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Article
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Transposable element-initiated enhancer-like elements generate the subgenome-biased spike specificity of polyploid wheat
The direct impacts of transposable element dynamics on polyploid regulation and developmental specificity remain unclear. Here, the authors show that a large proportion of enhancer-like elements (ELEs) are mainly originated from RLG_famc7.3 specifically expanded in subgenome A, producing active nascent transcripts and influencing wheat spike development.
- Yilin Xie
- , Songbei Ying
- & Yijing Zhang
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Article
| Open Access
Dynamics of transposable element accumulation in the non-recombining regions of mating-type chromosomes in anther-smut fungi
In the absence of recombination, the number of transposable elements (TEs) increases, but their accumulation dynamics are not well characterized. This study shows that TEs rapidly accumulated in non-recombining fungal mating-type chromosomes before reaching a plateau, possibly forming a TE reservoir.
- Marine Duhamel
- , Michael E. Hood
- & Tatiana Giraud
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Article
| Open Access
Insertion sequence transposition inactivates CRISPR-Cas immunity
CRISPR-Cas immunity systems safeguard prokaryotic genomes by inhibiting the invasion of mobile genetic elements. Here, the authors show that insertion sequences can efficiently insert into cas genes, thus inactivating CRISPR defenses and increasing bacterial susceptibility to foreign DNA invasion.
- Yong Sheng
- , Hengyu Wang
- & Qianjin Kang
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Article
| Open Access
Retrotransposon instability dominates the acquired mutation landscape of mouse induced pluripotent stem cells
Retrotransposons are mobile genetic elements normally repressed by DNA methylation in differentiated cells. Here, the authors show that DNA hypomethylation in mouse induced pluripotent stem cells allows retrotransposons to jump, but this can be blocked with a reverse transcriptase inhibitor.
- Patricia Gerdes
- , Sue Mei Lim
- & Geoffrey J. Faulkner
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Article
| Open Access
Transposable element-mediated rearrangements are prevalent in human genomes
Here the authors show that transposable element-mediated rearrangements impact more than 500 kbp of an average human genome, are a source of individual variation, a substrate for evolutionary change, and can occur through diverse mechanisms.
- Parithi Balachandran
- , Isha A. Walawalkar
- & Christine R. Beck
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Article
| Open Access
Transposable elements orchestrate subgenome-convergent and -divergent transcription in common wheat
How subgenome-divergent and -convergent transcription is mediated and harmonized in hexaploid common wheat genome remains unclear. Here, via characterizing the cistrome maps, the authors reveal that transposon elements with transcription factor binding ability have the potential to make the contribution.
- Yuyun Zhang
- , Zijuan Li
- & Yijing Zhang
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Article
| Open Access
Population genomics of Puccinia graminis f.sp. tritici highlights the role of admixture in the origin of virulent wheat rust races
Factors defining wheat stem rust pathogen (Pgt) virulence remain poorly characterized. Comparative population genomics based on Pgt haplotypes suggest that structural variation and admixture through somatic hybridization and sexual recombination play an important role in broadening Pgt virulence.
- Yuanwen Guo
- , Bliss Betzen
- & Eduard Akhunov
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Article
| Open Access
Frequency and mechanisms of LINE-1 retrotransposon insertions at CRISPR/Cas9 sites
The identification of events occurring at target sites is critical to determine the safety of CRISPRbased DNA editing tools. Here, the authors show that LINE-1 retrotranspositions can occur frequently at canonical CRISPR/Cas9 editing sites, but are rare with prime editors and base editors.
- Jianli Tao
- , Qi Wang
- & Roberto Chiarle
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Article
| Open Access
Strain-level characterization of broad host range mobile genetic elements transferring antibiotic resistance from the human microbiome
Here, Forster et al. compare 1354 cultured commensal strains (540 species) to 45,403 pathogen strains (12 species), identifying 64,188 MGE-mediated antibiotic resistance gene transfer events between the two groups, and show that 15 broad host range MGEs are able to transfer between phyla.
- Samuel C. Forster
- , Junyan Liu
- & Trevor D. Lawley
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Article
| Open Access
Whole-genome sequencing of 1,171 elderly admixed individuals from Brazil
Whole genome sequencing (WGS) data on non-European and admixed individuals remains scarce. Here, the authors analyse WGS data from 1,171 admixed elderly Brazilians from a census cohort, characterising population-specific genetic variation and exploring the clinical utility of this expanded dataset.
