazoan diversity, or whether entirely new clades were hiding in unexplored genomes, could not be answered with confidence from genome data alone.

The French team, based at the Station Biologique de Roscoff, Nantes University and the Muséum national d’Histoire naturelle, took a different route. Rather than relying on genomes, they mined transcriptomes, the sets of expressed RNA sequences, across 315 species, supplementing these with additional database searches. Transcriptomes are far more numerous than genomes, because RNA sequencing has been applied broadly across biodiversity sampling efforts, even for organisms whose genomes will never be assembled. The strategy pushed taxonomic coverage into 12 phyla that had previously gone unsampled, including many of the so-called minor taxa, small-bodied and evolutionarily pivotal groups such as springtails, two-pronged bristletails, velvet worms and tardigrades.

From this expanded dataset the researchers recovered 1,285 Copia elements, most of which could be confidently assigned to known clades through analysis of the reverse transcriptase and RNase H protein domains, the standard markers used to classify LTR-retrotransposons. Two major conclusions emerged. First, the diversity of Copia clades in animals appears to be close to exhaustive: despite broadening the search into a dozen new phyla, the team detected no previously unknown clades. This saturation is itself informative, suggesting that the catalog of animal Copia lineages assembled over the past two decades is nearly complete and that future discoveries, if any, will be rare.

Second, the marine-terrestrial dichotomy survived the broader test intact. Copia clades consistently fell into two environmental groups, one dominated by marine species and the other by terrestrial ones. The conservation of this pattern across such a wide range of animals implies that it is not a statistical artifact of sparse sampling but a genuine biological signal. What could explain it? The authors point to a combination of ecology and phylogeny. The water-to-land transition in animal history was a major evolutionary event, and the major lineages that made that transition carried with them a specific set of retrotransposon lineages. Environment and ancestry are therefore intertwined: the clades animals carry today reflect both where they live and who their ancestors were.

The study also refined the ranges of clades that appear restricted to particular animal groups. Most taxon-specific clades remain confined to their known hosts, although improved sampling tightened the estimates of their distribution. The most striking case concerns the CoCol clade, which had previously been found only in Collembola, the springtails, tiny hexapods that abound in soils worldwide. The new transcriptome survey confirmed the strong specificity of CoCol for springtails and, crucially, extended it to the Diplura, the two-pronged bristletails, another group of entognathous hexapods. This shared presence suggests that CoCol colonized the common ancestor of these early-diverging hexapod lineages, a single ancient invasion whose descendants persist in both groups today.

That finding becomes even more interesting when set against the broader arthropod context. Other terrestrial euarthropods, including the insects proper, crustaceans on land, arachnids and myriapods, display high Copia diversity, carrying representatives of many clades rather than a single host-specific lineage. The velvet worms, or Onychophora, close relatives of arthropods that live in moist terrestrial habitats, likewise show a rich complement of Copia elements. In other words, being terrestrial did not impose a uniform retrotransposon profile on all land animals. Springtails and bristletails stand out as exceptions, likely reflecting a distinctive early evolutionary history among the hexapods, whereas their terrestrial arthropod relatives accumulated a more diverse and dynamic Copia community.

Methodologically, the work demonstrates that transcriptomes, despite capturing only expressed sequences and typically only fragments of full-length retrotransposons, are a powerful resource for cataloguing transposable element diversity at the clade level. The reverse transcriptase and RNase H domains are conserved enough to be detected even in short expressed fragments, which is precisely what clade-level classification requires. The cost of this approach is that transcriptomes underestimate element copy number and may miss inactive, non-expressed families, so they complement rather than replace genome-based analyses. Used together, the two data types offer a far more comprehensive census of mobile element evolution than either alone.

