Genome Biology and Evolution

Retrotransposons are mobile, repetitive DNA sequences that are ubiquitous across eukaryotes and widely recognised as key drivers of both gene and genome evolution. The CR1 group of retrotransposons is thought to have been present in the most recent common ancestor of chordates [~]560 mya, and is the dominant retrotransposon in the majority of chordate species. The advent of long-read sequencing technologies has enabled the assembly of high-quality genomes from representatives of almost all major chordate orders, enabling comparative analysis with deeply divergent species. To better understand the composition of CR1-group elements (CGEs) in chordates, we systematically characterised full-length, recently active transposable elements across representative species from every available extant order of chordate. Our analysis uncovered previously unknown phylogenetic relationships of CGEs within and between species and has pushed back the origin of certain CR1-group subclades by tens of millions of years. Additionally, entirely novel elements with no close relatives in existing databases were uncovered within several of the species analysed. We also detected numerous putative horizontal transfer events, many of which had not been previously documented. Overall, this investigation has provided the first chordate-wide analysis of an element that is historically understudied yet plays a pivotal role in genome biology and evolution.

Histone variants are paralogs that replace canonical histones in nucleosomes, often imparting novel functions. Despite their importance, how histone variants arise and evolve is poorly understood. Reconstruction of histone protein evolution is challenging due to high amino acid conservation and large differences in evolutionary rates across gene lineages and sites. Here we combined amino acid sequences and intron position data from 108 nematode genomes to trace the evolutionary histories of the three H2A variants found in Caenorhabditis elegans: the ancient H2A.ZHTZ-1, the sperm-specific HTAS-1, and HIS-35, which differs from canonical H2A by a single glycine-to-alanine C-terminal change. We find disparate evolutionary histories. Although the H2A.ZHTZ-1 protein is highly conserved, its gene exhibits recurrent intron gain and loss. This pattern suggests that it is intron presence, rather than specific intron sequences or positions, that may be important to H2A.Z functionality. In contrast, for HTAS-1 and HIS-35, we find variant-specific intron positions that are conserved across species. HIS-35 arose in the ancestor of Caenorhabditis and its sister group, including the genus Diploscapter, while the sperm-specific variant HTAS-1 arose more recently in the ancestor of a subset of Caenorhabditis species. HIS-35 exhibits gene retention in some descendent lineages but also recurrent gene loss in others, suggesting that histone variant use or functionality is highly flexible in this case. We also find that the single amino acid differentiating HIS-35 from core H2A is ancestral and common across canonical Caenorhabditis H2A sequences and identify one nematode species that bear identical HIS-35 and canonical H2A proteins, findings that are not predicted from the hypothesis that HIS-35 has a distinct function. Instead, we speculate that HIS-35 enables H2A expression across the cell cycle or in distinct tissues; genes encoding such partially-redundant functions may be advantageous yet relatively replaceable over evolutionary times, consistent with the patchwork pattern of retention and loss of both genes. Our study shows the evolutionary trajectory for histone H2A variants with distinct functions and the utility of intron positions for reconstructing the evolutionary history of gene families, particularly those undergoing idiosyncratic sequence evolution.

Comparisons of multiple metazoan genomes have revealed the existence of ancestral linkage groups (ALGs), genomic scaffolds sharing sets of orthologous genes that have been inherited from ancestral animals for hundreds of millions of years (Simakov et al. 2022; Schultz et al. 2023) These ALGs have persisted across major animal taxa including Cnidaria, Deuterostomia, Ecdysozoa and Spiralia. Notwithstanding this general trend of chromosome-scale conservation, ALGs have been obliterated by extensive genome rearrangements in certain groups, most notably including Clitellata (oligochaetes and leeches), a group of easily overlooked invertebrates that is of tremendous ecological, agricultural and economic importance (Charles 2019; Barrett 2016). To further investigate these rearrangements, we have undertaken a comparison of 12 clitellate genomes (including four newly sequenced species) and 11 outgroup representatives. We show that these rearrangements began at the base of the Clitellata (rather than progressing gradually throughout polychaete annelids), that the inter-chromosomal rearrangements continue in several clitellate lineages and that these events have substantially shaped the evolution of the otherwise highly conserved Hox cluster.