- Michel S. Naslavsky
- , Marilia O. Scliar
- & Mayana Zatz
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Article
| Open Access
A transposon expression burst accompanies the activation of Y-chromosome fertility genes during Drosophila spermatogenesis
In this study, Lawlor et al. show that transposons on the Drosophila Y chromosome have evolved to exploit a specific stage of spermatogenesis when the Y chromosome is decondensed and the piRNA pathway is downregulated.
- Matthew A. Lawlor
- , Weihuan Cao
- & Christopher E. Ellison
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Article
| Open Access
Mouse strain-specific polymorphic provirus functions as cis-regulatory element leading to epigenomic and transcriptomic variations
How polymorphic elements can drive intra-species variation has not been clearly examined. Here the authors show that the polymorphic GLN endogenous retrovirus (ERV) functions as a cis-regulatory element for neighboring genes, leading to differences in how two mouse strains respond to stress.
- Xuemeng Zhou
- , Tsz Wing Sam
- & Danny Leung
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Article
| Open Access
Bacterial chromosomal mobility via lateral transduction exceeds that of classical mobile genetic elements
It is commonly thought that horizontal transfer of most bacterial chromosomal genes is limited, in comparison with the frequent transfer of mobile genetic elements. Humphrey et al. show that, actually, phage-mediated lateral transduction of core chromosomal genes can be more efficient than the transfer of mobile genetic elements via conjugation or generalized transduction.
- Suzanne Humphrey
- , Alfred Fillol-Salom
- & José R. Penadés
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Article
| Open Access
Insertion-sequence-mediated mutations both promote and constrain evolvability during a long-term experiment with bacteria
Insertion sequences (IS) are common mobile genetic elements in bacteria, but their effects on bacterial evolution are not well understood. Here, Consuegra and colleagues investigate the dynamics and fitness consequences of IS elements in E. coli over 50,000 generations.
- Jessika Consuegra
- , Joël Gaffé
- & Dominique Schneider
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| Open Access
Epigenetic conflict on a degenerating Y chromosome increases mutational burden in Drosophila males
Selfish DNA such as transposable elements cause intragenomic conflict. This study finds that on an evolutionarily young, gene-rich Drosophila Y chromosome, transposable elements evade heterochromatic suppression, leading to elevated transposition rates in males.
- Kevin H.-C. Wei
- , Lauren Gibilisco
- & Doris Bachtrog
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Article
| Open Access
Pathways for horizontal gene transfer in bacteria revealed by a global map of their plasmids
Plasmids can mediate gene transfer across bacterial populations. Here, the authors describe a global map of the prokaryotic plasmidome, where plasmids organize into discrete ‘plasmid taxonomic units’ based on their genomic composition and pairwise sequence identity.
- Santiago Redondo-Salvo
- , Raúl Fernández-López
- & Fernando de la Cruz
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Article
| Open Access
Transposable elements contribute to cell and species-specific chromatin looping and gene regulation in mammalian genomes
A fraction of mammalian CTCF binding sites fall within transposable elements (TEs) but their contribution to the evolution of 3D chromatin structure is unknown. Here the authors investigate the effect of TE-driven CTCF binding site expansions on chromatin looping in humans and mice, and provide evidence that TEs contribute to cell-specific and species-specific chromatin looping diversity and variable gene regulation in mammalian genomes.
- Adam G. Diehl
- , Ningxin Ouyang
- & Alan P. Boyle
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Article
| Open Access
Evolution of satellite plasmids can prolong the maintenance of newly acquired accessory genes in bacteria
Newly acquired plasmids are frequently lost due to fitness costs. Here, Zhang et al. show that the evolution of satellite plasmids with gene deletions can reduce fitness costs by driving down the copy number of full plasmids and thus favor maintenance of the full plasmid and its novel accessory genes.
- Xue Zhang
- , Daniel E. Deatherage
- & Jeffrey E. Barrick
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Article
| Open Access
Relaxed purifying selection in autopolyploids drives transposable element over-accumulation which provides variants for local adaptation
Why transposable elements (TEs) accumulate in polyploids and the evolutionary implications remain unclear. Here, the authors show that following whole genome duplication, relaxed purifying selection is the main driver of TE over-accumulation, which provides variants for rapid local adaptation.
- Pierre Baduel
- , Leandro Quadrana
- & Vincent Colot
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Article
| Open Access
Transposition favors the generation of large effect mutations that may facilitate rapid adaption
The contribution of transposable elements (TEs) to the creation of heritable mutations is unknown. Here the authors show in Arabidopsis that TEs accumulate exponentially once mobilized and that COPIA retrotransposons preferentially integrate in environmental response genes in a H2A.Z-dependent manner.
