Genome editing in plants using the TnpB transposase system.

The widely used clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated nuclease (Cas) system is thought to have evolved from IS200/IS605 transposons. TnpB proteins, encoded by one type of IS200/IS605 transposon, are considered to be the evolutionary ancestors of Cas12 nucleases, which have been engineered to function as RNA-guided DNA endonucleases for genome editing in bacteria and human cells. TnpB nucleases, which are smaller than Cas nucleases, have been engineered for use in genome editing in animal systems, but the feasibility of this approach in plants remained unknown. Here, we obtained stably transformed genome-edited mutants in rice (Oryza sativa) by adapting three recently identified TnpB genome editing vectors, encoding distinct TnpB nucleases (ISAam1, ISDra2, and ISYmu1), for use in plants, demonstrating that the hypercompact TnpB proteins can effectively edit plant genomes. ISDra2 and ISYmu1 precisely edited their target sequences, with no off-target mutations detected, showing that TnpB transposon nucleases are suitable for development into a new genome editing tool for plants. Future modifications improving the genome-editing efficiency of the TnpB system will facilitate plant functional studies and breeding programs. Supplementary Information: The online version contains supplementary material available at 10.1007/s42994-024-00172-6.

Low-input PacBio sequencing generates high-quality individual fly genomes and characterizes mutational processes.

Long-read sequencing, exemplified by PacBio, revolutionizes genomics, overcoming challenges like repetitive sequences. However, the high DNA requirement ( > 1 µg) is prohibitive for small organisms. We develop a low-input (100 ng), low-cost, and amplification-free library-generation method for PacBio sequencing (LILAP) using Tn5-based tagmentation and DNA circularization within one tube. We test LILAP with two Drosophila melanogaster individuals, and generate near-complete genomes, surpassing preexisting single-fly genomes. By analyzing variations in these two genomes, we characterize mutational processes: complex transpositions (transposon insertions together with extra duplications and/or deletions) prefer regions characterized by non-B DNA structures, and gene conversion of transposons occurs on both DNA and RNA levels. Concurrently, we generate two complete assemblies for the endosymbiotic bacterium Wolbachia in these flies and similarly detect transposon conversion. Thus, LILAP promises a broad PacBio sequencing adoption for not only mutational studies of flies and their symbionts but also explorations of other small organisms or precious samples.

Chasing Sequencing Perfection: Marching Toward Higher Accuracy and Lower Costs.

Next-generation sequencing (NGS), represented by Illumina platforms, has been an essential cornerstone of basic and applied research. However, the sequencing error rate of 1 per 1000 bp (10-3) represents a serious hurdle for research areas focusing on rare mutations, such as somatic mosaicism or microbe heterogeneity. By examining the high-fidelity sequencing methods developed in the past decade, we summarized three major factors underlying errors and the corresponding 12 strategies mitigating these errors. We then proposed a novel framework to classify 11 preexisting representative methods according to the corresponding combinatory strategies and identified three trends that emerged during methodological developments. We further extended this analysis to eight long-read sequencing methods, emphasizing error reduction strategies. Finally, we suggest two promising future directions that could achieve comparable or even higher accuracy with lower costs in both NGS and long-read sequencing.

Heterologous survey of 130 DNA transposons in human cells highlights their functional divergence and expands the genome engineering toolbox.

Experimental studies on DNA transposable elements (TEs) have been limited in scale, leading to a lack of understanding of the factors influencing transposition activity, evolutionary dynamics, and application potential as genome engineering tools. We predicted 130 active DNA TEs from 102 metazoan genomes and evaluated their activity in human cells. We identified 40 active (integration-competent) TEs, surpassing the cumulative number (20) of TEs found previously. With this unified comparative data, we found that the Tc1/mariner superfamily exhibits elevated activity, potentially explaining their pervasive horizontal transfers. Further functional characterization of TEs revealed additional divergence in features such as insertion bias. Remarkably, in CAR-T therapy for hematological and solid tumors, Mariner2_AG (MAG), the most active DNA TE identified, largely outperformed two widely used vectors, the lentiviral vector and the TE-based vector SB100X. Overall, this study highlights the varied transposition features and evolutionary dynamics of DNA TEs and increases the TE toolbox diversity.

Evaluation of body shape as a human body composition assessment in isolated conditions and remote environments.