The origin of meiotic sex was a key milestone in the evolution of the eukaryotic cell. The DNA recombinases Rad51 and DMC1 have been used previously to trace the timing and origins of the meiotic machinery, and warrant revisiting in the face of the recent increased diversity of reported asgardarchaeal taxa. Here we perform comparative genomics and phylogenetic analyses of RadA protein sequences from a broad sampling of eukaryotic and archaeal taxa. We show that even with increased and new sampling, the eukaryotic Rad51 and DMC1 proteins still resolve separately from any archaeal RadA sequences. Taking into account recent evolutionary cell biological discoveries, our data are most consistent with a scenario whereby the asgardarchaeal host cell was evolving cytoskeletal and membrane-protein machinery that was later incorporated into eukaryotic endomembrane systems following the acquisition of mitochondria and the evolution of sex.

BackgroundNotothenioids are a well characterised species flock endemic to the Antarctic and an important model group for the study of genome adaptation to extreme cold. We used a new reference assembly and clade-wide comparative genomic analysis to investigate cryonotothenioid evolution and the appearance of novel functionalities linked to cold adaptation. ResultsA new phased assembly of a model notothenioid, Harpagifer antarcticus, demonstrated low levels of haplotypic variability across the genome. Nevertheless, numerous insertions from multiple LINE-L2 clades were found, suggesting ongoing transposition with potential contribution to speciation. Contrary to expectations the afgp locus was highly similar between haplotypes, except for large length allelic variants of afgp genes. Analysis suggests a model for the afgp locus expansion in H. antarcticus through segmental tandem duplications involving two pairs of afgp genes at time. Syntenic reconstruction of genomes from across the clade demonstrates conserved macrosyntenic relationships and group specific chromosomal fusions of notothenioids. Quantification of genome gain and transposition rates during cryonotothenioid diversification showed a first ancestral slow genome expansion concurrent with historic temperature drops. This was followed by lineage-specific massive peaks of genomic gain and transposition activity. Finally, we identified a set of genes that underwent ancestral diversifying selection and acquired novel conserved non-coding elements during the cryonotothenioid emergence. These were related to antioxidants and proteostasis, which may have facilitated the notothenioid Antarctic radiation. ConclusionDiversifying selection and genomic gain linked to transposon activity are primary contributors to lineage-specific evolutionary dynamics through the clade which facilitated adaptation to life in the cold.

The process of evolutionary change remains poorly understood. By analyzing genomic data from 12 populations in Lenskis long-term evolution experiment (LTEE) over 60,000 generations, we identified a clear sequence in gene adaptation: growth-related genes evolved early, while survival-related genes evolved later. Early-evolving genes exhibited higher rates of both nonsynonymous and synonymous substitutions. We also observed a general decline in gene evolutionary rates across LTEE populations, with additional data highlighting the role of fitness gains in determining evolutionary rates. These findings suggest that, in a relatively stable environment, the fitness gains from beneficial mutations decrease as adaptation progresses. This diminishing return on fitness gains may represent a key evolutionary rule, potentially contributing to evolutionary stasis and the prevalence of neutral evolution.

Gene duplication is associated with the evolution of many novel biological functions at the molecular level. The dominant view, often referred to as "neofunctionalization", states that duplications precede many novel gene functions by creating functionally redundant copies which are less constrained than singletons. However, numerous alternative models have been formulated, including some in which novel functions emerge prior to duplication. Unfortunately, few studies have reconstructed the evolutionary history of a functionally diverse gene family sufficiently well to differentiate between these models. Here we examined the evolution of the g2 family of phospholipase A2 (EC 3.1.1.4) in the genomes of 93 species from all major lineages of Vertebrata. This family is evolutionarily important and has been co-opted for a diverse range of functions, including innate immunity and venom. The genomic region in which this family is located is remarkably syntenic. This allowed us to reconstruct all duplication events over hundreds of millions of years of evolutionary history using manual annotation of gene clusters, which enabled the discovery of a large number of previously un-annotated genes. Intriguingly, we found that the same ancestral gene in the phospholipase gene cluster independently acquired novel molecular functions in birds, mammals and snake, and all subsequent expansion of the cluster originates from this locus. This suggests that the locus has a deep ancestral propensity for multiplication, likely conferred by a structural arrangement of genomic material (i.e. the "genomic context" of the locus) that dates back at least the amniote MRCA. These results highlight the underlying complexity of gene family evolution, as well as the historical- and context-dependence of gene family evolution. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=137 SRC="FIGDIR/small/583344v3_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@1c3228forg.highwire.dtl.DTLVardef@12053forg.highwire.dtl.DTLVardef@11683c0org.highwire.dtl.DTLVardef@123eb3a_HPS_FORMAT_FIGEXP M_FIG C_FIG