- Leandro Quadrana
- , Mathilde Etcheverry
- & Vincent Colot
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Article
| Open Access
The Wolbachia mobilome in Culex pipiens includes a putative plasmid
Wolbachia bacteria live within the cells of many insects, including the mosquito Culex pipiens. Here, the authors analyse new and existing Wolbachia metagenomes from C. pipiens mosquitoes and find evidence of a plasmid, which may facilitate genetic manipulation of these bacteria for vector control applications.
- Julie Reveillaud
- , Sarah R. Bordenstein
- & A. Murat Eren
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Article
| Open Access
Tracking the origin of two genetic components associated with transposable element bursts in domesticated rice
Transposable element (TE) bursts shape genome evolution but their origin remains unclear. Here, the authors show that a burst is restricted to only a few domesticated rice accessions and is associated with the acquisition of two TE variants, Ping16A and Ping16A_Stow, not the loss of TE silencing.
- Jinfeng Chen
- , Lu Lu
- & Susan R. Wessler
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Article
| Open Access
Squamate reptiles challenge paradigms of genomic repeat element evolution set by birds and mammals
Large-scale patterns of genomic repeat element evolution have been studied mainly in birds and mammals. Here, the authors analyze the genomes of over 60 squamate reptiles and show high variation in repeat elements compared to mammals and birds, and particularly high microsatellite seeding in snakes.
- Giulia I. M. Pasquesi
- , Richard H. Adams
- & Todd A. Castoe
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| Open Access
Parallels between experimental and natural evolution of legume symbionts
It is unclear if experimental evolution is a good model for natural processes. Here, Clerissi et al. find parallels between the evolution of symbiosis in rhizobia after horizontal transfer of a plasmid over 10 million years ago and experimentally evolved symbionts.
- Camille Clerissi
- , Marie Touchon
- & Eduardo P. C. Rocha
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Article
| Open Access
High-frequency recombination between members of an LTR retrotransposon family during transposition bursts
Retrotransposons are abundant in eukaryotic genomes. Here, Sanchez et al. show evidence of high-frequency recombination between members of an LTR retrotransposon family during transposition bursts in Arabidopsis.
- Diego H. Sanchez
- , Hervé Gaubert
- & Jerzy Paszkowski
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Article
| Open Access
Complete fusion of a transposon and herpesvirus created the Teratorn mobile element in medaka fish
Teratorn is a large mobile genetic element originally identified in the small teleost fish medaka. Here, the authors show that Teratorn is derived from the fusion of a piggyBac superfamily DNA transposon and an alloherpesvirus and that it is widely found across teleost fish.
- Yusuke Inoue
- , Tomonori Saga
- & Hiroyuki Takeda
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Article
| Open Access
A Helitron transposon reconstructed from bats reveals a novel mechanism of genome shuffling in eukaryotes
Helitron elements are proposed rolling-circle transposons in eukaryotic genomes, but experimental evidence for their transposition has been lacking. Here, Grabundzija et al. reconstruct an active Helitron from bats which they name Helraiser, and characterize its mechanism of transposition in cell-free reactions and in human cell cultures in vitro.
- Ivana Grabundzija
- , Simon A. Messing
- & Zoltán Ivics
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Article
| Open Access
Interactions between horizontally acquired genes create a fitness cost in Pseudomonas aeruginosa
Horizontal gene transfer is important for bacterial evolution but the molecular basis of its fitness costs remain unclear. Here the authors show that fitness costs produced by a plasmid in P. aeruginosaare alleviated by mutations in recently acquired genes encoded in mobile genetic elements.
- Alvaro San Millan
- , Macarena Toll-Riera
- & R. Craig MacLean
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Article
| Open Access
Mobile elements drive recombination hotspots in the core genome of Staphylococcus aureus
Horizontal gene transfer occurs in most bacteria, yet it is unclear whether it happens in clonal species. Here, Everitt et al. show widespread within-species recombination, driven by mobile elements, in the genome of the pathogen Staphylococcus aureus, but no recombination between closely related strains.
- Richard G. Everitt
- , Xavier Didelot
- & Daniel J. Wilson
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Article
| Open Access
Wall teichoic acid structure governs horizontal gene transfer between major bacterial pathogens
Horizontal gene transfer of mobile genetic elements contributes to bacterial evolution and emergence of new pathogens. Here the authors demonstrate that the highly diverse structure of wall teichoic acid polymers governs horizontal gene transfer among Gram-positive pathogens, even across long phylogenetic distances.
- Volker Winstel
- , Chunguang Liang
- & Guoqing Xia
JUN upregulation drives aberrant transposable element mobilization, associated innate immune response, and impaired neurogenesis in Alzheimer’s disease