The broader significance of the study lies in what it says about genome evolution across the animal kingdom. Transposable elements are key drivers of genome change, influencing genome size, recombination, gene regulation and adaptation. Understanding which element lineages are present in which animals provides a baseline for interpreting these processes. The confirmation that Copia clade diversity is nearly saturated, the robustness of the marine-terrestrial partition, and the phylogenetic resolution of the CoCol clade within early hexapods together sketch a coherent picture: the mobile element complement of an animal is a mosaic of deep ancestry and ecological circumstance. Minor taxa, often overlooked in genomic surveys, proved essential to seeing that picture clearly. As transcriptomic data continue to accumulate for understudied phyla, similar surveys promise to sharpen our understanding not only of Copia but of the full repertoire of mobile DNA that has accompanied animal evolution from the oceans onto land.

Subject of Research: Distribution and evolution of Copia LTR-retrotransposon clades across metazoans

Article Title: The analysis of minor taxa highlights the role of the environment and phylogeny in the distribution of the LTR-retrotransposon Copia clades

Article References: Lamothe, L., Klai, K., Farhat, S., & Bonnivard, E. (2026). The analysis of minor taxa highlights the role of the environment and phylogeny in the distribution of the LTR-retrotransposon Copia clades. Heredity. https://doi.org/10.1038/s41437-026-00888-9

Image Credits: AI Generated

DOI: 10.1038/s41437-026-00888-9

Keywords: Copia retrotransposons, LTR-retrotransposons, transposable elements, metazoans, transcriptomics, marine-terrestrial dichotomy, Collembola, Diplura, Hexapoda, genome evolution, phylogeny, Heredity

An international team of researchers led by Dmitrii I. Ostromyshenskii and Aleksandra O. Travina of the Institute of Cytology of the Russian Academy of Sciences, together with colleagues from The Center for Bio- and Medical Technologies in Moscow, carried out a genome-wide analysis of tandem repeats in nine species of ranid frogs. The species surveyed span a broad evolutionary range within the family, including the European common frog Rana temporaria, the Cascades frog Amerana muscosa, the Siberianewood frog relative Rana kukunoris, the moor frog relative Pelophylax lessonae, the northern leopard frog Lithobates pipiens, the American bullfrog Aquarana catesbeiana, Aquarana septentrionalis, the wood frog Boreorana sylvatica, and the torrent frog Staurois parvus. This choice of species allowed the team to examine repeat repertoires across multiple genera and lineages, giving the analysis genuine comparative power.

The technical foundation of the study was a systematic computational search for tandem repeats, sequences in which a repeating unit, or monomer, is arranged head to tail in long arrays. Using the Tandem Repeats Finder algorithm on genome assemblies of all nine species, the researchers catalogued thousands of repeat families, characterized their monomer lengths, GC content, array lengths, and copy numbers, and grouped them into families based on sequence similarity. The scale of the result was remarkable. Tandem repeat content in these frog genomes proved to be exceptionally high, and, crucially, it correlated positively with overall genome size. In other words, the frogs with the largest genomes also carried the largest loads of satellite DNA, a finding that supports the long-standing hypothesis that non-coding repetitive sequence accumulation, rather than gene duplication alone, is a major driver of genome size expansion in amphibians.

Perhaps the most eye-catching figure in the study concerns the origin of these repeats. When the researchers searched the repeat monomers against databases of known transposable elements, they found that a very large proportion of the tandem repeats shared sequence homology with transposable element families. Depending on the species, repeats with recognizable transposable element ancestry accounted for between 43 and 91 percent of the total tandem repeat length in the genome. These TE-based tandem repeats, the authors note, correlated not only with genome size but also with overall tandem repeat content, suggesting that the flux of transposable element sequence into satellite DNA is a continuous and quantitatively significant process in ranid evolution rather than a rare curiosity.