Individuals in isolated and extreme environments can experience debilitating side-effects including significant decreases in fat-free mass (FFM) from disuse and inadequate nutrition. The objective of this study was to determine the strengths and weaknesses of three-dimensional optical (3DO) imaging for monitoring body composition in either simulated or actual remote environments. Thirty healthy adults (ASTRO, male = 15) and twenty-two Antarctic Expeditioners (ABCS, male = 18) were assessed for body composition. ASTRO participants completed duplicate 3DO scans while standing and inverted by gravity boots plus a single dual-energy X-ray absorptiometry (DXA) scan. The inverted scans were an analog for fluid redistribution from gravity changes. An existing body composition model was used to estimate fat mass (FM) and FFM from 3DO meshes. 3DO body composition estimates were compared to DXA with linear regression and reported with the coefficient of determination (R2) and root mean square error (RMSE). ABCS participants received only duplicate 3DO scans on a monthly basis. Standing ASTRO meshes achieved an R2 of 0.76 and 0.97 with an RMSE of 2.62 and 2.04 kg for FM and FFM, while inverted meshes achieved an R2 of 0.52 and 0.93 with an RMSE of 2.84 and 3.23 kg for FM and FFM, respectively, compared to DXA. For the ABCS arm, mean weight, FM, and FFM changes were -0.47, 0.06, and -0.54 kg, respectively. Simulated fluid redistribution decreased the accuracy of estimated body composition values from 3DO scans. However, FFM stayed robust. 3DO imaging showed good absolute accuracy for body composition assessment in isolated and remote environments.

Generative deep learning furthers the understanding of local distributions of fat and muscle on body shape and health using 3D surface scans.

BACKGROUND: Body shape, an intuitive health indicator, is deterministically driven by body composition. We developed and validated a deep learning model that generates accurate dual-energy X-ray absorptiometry (DXA) scans from three-dimensional optical body scans (3DO), enabling compositional analysis of the whole body and specified subregions. Previous works on generative medical imaging models lack quantitative validation and only report quality metrics. METHODS: Our model was self-supervised pretrained on two large clinical DXA datasets and fine-tuned using the Shape Up! Adults study dataset. Model-predicted scans from a holdout test set were evaluated using clinical commercial DXA software for compositional accuracy. RESULTS: Predicted DXA scans achieve R2 of 0.73, 0.89, and 0.99 and RMSEs of 5.32, 6.56, and 4.15 kg for total fat mass (FM), fat-free mass (FFM), and total mass, respectively. Custom subregion analysis results in R2s of 0.70-0.89 for left and right thigh composition. We demonstrate the ability of models to produce quantitatively accurate visualizations of soft tissue and bone, confirming a strong relationship between body shape and composition. CONCLUSIONS: This work highlights the potential of generative models in medical imaging and reinforces the importance of quantitative validation for assessing their clinical utility.

Body composition, measured quantities of muscle, fat, and bone, is typically assessed through dual energy X-ray absorptiometry (DXA) scans, which requires specialized equipment, trained technicians and involves exposure to radiation. Exterior body shape is dependent on body composition and recent technological advances have made three-dimensional (3D) scanning for body shape accessible and virtually ubiquitous. We developed a model which uses 3D body surface scan inputs to generate DXA scans. When analyzed with commercial software that is used clinically, our model generated images yielded accurate quantities of fat, lean, and bone. Our work highlights the strong relationship between exterior body shape and interior composition. Moreover, it suggests that with enhanced accuracy, such medical imaging models could be more widely adopted in clinical care, making the analysis of body composition more accessible and easier to obtain.

Hagfish genome elucidates vertebrate whole-genome duplication events and their evolutionary consequences.

Polyploidy or whole-genome duplication (WGD) is a major event that drastically reshapes genome architecture and is often assumed to be causally associated with organismal innovations and radiations. The 2R hypothesis suggests that two WGD events (1R and 2R) occurred during early vertebrate evolution. However, the timing of the 2R event relative to the divergence of gnathostomes (jawed vertebrates) and cyclostomes (jawless hagfishes and lampreys) is unresolved and whether these WGD events underlie vertebrate phenotypic diversification remains elusive. Here we present the genome of the inshore hagfish, Eptatretus burgeri. Through comparative analysis with lamprey and gnathostome genomes, we reconstruct the early events in cyclostome genome evolution, leveraging insights into the ancestral vertebrate genome. Genome-wide synteny and phylogenetic analyses support a scenario in which 1R occurred in the vertebrate stem-lineage during the early Cambrian, and 2R occurred in the gnathostome stem-lineage, maximally in the late Cambrian-earliest Ordovician, after its divergence from cyclostomes. We find that the genome of stem-cyclostomes experienced an additional independent genome triplication. Functional genomic and morphospace analyses demonstrate that WGD events generally contribute to developmental evolution with similar changes in the regulatory genome of both vertebrate groups. However, appreciable morphological diversification occurred only in the gnathostome but not in the cyclostome lineage, calling into question the general expectation that WGDs lead to leaps of bodyplan complexity.