Bacteria, Archaea, and Eukarya all share a common set of metabolic reactions. This implies that the function and topology of central metabolism has been evolving under purifying selection over deep time. Central metabolism may similarly evolve under purifying selection during longterm evolution experiments, although it is unclear how long such experiments would have to run (decades, centuries, millennia) before signs of purifying selection on metabolism appear. I hypothesized that central and superessential metabolic enzymes would show evidence of purifying selection in the long-term evolution experiment with Escherichia coli (LTEE). I also hypothesized that enzymes that specialize on single substrates would show stronger evidence of purifying selection in the LTEE than generalist enzymes that catalyze multiple reactions. I tested these hypotheses by analyzing metagenomic time series covering 62,750 generations of the LTEE. I find mixed support for these hypotheses, because the observed patterns of purifying selection are idiosyncratic and population-specific. To explain this finding, I propose the Jenga hypothesis, named after a childrens game in which blocks are removed from a tower until it falls. The Jenga hypothesis postulates that loss-of-function mutations degrade costly, redundant, and nonessential metabolic functions. Replicate populations can therefore follow idiosyncratic trajectories of lost redundancies, despite purifying selection on overall function. I tested the Jenga hypothesis by simulating the evolution of 1,000 minimal genomes under strong purifying selection. As predicted, the minimal genomes converge to different metabolic networks. Strikingly, the core genes common to all 1,000 minimal genomes show consistent signatures of purifying selection in the LTEE. Significance StatementPurifying selection conserves organismal function over evolutionary time. However, few studies have examined the role of purifying selection during adaptation to novel environments. I tested metabolic enzymes for purifying selection in an ongoing long-term evolution experiment with Escherichia coli. While some populations show signs of purifying selection, the overall pattern is inconsistent. To explain these findings, I propose the Jenga hypothesis, in which loss-of-function mutations first degrade costly, redundant, and nonessential metabolic functions, after which purifying selection begins to dominate. I then tested several predictions of the Jenga hypothesis using computational simulations. On balance, the simulations confirm that we should find evidence of purifying selection on the metabolic pathways that sustain growth in a novel environment.

Genomic repeats, particularly simple sequence repeats, influence genome stability and gene regulation. While many genomic traits exhibit phylogenetic signal and pulsed evolution, repeat elements have rarely been examined in a comparative framework, and their evolutionary relationships with other genome features remain poorly understood. We contrasted the trait evolution of genomic repeats with non-repeat traits across diverse actinobacterial orders, testing for phylogenetic signal, evolutionary mode, and pulsed dynamics using time-calibrated, 16S rRNA, and whole-genome sequence (WGS) trees. Non-repeat traits consistently exhibited signs of punctuated evolution, with larger pulses in species-rich orders such as Mycobacteriales and Actinomycetales; repeats, by contrast, were evolutionarily labile, lacking phylogenetic signal and largely decoupled from other genomic traits. Bifidobacteriales was the sole exception, with repeats exhibiting phylogenetic signal only under the WGS tree. The WGS tree also recovered a stronger signal for genome-level traits, highlighting its utility in comparative analyses. Genome size evolution in Actinomycetota appears driven primarily by protein-coding gene expansion rather than repeat accumulation.

Since the formation of the first proto-eukaryotes, more than 1.5 billion years ago, eukaryotic gene repertoire as well as genome complexity has significantly increased. Among genetic elements that are responsible for this increase in genome coding capacity and plasticity are tandem repeats such as microsatellites, minisatellites and their bigger brothers, megasatellites. Although microsatellites have been thoroughly studied in many organisms for the last 20 years, little is known about the distribution and evolution of mini- and megasatellites. Here, we describe the first genome-wide analysis of megasatellites in 58 vertebrate genomes, belonging to 12 monophyletic groups. We show that two bursts of megasatellite formation occurred, one after the radiation between agnatha et gnathostomata fishes and the second one later, in therian mammals. Megasatellites are frequently encoded in genes involved in transcription regulation (zinc-finger proteins) and intracellular trafficking, but also in cell membrane metabolism, reminiscent of what was observed in fungi genomes. The presence of many introns within young megasatellites suggests a model in which an exon-intron DNA segment is first duplicated and amplified before the accumulation of mutations in intronic parts partially erase the tandem repeat in such a way that it becomes detectable only in exonic regions. In addition, evidence for the genetic transfer of megasatellites between unrelated genes suggests that megasatellite formation and evolution is a very dynamic and still ongoing process in vertebrate genomes.