The transposable element classes implicated include some of the most widespread mobile genetic elements in eukaryotes: LINEs, or long interspersed nuclear elements; SINEs, or short interspersed nuclear elements; LTR retrotransposons, which move via an RNA intermediate; and MITEs, miniature inverted-repeat transposable elements, along with DNA transposons of the Tc1-Mariner superfamily. Sequence alignments revealed fragments of these elements embedded within repeat monomers and arrays, providing a molecular fingerprint of their conversion into tandemly repeated satellite DNA. The mechanistic picture that emerges is one in which insertions of transposable elements, or fragments thereof, occasionally seed new tandem repeat arrays, which can then expand through processes such as replication slippage, unequal crossing over, and rolling circle-like amplification into large satellite families.

Beyond their sheer abundance, the repeat families displayed a hierarchical pattern of conservation across the nine species. At one end of the spectrum, the team identified widely conserved repeat families whose sequences could be detected by similarity searches in many or even all of the sampled frogs, hinting at ancient repeat lineages that predate the diversification of the family. At the other end, many repeat families were lineage-restricted or entirely species-specific, detectable in only one of the nine genomes. This layered organization, from ancient shared repeats to young species-private satellites, mirrors patterns seen in other organisms and underscores the rapid turnover of satellite DNA, which can expand, degrade, and be replaced over relatively short evolutionary timescales.

Computational mapping of the repeats onto genome assemblies suggested that the tandem repeats were broadly distributed across chromosomes rather than confined to a single genomic compartment. To test this at the cytogenetic level, the researchers performed fluorescence in situ hybridization, or FISH, using probes derived from representative repeat families. The FISH experiments confirmed the in silico predictions, showing that both the transposable element-derived repeats and the repeats without detectable TE homology occupy pericentromeric regions near the centromeres, subtelomeric regions near chromosome ends, and interstitial positions along chromosome arms. This widespread chromosomal distribution distinguishes the frog repeats from the classic model of satellite DNA as material concentrated exclusively at centromeres.

The comparative presence-absence analysis across the nine species, compiled in a BLAST score-based matrix in the supplementary materials, allowed the team to quantify how repeat families diverge in sequence similarity between relatives and how quickly new families appear in individual lineages. Species such as Rana temporaria, Amerana muscosa, and Staurois parvus served as reference points for characterizing the transposable element composition of their repeat arrays, and the patterns consistently reinforced the conclusion that TE-derived satellites are a pervasive feature of ranid genomes. The coexistence of conserved and lineage-restricted repeat families, many of which carry transposable element signatures, indicates that transposable elements have been recruited repeatedly, and independently, in the emergence of new satellite repeats throughout the evolutionary history of the family.

The findings carry broader implications for understanding amphibian genome evolution and genome biology in general. Amphibian genomes can reach sizes many times larger than the human genome, and the sustained accumulation and expansion of tandem repeats documented in this study offers a compelling explanation for much of that bulk. More broadly, the study adds frogs to the growing list of organisms in which transposable elements act as raw material for the birth of satellite DNA, contributing to centromere structure, heterochromatin formation, and potentially to the reproductive isolation of lineages through rapid satellite divergence. The work was supported by the Russian Science Foundation under grant 25-24-01071, and all data and supplementary tables, including family-by-family repeat catalogues and comparative matrices, are openly available alongside the open-access publication, providing a valuable resource for anyone seeking to decode the repetitive architecture of these extraordinary genomes.

Subject of Research: Genome-wide analysis of tandem repeat repertoires and transposable element contributions in ranid frog genomes

Article Title: Extensive tandem repeat repertoires in ranid frogs and the role of transposable elements in their evolution

Article References: Ostromyshenskii, D. I., Ivanova, N. G., Popova, M. A., Pasynkova, R. A., Podgornaya, O. I., Litvinchuk, S. N., & Travina, A. O. (2026). Extensive tandem repeat repertoires in ranid frogs and the role of transposable elements in their evolution. BMC Biology. https://doi.org/10.1186/s12915-026-02718-0

Image Credits: AI Generated

DOI: 10.1186/s12915-026-02718-0

Keywords: tandem repeats, satellite DNA, transposable elements, Ranidae, amphibian genomes, genome evolution, Anura, FISH, genome size, LINE, SINE, LTR retrotransposons