Forces driving transposable element load variation during Arabidopsis range expansion.

Genetic load refers to the accumulated and potentially life-threatening deleterious mutations in populations. Understanding the mechanisms underlying genetic load variation of transposable element (TE) insertion, a major large-effect mutation, during range expansion is an intriguing question in biology. Here, we used 1,115 global natural accessions of Arabidopsis (Arabidopsis thaliana) to study the driving forces of TE load variation during its range expansion. TE load increased with range expansion, especially in the recently established Yangtze River basin population. Effective population size, which explains 62.0% of the variance in TE load, high transposition rate, and selective sweeps contributed to TE accumulation in the expanded populations. We genetically mapped and identified multiple candidate causal genes and TEs, and revealed the genetic architecture of TE load variation. Overall, this study reveals the variation in TE genetic load during Arabidopsis expansion and highlights the causes of TE load variation from the perspectives of both population genetics and quantitative genetics.

Arthralgia in midlife Singaporean women: the Integrated Women's Health Program (IWHP).

OBJECTIVE: Arthralgia is a common menopausal complaint in midlife women, and its causes remain unclear. We examined the prevalence of menopausal arthralgia with various factors including sleep quality, depression/anxiety, muscle strength and physical performance among midlife Singaporean women. METHODS: The Integrated Women's Health Program (IWHP) comprised 1120 healthy, community-dwelling women of Chinese, Malay or Indian ethnicities (aged 45-69 years) attending well-women clinics at the National University Hospital, Singapore. Sociodemographic, menopausal, reproductive and health data were obtained with validated questionnaires. Muscle strength, physical performance and dual-energy X-ray absorptiometry were measured. Women with moderate to very severe symptoms using the Menopause Rating Scale were classified as having arthralgia. Multivariable logistic regression analyses examined risk factors for arthralgia. RESULTS: One-third of the participants reported arthralgia, and 12.7%, 16.2% and 71.2% were in the premenopausal, perimenopausal and postmenopausal period, respectively. Menopausal symptoms, such as vaginal dryness (adjusted odds ratio [aOR]: 2.64, 95% confidence interval [CI]: 1.64, 4.24) and physical/mental exhaustion (aOR: 2.83, 95% CI: 1.79, 4.47), were independent risk factors for arthralgia. Poor muscle strength (aOR: 2.20, 95% CI: 1.29, 3.76), obesity (aOR: 1.94, 95% CI: 1.13, 3.32) and rheumatoid arthritis (aOR: 7.73, 95% CI: 4.47, 13.36) were also independently associated with arthralgia after adjustment for confounders. CONCLUSIONS: Arthralgia in midlife Singaporean women was associated with menopausal symptoms of vaginal dryness and physical and mental exhaustion. Women with poor muscle strength were more likely to experience menopausal arthralgia.

Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection.

New genes (or young genes) are structural novelties pivotal in mammalian evolution. Their phenotypic impacts on humans, however, remain elusive due to the technical and ethical complexities in functional studies. Through combining gene age dating with Mendelian disease phenotyping, our research reveals a steady integration of new genes with biomedical phenotypes into the human genome over macroevolutionary timescales (~0.07% per million years). Despite this stable pace, we observe distinct patterns in phenotypic enrichment, pleiotropy, and selective pressures shaped by different gene ages. Notably, young genes show significant enrichment in the male reproductive system, indicating strong sexual selection. Young genes also exhibit functions in tissues and systems potentially linked to human phenotypic innovations, such as increased brain size, musculoskeletal phenotypes, and color vision. Our findings further reveal increasing levels of pleiotropy over evolutionary time, which accompanies stronger selective constraints. We propose a "pleiotropy-barrier" model that delineates different potentials for phenotypic innovation between young and older genes subject to natural selection. Our study demonstrates that evolutionary new genes are critical in influencing human reproductive evolution and adaptive phenotypic innovations driven by sexual and natural selection, with low pleiotropy as a selective advantage.