Bacterial strains evolve in response to the gut environment of their hosts, with genomic changes that influence their interactions with hosts as well as with other members of the gut community. Great apes in captivity have acquired strains of Bacteroides xylanisolvens, which are common within gut microbiome of humans but not typically found other apes, thereby enabling characterization of strain evolution following colonization. Here, we isolate, sequence and reconstruct the history of gene gain and loss events in numerous captive-ape-associated strains since their divergence from their closest human-associated strains. We show that multiple captive-ape-associated B. xylanisolvens lineages have independently acquired gene complexes that encode functions related to host mucin metabolism. Our results support the finding of high genome fluidity in Bacteroides, in that several strains, in moving from humans to captive apes, have rapidly gained large genomic regions that augment metabolic properties not previously present in their relatives. Significance statementChronicling the changes that occur in bacterial genomes after a host-switch event is normally difficult due to age of most bacteria-host associations, which renders uncertainties about the bacterial ancestor (and ancestral genome) prior to colonization of the new host. However, the gut microbiomes of great apes in captivity contain bacterial strains that are unique to humans, allowing fine-scale assessment and reconstruction of the genomic changes that follow colonization. By sequencing and comparing closely related strains of Bacteroides that are restricted both to human and to captive great apes, we found that multiple bacterial lineages convergently acquired sets of genes involved in the metabolism of dietary polysaccharides. These results show that over relatively short timescales, the incorporation of strains into microbiomes involves large-scale genomic events that correspond to characteristics of the new host environment.

Genome size has been measurable since the 1940s but we still do not understand the basis of genome size variation. Caenorhabditis nematodes show strong conservation of chromosome number but vary in genome size between closely related species. Androdioecy, where populations are composed of males and self-fertile hermaphrodites, has evolved from outcrossing, female-male dioecy, three times in this group. Androdioecious genomes are 10-30% smaller than dioecious species but large phylogenetic distances and rapid protein evolution have made it difficult to pinpoint the basis of these changes. Here, we analyze the genome sequences of Caenorhabditis and and test three hypotheses explaining genome evolution: 1) genomes evolve through deletions and genome shrinkage in androdioecious species; 2) genome size is determined by transposable element (TE) expansion and DNA loss through large deletions (the accordion model); and 3) TE dynamics differ in androdioecious and dioecious species. We find no evidence for these hypotheses in Caenorhabditis. Across both short and long evolutionary distances Caenorhabditis genomes evolve through small structural variant (SV) mutations including frequent duplications and insertions, predominantly in genic regions. Caenorhabditis have rapid rates of gene family expansion and contraction and we identify 71 protein families with significant, parallel decreases across self-fertile Caenorhabditis. These include genes involved in the sensory system, regulatory proteins and membrane-associated immune responses, reflecting the shifting selection pressures that result from self-fertility. Our results suggest that the rules governing genome evolution differ between organisms based on ecology, life style and reproductive system.

Octopuses are phenotypically distinctive organisms, and recent genomic work raises questions about the contributions of transposable elements (TE) to their genomic architecture. We leveraged a robust repeat annotation pipeline, in combination with manual and automated curatorial techniques, to produce a more comprehensive repeat annotation of Octopus vulgaris. This revealed that [~]66% of the genome are repeats, in contrast to previous estimates of 43-50%. Whereas previous studies of TE expansion in Octopus bimaculoides identified two bursts of activity, 25 and 56 MYA, our re-annotation revealed four such expansions at 18, 25, 33, and 56 MYA. We further identified a landscape of TE hot- and cold spots. This much refined TE timescape and landscape will serve as a useful basis for understanding TE contributions to O. vulgaris evolution, and also for identifying factors contributing to variation in the TE community across genomic space and evolutionary time.

