The genomic distribution of transposable elements is driven by spatially variable purifying selection DOI Creative Commons
Anna Maria Langmüller, Viola Nolte,

Marlies Dolezal

et al.

Nucleic Acids Research, Journal Year: 2023, Volume and Issue: 51(17), P. 9203 - 9213

Published: July 19, 2023

Abstract It is widely accepted that the genomic distribution of transposable elements (TEs) mainly reflects outcome purifying selection and insertion bias (1). Nevertheless, relative importance these two evolutionary forces could not be tested thoroughly. Here, we introduce an experimental system, which allows separating from TE bias. We used evolution to study patterns in Drosophila simulans founder populations harboring 1040 insertions active P-element. After 10 generations at a large population size, detected strong against P-element insertions. The exception were regions for has been proposed (2–4). Because recurrent cannot explain this pattern, conclude selection, with variable strength along chromosomes, major determinant P-elements. Genomic relaxed exhibit normal levels base substitutions. This suggests different types operate on substitutions Our results highlight power understand basic processes, are difficult infer natural variation alone.

Language: Английский

Gene drives gaining speed DOI Creative Commons
Ethan Bier

Nature Reviews Genetics, Journal Year: 2021, Volume and Issue: 23(1), P. 5 - 22

Published: Aug. 6, 2021

Gene drives are selfish genetic elements that transmitted to progeny at super-Mendelian (>50%) frequencies. Recently developed CRISPR–Cas9-based gene-drive systems highly efficient in laboratory settings, offering the potential reduce prevalence of vector-borne diseases, crop pests and non-native invasive species. However, concerns have been raised regarding unintended impacts systems. This Review summarizes phenomenal progress this field, focusing on optimal design features for full-drive (drives with linked Cas9 guide RNA components) either suppress target mosquito populations or modify them prevent pathogen transmission, allelic updating elements, mitigating strategies including trans-complementing split-drives neutralizing adaptation drive technology other organisms. These scientific advances, combined ethical social considerations, will facilitate transparent responsible advancement these technologies towards field implementation. In Review, Ethan Bier discusses how several impactful technical advancements, particularly involving CRISPR-based methods, providing a diverse toolkit control such as insect vectors disease.

Language: Английский

Citations

163
Earl Grey: A Fully Automated User-Friendly Transposable Element Annotation and Analysis Pipeline DOI Creative Commons
Tobias Baril, James D. Galbraith, Alexander Hayward

et al.

Molecular Biology and Evolution, Journal Year: 2024, Volume and Issue: 41(4)

Published: April 1, 2024

Transposable elements (TEs) are major components of eukaryotic genomes and implicated in a range evolutionary processes. Yet, TE annotation characterization remain challenging, particularly for nonspecialists, since existing pipelines typically complicated to install, run, extract data from. Current methods automated also subject issues that reduce overall quality, (i) fragmented overlapping annotations, leading erroneous estimates count coverage, (ii) repeat models represented by short sections total length, with poor capture 5' 3' ends. To address these issues, we present Earl Grey, fully pipeline designed user-friendly curation TEs genome assemblies. Using nine simulated an Drosophila melanogaster, show Grey outperforms current widely used methodologies ameliorating the mentioned above while scoring highly benchmarking classification being robust across genomic contexts. provides comprehensive toolkit researchers paper-ready summary figures outputs standard formats compatible other bioinformatics tools. has modular format, great scope inclusion additional modules focused on further quality control tailored analyses future releases.

Language: Английский

Citations

52
Autonomous transposons tune their sequences to ensure somatic suppression DOI Creative Commons
İbrahim Ilik, Petar Glažar, Kevin Tse

et al.

Nature, Journal Year: 2024, Volume and Issue: 626(8001), P. 1116 - 1124

Published: Feb. 14, 2024

Abstract Transposable elements (TEs) are a major constituent of human genes, occupying approximately half the intronic space. During pre-messenger RNA synthesis, TEs transcribed along with their host genes but rarely contribute to final mRNA product because they spliced out together intron and rapidly degraded. Paradoxically, an abundant source RNA-processing signals through which can create new introns 1 , also functional 2 or non-functional chimeric transcripts 3 . The rarity these events implies existence resilient splicing code that is able suppress TE exonization without compromising pre-mRNA processing. Here we show SAFB proteins protect genome integrity by preventing retrotransposition L1 while maintaining integrity, via prevention previously integrated TEs. This unique dual role possible L1’s conserved adenosine-rich coding sequences bound proteins. suppressive activity extends tissue-specific, giant protein-coding cassette exons, nested Tigger DNA transposons. Moreover, suppresses LTR/ERV in species still active, such as mice flies. A significant subset suppressed somatic cells activated testis, coinciding low expression postmeiotic spermatids. Reminiscent division labour between innate adaptive immune systems fight external pathogens, our results uncover RNA-based, pattern-guided, non-adaptive defence system against soma, complementing Piwi-interacting pathway germline.

Language: Английский

Citations

16
Transposable Elements: Major Players in Shaping Genomic and Evolutionary Patterns DOI Creative Commons
Nunzia Colonna Romano, Laura Fanti

Cells, Journal Year: 2022, Volume and Issue: 11(6), P. 1048 - 1048

Published: March 19, 2022

Transposable elements (TEs) are ubiquitous genetic elements, able to jump from one location of the genome another, in all organisms. For this reason, on hand, TEs can induce deleterious mutations, causing dysfunction, disease and even lethality individuals. On other increase variability, making populations better equipped respond adaptively environmental change. To counteract effects TEs, organisms have evolved strategies avoid their activation. However, mobilization does occur. Usually, maintained silent through several mechanisms, but they be reactivated during certain developmental windows. Moreover, become de-repressed because drastic changes external environment. Here, we describe ‘double life’ being both ‘parasites’ ‘symbionts’ genome. We also argue that transposition contributes two important evolutionary processes: temporal dynamic evolution induction variability. Finally, discuss how interplay between TE-dependent phenomena, insertional mutagenesis epigenetic plasticity, plays a role process evolution.