The Morphological Transformation of the Thorax during the Eclosion of Drosophila melanogaster (Diptera: Drosophilidae).

The model organism Drosophila melanogaster, as a species of Holometabola, undergoes a series of transformations during metamorphosis. To deeply understand its development, it is crucial to study its anatomy during the key developmental stages. We describe the anatomical systems of the thorax, including the endoskeleton, musculature, nervous ganglion, and digestive system, from the late pupal stage to the adult stage, based on micro-CT and 3D visualizations. The development of the endoskeleton causes original and insertional changes in muscles. Several muscles change their shape during development in a non-uniform manner with respect to both absolute and relative size; some become longer and broader, while others shorten and become narrower. Muscular shape may vary during development. The number of muscular bundles also increases or decreases. Growing muscles are probably anchored by the tissues in the stroma. Some muscles and tendons are absent in the adult stage, possibly due to the hardened sclerites. Nearly all flight muscles are present by the third day of the pupal stage, which may be due to the presence of more myofibers with enough mitochondria to support flight power. There are sexual differences in the same developmental period. In contrast to the endodermal digestive system, the functions of most thoracic muscles change in the development from the larva to the adult in order to support more complex locomotion under the control of a more structured ventral nerve cord based on the serial homology proposed herein.

Cross-sectional assessment of body composition and detection of malnutrition risk in participants with low body mass index and eating disorders using 3D optical surface scans.

BACKGROUND: New recommendations for the assessment of malnutrition and sarcopenia include body composition, specifically reduced muscle mass. Three-dimensional optical imaging (3DO) is a validated, accessible, and affordable alternative to dual X-ray absorptiometry (DXA). OBJECTIVE: Identify strengths and weaknesses of 3DO for identification of malnutrition in participants with low body mass index (BMI) and eating disorders. DESIGN: Participants were enrolled in the cross-sectional Shape Up! Adults and Kids studies of body shape, metabolic risk, and functional assessment and had BMI of <20 kg/m2 in adults or <85% of median BMI (mBMI) in children and adolescents. A subset was referred for eating disorders evaluation. Anthropometrics, scans, strength testing, and questionnaires were completed in clinical research centers. Lin's Concordance Correlation Coefficient (CCC) assessed agreement between 3DO and DXA; multivariate linear regression analysis examined associations between weight history and body composition. RESULTS: Among 95 participants, mean ± SD BMI was 18.3 ± 1.4 kg/m2 in adult women (N = 56), 19.0 ± 0.6 in men (N = 14), and 84.2% ± 4.1% mBMI in children (N = 25). Concordance was excellent for fat-free mass (FFM, CCC = 0.97) and strong for appendicular lean mass (ALM, CCC = 0.86) and fat mass (FM, CCC = 0.87). By DXA, 80% of adults met the low FFM index criterion for malnutrition, and 44% met low ALM for sarcopenia; 52% of children and adolescents were <-2 z-score for FM. 3DO identified 95% of these cases. In the subset, greater weight loss predicted lower FFM, FM, and ALM by both methods; a greater percentage of weight regained predicted a higher percentage of body fat. CONCLUSIONS: 3DO can accurately estimate body composition in participants with low BMI and identify criteria for malnutrition and sarcopenia. In a subset, 3DO detected changes in body composition expected with weight loss and regain secondary to eating disorders. These findings support the utility of 3DO for body composition assessment in patients with low BMI, including those with eating disorders. This trial was registered at clinicaltrials.gov as NCT03637855.

A novel AIE material for sensing of Erythromycin in pure water by hydrogen bond in portable test strips and cellular imaging applications.

Erythromycin could be used to treat various bacterial infection, but it was harmful to the colonic microflora. Therefore, it is highly desirable to develop a fluorescence probe that could selectively and sensitively detect Erythromycin in pure water. In this work, a fluorescent probe named EHMC, which exhibited aggregation-induced emission (AIE) characteristic in solid state and water/EtOH binary solvent was developed for "turn on" sensing Erythromycin in pure water with high selectivity and sensitivity (detection limit: 1.78 × 10-8 M). Also, there are fewer interference from other antibiotics in the detection process of probe EHMC for Erythromycin. Moreover, probe EHMC could as a portable test strips for highly selective detection of Erythromycin and identification of different concentrations of Erythromycin. In addition, living cells imaging experiments displayed that probe EHMC could detect Erythromycin in A549 cells and BEAS-2B cells successfully. Combined with the theoretical calculation results The sensing mechanisms that the CO in Erythromycin and OH in EHMC formed intermolecular hydrogen bond and further formed new aggregates were confirmed by job' plot, 1H NMR, FT-IR, ESI-MS, DLS and TEM and DFT calculation.