The haplochromine cichlid fishes of Lake Malawi form one of the most dramatic examples of recent rapid radiation in vertebrates. Here we describe nine new diploid telomere-to-telomere (T2T) genome sequences generated using ultra-long ONT reads, which include 78 ungapped chromosomes. We provide accurate annotations of transposable elements and tandem repeats, identify rDNA cluster regions and putative centromeres, and confirm previously reported large chromosomal inversions. The putative centromeres are primarily composed of satellite tandem arrays of previously reported 237 bp repeats, but notably on most chromosomes these are organised in a novel structure in which four blocks of satellites in alternating orientation are separated by an inverted pair of ~15 kb sequences we term 'centroids', which have similarity to a non-autonomous DNA transposable element and containing potential CENP-B binding boxes. The methylation dip region indicating the likely active centromere always lies between the centroids, whose separation is almost always around 200 kb (interquartile range 151-221kb). A structurally equivalent but non-homologous organisation is seen in the distantly related Etroplus cichlid genera from South Asia. By comparing these structures across chromosomes and species, we suggest how they may have evolved, and potentially how they could contribute to the rampant sympatric speciation seen in these species, based on meiotic drive and chromosome missegregation.

The placement of a non-hyperthermophilic order Mesoaciditogales at the base of Thermotogota tree challenges the prevailing hypothesis that the last common ancestor of Thermotogota was a hyperthermophile. Yet, given the long branch leading to the only two Mesoaciditogales described to-date, the phylogenetic position of the order may be due to the long branch attraction artifact. By testing various models and applying data recoding in phylogenetic reconstructions, we observed that Mesoaciditogales basal placement is strongly supported by the conserved marker genes assumed to be vertically inherited. However, based on the taxonomic content of 1,181 gene families and a phylogenetic analysis of 721 gene family trees, we also found that a substantial number of Mesoaciditogales genes are more closely related to species from the order Petrotogales. These genes contribute to coenzyme transport and metabolism, fatty acid biosynthesis, genes known to respond to heat and cold stressors, and include many genes of unknown functions. The Petrotogales comprise moderately thermophilic and mesophilic species with similar temperature tolerances to that of Mesoaciditogales. Our findings hint at extensive horizontal gene transfer between, or parallel independent gene gains by, the two ecologically similar lineages, and suggest that the exchanged genes may be important for adaptation to comparable temperature niches. SignificanceThe high-temperature phenotype is often referenced when conjecturing about characteristics of the last common ancestor of all present-day organisms. Such inferences rely on accuracy of phylogenetic trees, especially with respect to lineages that branch closest to the last common ancestor. Here, we examined evolutionary history of Mesoaciditogales, an early-branching lineage within Thermotogota phylum, which is one of the early-diverging groups of bacteria. Thermotogota is composed of thermophiles, hyperthermophiles and mesophiles, who collectively can grow between 20 to 90 degrees Celsius, making it challenging to infer the growth temperature of their common ancestor. Our analysis revealed a complex evolutionary history of Mesoaciditogales genome content impacted by horizontal gene transfer, highlighting the challenges of ancestral phenotype inferences using present-day genomes.

Size evolution among gigantic genomes involves gain and loss of many gigabases of transposable elements (TEs), sequences that parasitize host genomes. Animals suppress TEs using piRNA and KRAB-ZFP pathways. TEs and hosts coevolve in an arms race, where suppression strength reflects TE fitness costs. In enormous genomes, additional TE costs become miniscule. How, then, do TEs and host suppression invoke further addition of massive DNA amounts? We analyzed TE proliferation histories, deletion rates, and community diversities in six salamander genomes (21.3 - 49.9 Gb), alongside gonadal expression of TEs and suppression pathways. TE activity is higher in testes than ovaries, attributable to lower KRAB-ZFP suppression. Unexpectedly, genome size/expansion is uncorrelated with TE deletion rate, proliferation history, expression, and host suppression. Also, TE community diversity increases with genome size, contrasting theoretical predictions. TE/host antagonism in gigantic genomes likely produces stochastic TE accumulation, determined by noisy intermolecular interactions in huge genomes/cells.

