4.6 Article

Comparative Analysis of Transposable Elements Reveals the Diversity of Transposable Elements in Decapoda and Their Effects on Genomic Evolution

Related references

Note: Only part of the references are listed.
Article Entomology

Genome-Wide Screening of Transposable Elements in the Whitefly, Bemisia tabaci (Hemiptera: Aleyrodidae), Revealed Insertions with Potential Insecticide Resistance Implications

Marwa Zidi et al.

Summary: The genome-wide screening of TEs in the B. tabaci genome revealed the presence of numerous clustered TE copies. The analysis of TE insertion sites identified insertions within or near defensome genes.

INSECTS (2022)

Article Entomology

Miniature Inverted-Repeat Transposable Elements (MITEs) in the Two Lepidopteran Genomes of Helicoverpa armigera and Helicoverpa zea

Khouloud Klai et al.

Summary: MITEs are ubiquitous, non-autonomous class II transposable elements. The moths Helicoverpa armigera and Helicoverpa zea are recognized as the two most serious pest species within the genus. Moreover, these pests have the ability to develop insecticide resistance. In this study, a genome-wide analysis of MITEs present in H. armigera and H. zea genomes was conducted using the bioinformatics tool MITE tracker. A total of 3570 and 7405 MITE sequences were identified in the H. armigera and H. zea genomes, respectively. Comparative analysis of the identified MITE sequences led to the identification of 18 families, comprising 140 MITE members in H. armigera and 161 MITE members in H. zea. The analysis of MITE insertion sites in defensome genes showed intronic insertions of 11 MITEs in H. armigera and one MITE in H. zea. These insertions could be involved in the insecticide resistance observed in these pests.

INSECTS (2022)

Article Agriculture, Dairy & Animal Science

Diversity of Harbinger-like Transposons in Teleost Fish Genomes

Ema Etchegaray et al.

Summary: Transposable elements are repeated DNA sequences that can insert into new locations in genomes. Harbinger-like DNA transposons are widespread in plants and vertebrates, but absent from mammalian genomes. This study focuses on the variability in the genomic composition of Harbinger-like sequences in teleost fish and the unique origin of the association between transposase and Myb-like protein.

ANIMALS (2022)

Article Genetics & Heredity

Recurrent co-domestication of PIF/Harbinger transposable element proteins in insects

Dragomira N. Markova et al.

Summary: This study identified at least six independent PIF transposable element protein domestication events in insects, including two co-domestications in Anopheles (Diptera) of both transposase and MADF proteins, one transposase-only event and one co-domestication in butterflies and moths (Lepidoptera), and two transposases-only events in cockroaches (Blattodea). Predicted nuclear localization signals and dicistronic transcription in some proteins support the functional associations of co-domesticated transposase and MADF proteins.

MOBILE DNA (2022)

Article Biochemistry & Molecular Biology

Horizontal transfer of Buster transposons across multiple phyla and classes of animals

Zhongxia Guan et al.

Summary: This study conducted a systematic analysis of the evolutionary landscape of the Buster family and found that it is widely distributed in various species, showing characteristics of youth and high activity. Buster transposons have high percentages of intact copies in multiple lineages of animals, possibly indicating their spread through horizontal transfer events.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2022)

Article Biotechnology & Applied Microbiology

Comparative genomics of tadpole shrimps (Crustacea, Branchiopoda, Notostraca): Dynamic genome evolution against the backdrop of morphological stasis

Andrea Luchetti et al.

Summary: The study reveals that despite the morphological stability of Notostraca, their genome evolution is dynamic, characterized by gene family expansion/contraction and variability in transposable element content. Additionally, the research suggests a link between the transposable element content of Triops cancriformis and its reproductive strategies.

GENOMICS (2021)

Article Infectious Diseases

Genome-Wide Identification, Characterization, and Expression Analysis of DDE_Tnp_4 Family Genes in Eriocheir sinensis

Yuanfeng Xu et al.

Summary: In this study, 39 DDE_Tnp_4 family genes were identified in the Eriocheir sinensis genome using HMMER, and were classified into four subfamilies based on phylogenetic analysis. Gene expansions in E. sinensis were found to be mainly caused by tandem duplication. Up-regulation of some DDE_Tnp_4 family genes in response to acute high salinity and air exposure stress was observed in E. sinensis.

ANTIBIOTICS-BASEL (2021)

Review Genetics & Heredity

Transposable elements shape the evolution of mammalian development

Anna D. Senft et al.

Summary: Transposable elements (TEs) play a significant role in mammalian development and evolution by directly contributing genetic materials and indirectly affecting the evolution of TE repression systems such as KRAB-ZFPs. Despite the threats to genome stability, TEs actively shape mammalian-specific developmental processes and continue to impact mammalian development through ongoing co-evolution.

NATURE REVIEWS GENETICS (2021)

Article Multidisciplinary Sciences

Eusociality in snapping shrimps is associated with larger genomes and an accumulation of transposable elements

Solomon T. C. Chak et al.

Summary: Research has found that eusocial species have larger genomes with more transposable elements and microsatellite repeats, and different subclasses of transposable elements contribute to accumulation in different species. It appears that transposable elements modulate the relationship between sociality and genome architecture, highlighting a complex and dynamic relationship between genome and social evolution.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2021)

Article Ecology

High genetic and epigenetic variation of transposable elements: Potential drivers to rapid adaptive evolution for the noxious invasive weed Mikania micrantha

Yingjuan Su et al.