Adaptive evolution of the enigmatic Takakia now facing climate change in Tibet.

The most extreme environments are the most vulnerable to transformation under a rapidly changing climate. These ecosystems harbor some of the most specialized species, which will likely suffer the highest extinction rates. We document the steepest temperature increase (2010-2021) on record at altitudes of above 4,000 m, triggering a decline of the relictual and highly adapted moss Takakia lepidozioides. Its de-novo-sequenced genome with 27,467 protein-coding genes includes distinct adaptations to abiotic stresses and comprises the largest number of fast-evolving genes under positive selection. The uplift of the study site in the last 65 million years has resulted in life-threatening UV-B radiation and drastically reduced temperatures, and we detected several of the molecular adaptations of Takakia to these environmental changes. Surprisingly, specific morphological features likely occurred earlier than 165 mya in much warmer environments. Following nearly 400 million years of evolution and resilience, this species is now facing extinction.

Automated body composition estimation from device-agnostic 3D optical scans in pediatric populations.

BACKGROUND: Excess adiposity in children is strongly correlated with obesity-related metabolic disease in adulthood, including diabetes, cardiovascular disease, and 13 types of cancer. Despite the many long-term health risks of childhood obesity, body mass index (BMI) Z-score is typically the only adiposity marker used in pediatric studies and clinical applications. The effects of regional adiposity are not captured in a single scalar measurement, and their effects on short- and long-term metabolic health are largely unknown. However, clinicians and researchers rarely deploy gold-standard methods for measuring compartmental fat such as magnetic resonance imaging (MRI) and dual X-ray absorptiometry (DXA) on children and adolescents due to cost or radiation concerns. Three-dimensional optical (3DO) scans are relatively inexpensive to obtain and use non-invasive and radiation-free imaging techniques to capture the external surface geometry of a patient's body. This 3D shape contains cues about the body composition that can be learned from a structured correlation between 3D body shape parameters and reference DXA scans obtained on a sample population. STUDY AIM: This study seeks to introduce a radiation-free, automated 3D optical imaging solution for monitoring body shape and composition in children aged 5-17. METHODS: We introduce an automated, linear learning method to predict total and regional body composition of children aged 5-17 from 3DO scans. We collected 145 male and 206 female 3DO scans on children between the ages of 5 and 17 with three scanners from independent manufacturers. We used an automated shape templating method first introduced on an adult population to fit a topologically consistent 60,000 vertex (60 k) mesh to 3DO scans of arbitrary scanning source and mesh topology. We constructed a parameterized body shape space using principal component analysis (PCA) and estimated a regression matrix between the shape parameters and their associated DXA measurements. We automatically fit scans of 30 male and 38 female participants from a held-out test set and predicted 12 body composition measurements. RESULTS: The coefficient of determination (R2) between 3DO predicted body composition and DXA measurements was at least 0.85 for all measurements with the exception of visceral fat on 3D scan predictions. Precision error was 1-4 times larger than that of DXA. No predicted variable was significantly different from DXA measurement except for male trunk lean mass. CONCLUSION: Optical imaging can quickly, safely, and inexpensively estimate regional body composition in children aged 5-17. Frequent repeat measurements can be taken to chart changes in body adiposity over time without risk of radiation overexposure.

Accuracy and Precision of 3-dimensional Optical Imaging for Body Composition by Age, BMI, and Ethnicity.