Ciliates are a diverse group of single-celled eukaryotes that can exhibit a wide range of genetic diversity within morphologically indistinguishable species. However, they are still not well studied as their mechanisms of speciation and the extent of diversification remain unknown. Mitochondrial genomes offer an effective framework for resolving species relationships and evolutionary changes. Here, we analyzed a globally sampled dataset of Paramecium to understand the evolution of mitochondrial genomes in ciliates. Phylogenetic analysis of linear mitochondrial genomes shows the presence of cryptic diversity beyond the P. aurelia complex, with P. bursaria lineage appearing as a deeply diverging out-group. Protein-coding genes are largely conserved, with limited rearrangements, and some ciliate-specific genes appear to be missing in P. bursaria. Population genetic analysis show little to no evidence of recombination along with substantial differences in effective population size across species. Patterns of molecular evolution also indicate purifying selection as the predominant force, the strength of which is at least as strong as in the nucleus and consistent with mitochondrial effective population sizes that are similar or larger than those of the nucleus. Across the functional groups, the electron transport chain and ribosomal genes are highly constrained, while ciliate-specific ymf genes show reduced efficacy of selection compared to the others. These findings offer a basis for connecting mitochondrial variation to evolutionary divergence, functional constraint, and speciation in microbial eukaryotes.

Repetitive DNA make up a considerable fraction of most eukaryotic genomes. In fish, transposable element (TE) activity have coincided with rapid species diversification. Here, we annotated the repetitive content in 100 genome assemblies, covering the major branches of the diverse lineage of teleost fish. We investigated if TE content correlates with family level net diversification rates and found support for a weak negative correlation. Further, we found that TE content, the degree of parental care and short tandem repeat (STR) content contributed to genome size variability. In contrast to TEs, STR content showed a negative relationship with genome size. STR content did not correlate with TE content, which implies independent evolutionary paths. Last, marine and freshwater fish have large differences in STR content. The most extreme propagation was found in the genomes of codfish species and Atlantic herring. Such a high density of STRs is likely to increase the mutational load, which we propose could be counterbalanced by high fecundity as seen in codfishes and herring.

The evolution of the nervous system has been shrouded in controversy since the onset of the genomics era. A large part of this controversy stems from the lack of phylogenetic consensus for the main branches of the animal tree, where often animals with nervous systems do not form a monophyletic group. However, this question can be informed from other non-phylogenetic perspectives, such as comparative genomics. Here we ask how similar are genes differentially expressed in neurons across a representative set of eight animals with a nervous system and tally the presence or absence of their homologs in 10 other animals and two choanoflagellates. We show that proteins from 39 families are differentially expressed in all neurons, regardless of the phylogenetic placement of their lineage, and that the majority of these gene families are present in the (unicellular) closest relatives of animals, choanoflagellates. We found that the members of these 39 gene families are enriched in domains for ion transport and juxtacrine signalling, and that there is one gene family of zinc-dependent extracellular matrix-remodelling proteins which is only found in animals bearing a nervous system. Our results show that common genetic toolkits are in place for the function of nervous systems. We identify a large number of potential new genomic markers linked to the nervous system and hope they can complement ongoing research efforts to better understand this quintessentially animal system.

BackgroundTransposable elements (TEs) are repetitive genetic elements that can jump to new loci causing genome expansions, structural rearrangements, and can, ultimately, propel the evolution of genomes. Despite their significance, the role of TEs in the evolution of genomes and phylogenetic groups remains largely understudied in early diverging lineages. Further, the extent to which TE content varies across species is still an open question. Medusozoa, a group within Cnidaria encompassing jellyfish and hydroids, exhibits an exceptional diversity of life history strategies, body plans, and physiological capabilities. These characteristics, along with its early-diverging phylogenetic position, establish Medusozoa as an ideal system for investigating the composition and evolutionary history of TEs within the group. ResultsWe generated a custom repeat library built from annotations of 25 Medusozoan genomes and used it to characterize TEs, aiming to identify lineage-specific TE content and activity that may correlate with the diversity observed within the group. We found that repetitive element percentage and genome size varied considerably, with Hydrozoa exhibiting the most variation among classes in both respects. DNA transposons were the most prevalent TE classification in all but two genomes, averaging 28% of all genomes. Intra-genus comparisons revealed a surprising degree of differences in TE content. In the genus Aurelia, the expansion of a single DNA transposon superfamily accounted for much of the difference in repetitive element percentage between two species, whereas in the genus Turritopsis, a similar divergence resulted from the proliferation of multiple superfamilies. Interestingly, most genomes showed evidence of recent TE expansions, suggesting ongoing activity in many medusozoan species. ConclusionWe present the first comparative analysis of TEs across all medusozoan classes. Our results reveal class-specific TE dynamics and highlight cases of TE proliferations as lineages diverge. This research provides data on TE activity and diversity that can be used as a resource for future study and fills important gaps in our understanding of TEs in early diverging animal lineages.