Language: Английский

Citations

39
Repetitive elements in aging and neurodegeneration DOI Creative Commons
Katie E. Copley, James Shorter

Trends in Genetics, Journal Year: 2023, Volume and Issue: 39(5), P. 381 - 400

Published: March 17, 2023

Language: Английский

Citations

39
Variation in mutation, recombination, and transposition rates inDrosophila melanogasterandDrosophila simulans DOI Creative Commons
Yiguan Wang,

Paul McNeil,

R. Abdulazeez

et al.

Genome Research, Journal Year: 2023, Volume and Issue: 33(4), P. 587 - 598

Published: April 1, 2023

The rates of mutation, recombination, and transposition are core parameters in models evolution. They impact genetic diversity, responses to ongoing selection, levels load. However, even for key evolutionary model species such as Drosophila melanogaster simulans, few estimates these available, we have little idea how vary between individuals, sexes, or populations. Knowledge this variation is fundamental parameterizing genome Here, provide direct their a West African European population D. simulans Across 89 flies, observe 58 single-nucleotide mutations, 286 crossovers, transposable element (TE) insertions. Compared the melanogaster, find has lower mutation rate (1.67 × 10-9 site-1 gen-1 vs. 4.86 gen-1) (8.99 10-5 copy-1 23.36 gen-1), but higher recombination (3.44 cM/Mb 2.06 cM/Mb). similar significantly lower, not different, rate. Overall, paternal-derived mutations more frequent than maternal ones both species. Our study quantifies among different populations our will benefit future studies genetics.

Language: Английский

Citations

26
The role of mobile DNA elements in the dynamic of plants genome plasticity DOI Creative Commons
Robyn Emmerson, Marco Catoni

Journal of Experimental Botany, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 10, 2025

Abstract Plants host a range of DNA elements capable self-replication. These molecules, usually associated to the activity transposable or viruses, are found integrated in genome form extrachromosomal DNA. The these can impact plasticity by variety mechanisms, including generation structural variants, shuffling regulatory coding sequences across genome, and endoduplication. This dynamically alter gene expression stability, ultimately affecting plant development response environmental changes. While activation is often considered deleterious their role creating variation important adaptation evolution. Moreover, mechanisms which mobile proliferate have been exploited for engineering, contributed understand how desirable traits be generated crops. In this review, we discuss origins roles element on biology, as well potential function current application biotechnology.

Language: Английский

Citations

1
Genomics of Triatominae, the Chagas Disease Vectors DOI
Antonella Bacigalupo, Sebastián Pita

Published: Jan. 1, 2025

Language: Английский

Citations

1
The Worldwide Invasion ofDrosophila suzukiiIs Accompanied by a Large Increase of Transposable Element Load and a Small Number of Putatively Adaptive Insertions DOI Creative Commons
Vincent Mérel, Patricia Gibert,

Inessa Buch

et al.

Molecular Biology and Evolution, Journal Year: 2021, Volume and Issue: 38(10), P. 4252 - 4267

Published: May 21, 2021

Transposable elements (TEs) are ubiquitous and mobile repeated sequences. They major determinants of host fitness. Here, we characterized the TE content spotted wing fly Drosophila suzukii. Using a recently improved genome assembly, reconstructed sequences de novo found that TEs occupy 47% mostly located in gene-poor regions. The majority insertions segregate at low frequencies, indicating recent probably ongoing activity. To explore dynamics context biological invasions, studied variation abundance genomic data from 16 invasive six native populations D. We large increase load correlated with reduced Watterson estimate genetic diversity θw^ proxy effective population size. did not find any correlation between contents bioclimatic variables, minor effect environmentally induced A genome-wide association study revealed ca. 2,000 regions associated abundance. find, however, evidence such an enrichment for genes known to interact activity (e.g., transcription factor encoding or piRNA pathway). Finally, insertion frequencies 15 putatively adaptive insertions, them being likely invasion history species.

Language: Английский

Citations

42
Earl Grey: a fully automated user-friendly transposable element annotation and analysis pipeline DOI Open Access
Tobias Baril, James D. Galbraith, Alexander Hayward

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2022, Volume and Issue: unknown

Published: July 2, 2022

ABSTRACT Transposable elements (TEs) are major components of eukaryotic genomes and implicated in a range evolutionary processes. Yet, TE annotation characterisation remains challenging, particularly for non-specialists, since existing pipelines typically complicated to install, run, extract data from. Current methods automated also subject issues that reduce overall quality, particularly: (i) fragmented overlapping annotations, leading erroneous estimates count coverage; (ii) repeat models represented by short sections total length, with poor capture 5’ 3’ ends. To address these issues, we present Earl Grey, fully pipeline designed user-friendly curation TEs genome assemblies. Using nine simulated an Drosophila melanogaster , show Grey outperforms current widely-used methodologies ameliorating the mentioned above, whilst scoring highly benchmarking classification, being robust across genomic contexts. provides comprehensive toolkit researchers paper-ready summary figures outputs standard formats compatible other bioinformatics tools. has modular format, great scope inclusion additional modules focussed on further quality control tailored analyses future releases.

Language: Английский

Citations

33