BACKGROUND: The obesity epidemic brought a need for accessible methods to monitor body composition, as excess adiposity has been associated with cardiovascular disease, metabolic disorders, and some cancers. Recent 3-dimensional optical (3DO) imaging advancements have provided opportunities for assessing body composition. However, the accuracy and precision of an overall 3DO body composition model in specific subgroups are unknown. OBJECTIVES: This study aimed to evaluate 3DO's accuracy and precision by subgroups of age, body mass index, and ethnicity. METHODS: A cross-sectional analysis was performed using data from the Shape Up! Adults study. Each participant received duplicate 3DO and dual-energy X-ray absorptiometry (DXA) scans. 3DO meshes were digitally registered and reposed using Meshcapade. Principal component analysis was performed on 3DO meshes. The resulting principal components estimated DXA whole-body and regional body composition using stepwise forward linear regression with 5-fold cross-validation. Duplicate 3DO and DXA scans were used for test-retest precision. Student's t tests were performed between 3DO and DXA by subgroup to determine significant differences. RESULTS: Six hundred thirty-four participants (females = 346) had completed the study at the time of the analysis. 3DO total fat mass in the entire sample achieved R2 of 0.94 with root mean squared error (RMSE) of 2.91 kg compared to DXA in females and similarly in males. 3DO total fat mass achieved a % coefficient of variation (RMSE) of 1.76% (0.44 kg), whereas DXA was 0.98% (0.24 kg) in females and similarly in males. There were no mean differences for total fat, fat-free, percent fat, or visceral adipose tissue by age group (P > 0.068). However, there were mean differences for underweight, Asian, and Black females as well as Native Hawaiian or other Pacific Islanders (P < 0.038). CONCLUSIONS: A single 3DO body composition model produced accurate and precise body composition estimates that can be used on diverse populations. However, adjustments to specific subgroups may be warranted to improve the accuracy in those that had significant differences. This trial was registered at clinicaltrials.gov as NCT03637855 (Shape Up! Adults).

Evolutionary mining and functional characterization of TnpB nucleases identify efficient miniature genome editors.

As the evolutionary ancestor of Cas12 nuclease, the transposon (IS200/IS605)-encoded TnpB proteins act as compact RNA-guided DNA endonucleases. To explore their evolutionary diversity and potential as genome editors, we screened TnpBs from 64 annotated IS605 members and identified 25 active in Escherichia coli, of which three are active in human cells. Further characterization of these 25 TnpBs enables prediction of the transposon-associated motif (TAM) and the right-end element RNA (reRNA) directly from genomic sequences. We established a framework for annotating TnpB systems in prokaryotic genomes and applied it to identify 14 additional candidates. Among these, ISAam1 (369 amino acids (aa)) and ISYmu1 (382 aa) TnpBs demonstrated robust editing activity across dozens of genomic loci in human cells. Both RNA-guided genome editors demonstrated similar editing efficiency as SaCas9 (1,053 aa) while being substantially smaller. The enormous diversity of TnpBs holds potential for the discovery of additional valuable genome editors.

Decadal stability in coral cover could mask hidden changes on reefs in the East Asian Seas.

Coral reefs in the Central Indo-Pacific region comprise some of the most diverse and yet threatened marine habitats. While reef monitoring has grown throughout the region in recent years, studies of coral reef benthic cover remain limited in spatial and temporal scales. Here, we analysed 24,365 reef surveys performed over 37 years at 1972 sites throughout East Asia by the Global Coral Reef Monitoring Network using Bayesian approaches. Our results show that overall coral cover at surveyed reefs has not declined as suggested in previous studies and compared to reef regions like the Caribbean. Concurrently, macroalgal cover has not increased, with no indications of phase shifts from coral to macroalgal dominance on reefs. Yet, models incorporating socio-economic and environmental variables reveal negative associations of coral cover with coastal urbanisation and sea surface temperature. The diversity of reef assemblages may have mitigated cover declines thus far, but climate change could threaten reef resilience. We recommend prioritisation of regionally coordinated, locally collaborative long-term studies for better contextualisation of monitoring data and analyses, which are essential for achieving reef conservation goals.

The power of "controllers": Transposon-mediated duplicated genes evolve towards neofunctionalization.

Since the discovery of the first transposon by Dr. Barbara McClintock, the prevalence and diversity of transposable elements (TEs) have been gradually recognized. As fundamental genetic components, TEs drive organismal evolution not only by contributing functional sequences (e.g., regulatory elements or "controllers" as phrased by Dr. McClintock) but also by shuffling genomic sequences. In the latter respect, TE-mediated gene duplications have contributed to the origination of new genes and attracted extensive interest. In response to the development of this field, we herein attempt to provide an overview of TE-mediated duplication by focusing on common rules emerging across duplications generated by different TE types. Specifically, despite the huge divergence of transposition machinery across TEs, we identify three common features of various TE-mediated duplication mechanisms, including end bypass, template switching, and recurrent transposition. These three features lead to one common functional outcome, namely, TE-mediated duplicates tend to be subjected to exon shuffling and neofunctionalization. Therefore, the intrinsic properties of the mutational mechanism constrain the evolutionary trajectories of these duplicates. We finally discuss the future of this field including an in-depth characterization of both the duplication mechanisms and functions of TE-mediated duplicates.