Summary: The genetic paradox of invasive species, which refers to their ability to rapidly adapt to novel environments, can be explained by the activity of transposable elements (TEs). Mikania micrantha serves as a good example to test this explanation, as shown in a study of 21 invasive populations in southern China. The research found that M. micrantha populations exhibit high levels of TE-related genetic and epigenetic variation, and are differentiated into subpopulations.

ECOLOGY AND EVOLUTION (2021)

Article Biology

Horizontal transfer and subsequent explosive expansion of a DNA transposon in sea kraits (Laticauda)

James D. Galbraith et al.

Summary: Transposable elements (TEs) are self-replicating genetic sequences considered as drivers of evolution, promoting genomic novelty. Most TE insertions may have harmful outcomes, but can rapidly proliferate in new host genomes through horizontal transposon transfer (HTT). The HTT of Harbinger-Snek DNA transposon into sea kraits led to rapid genomic changes contributing to adaptation to amphibious-marine habitat.

BIOLOGY LETTERS (2021)

Article Plant Sciences

Genomic re-assessment of the transposable element landscape of the potato genome

Diego Zavallo et al.

PLANT CELL REPORTS (2020)

Article Multidisciplinary Sciences

RepeatModeler2 for automated genomic discovery of transposable element families

Jullien M. Flynn et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

Article Biochemical Research Methods

Impact of transposable elements on genome size variation between two closely related crustacean species

Thomas Becking et al.

ANALYTICAL BIOCHEMISTRY (2020)

Article Genetics & Heredity

Transposable element abundance correlates with mode of transmission in microsporidian parasites

Nathalia Ramme Medeiros de Albuquerque et al.

MOBILE DNA (2020)

Review Genetics & Heredity

A Field Guide to Eukaryotic Transposable Elements

Jonathan N. Wells et al.

ANNUAL REVIEW OF GENETICS, VOL 54, 2020 (2020)

Article Genetics & Heredity

Mosquito genomes are frequently invaded by transposable elements through horizontal transfer

Elverson Soares de Melo et al.

PLOS GENETICS (2020)

Article Biochemistry & Molecular Biology

The impact of transposable elements in adaptive evolution

Lukas Schrader et al.

MOLECULAR ECOLOGY (2019)

Review Microbiology

Evolution of Immune Systems From Viruses and Transposable Elements

Felix Broecker et al.

FRONTIERS IN MICROBIOLOGY (2019)

Article Genetics & Heredity

High frequency of horizontal transfer in Jockey families (LINE order) of drosophilids

Izabella L. Tambones et al.

MOBILE DNA (2019)

Article Multidisciplinary Sciences

Horizontal transfer of retrotransposons between bivalves and other aquatic species of multiple phyla

Michael J. Metzger et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)

Review Genetics & Heredity

The Role of Transposable Elements in Speciation

Antonio Serrato-Capuchina et al.

GENES (2018)

Review Biotechnology & Applied Microbiology

Ten things you should know about transposable elements

Guillaume Bourque et al.

GENOME BIOLOGY (2018)

Article Biochemistry & Molecular Biology

Analyzing Horizontal Transfer of Transposable Elements on a Large Scale: Challenges and Prospects

Jean Peccoud et al.

BIOESSAYS (2018)

Review Genetics & Heredity

Transposable Element Domestication As an Adaptation to Evolutionary Conflicts

Diwash Jangam et al.

TRENDS IN GENETICS (2017)

Review Cell Biology

The Developmental Control of Transposable Elements and the Evolution of Higher Species

Marc Friedli et al.

ANNUAL REVIEW OF CELL AND DEVELOPMENTAL BIOLOGY, VOL 31 (2015)

Article Evolutionary Biology

Characterization of fossilized relatives of the White Spot Syndrome Virus in genomes of decapod crustaceans

Andrey Rozenberg et al.

BMC EVOLUTIONARY BIOLOGY (2015)

Article Evolutionary Biology

Comparative Analysis of Transposable Elements Highlights Mobilome Diversity and Evolution in Vertebrates

Domitille Chalopin et al.

GENOME BIOLOGY AND EVOLUTION (2015)

Article Biotechnology & Applied Microbiology

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

Mihaela Pertea et al.

NATURE BIOTECHNOLOGY (2015)

Article Biochemical Research Methods

HISAT: a fast spliced aligner with low memory requirements

Daehwan Kim et al.

NATURE METHODS (2015)

Article Biochemical Research Methods

Trimmomatic: a flexible trimmer for Illumina sequence data

Anthony M. Bolger et al.

BIOINFORMATICS (2014)

Article Biochemical Research Methods

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

Alexandros Stamatakis

BIOINFORMATICS (2014)

Article Evolutionary Biology

Remarkable Diversity of Endogenous Viruses in a Crustacean Genome

Julien Theze et al.

GENOME BIOLOGY AND EVOLUTION (2014)

Book Review Social Sciences, Mathematical Methods

ggplot2: Elegant Graphics for Data Analysis

Cedric Ginestet

JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES A-STATISTICS IN SOCIETY (2011)

Review Cell Biology

Small RNA-Mediated Quiescence of Transposable Elements in Animals

Kuniaki Saito et al.

DEVELOPMENTAL CELL (2010)

Article Biochemistry & Molecular Biology

Widespread occurence of mariner transposons in coastal crabs

Q. -T. Bui et al.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2008)

Review Genetics & Heredity

A unified classification system for eukaryotic transposable elements

Thomas Wicker et al.

NATURE REVIEWS GENETICS (2007)