4.5 Article

Horizontal Transposon Transfer and Their Ecological Drivers: The Case of Flower-breeding Drosophila

Related references

Note: Only part of the references are listed.
Article Biochemistry & Molecular Biology

Widespread introgression across a phylogeny of 155 Drosophila genomes

Anton Suvorov et al.

Summary: Genome-scale sequence data has provided new opportunities for studying introgression in the genus Drosophila. By combining 155 genome assemblies with a fossil-calibrated phylogeny, we found widespread introgression across the evolutionary history of Drosophila.

CURRENT BIOLOGY (2022)

Article Biochemistry & Molecular Biology

Paleozoic Protein Fossils Illuminate the Evolution of Vertebrate Genomes and Transposable Elements

Martin C. Frith

Summary: Protein fossils in genomes provide valuable insights into the ancient evolution of TEs and genomes. A recent study discovered ancient fossils in the human genome, which exhibit extreme sequence conservation and may have gene-regulatory functions.

MOLECULAR BIOLOGY AND EVOLUTION (2022)

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 Biology

Highly contiguous assemblies of 101 drosophilid genomes

Bernard Y. Kim et al.

Summary: Over 100 years of research on Drosophila melanogaster and related species have led to key discoveries in genetics, genomics, and evolution. Recent advances in long-read sequencing have enabled the generation of high-quality genome assemblies for tens or even hundreds of species. Utilizing Oxford Nanopore sequencing, a community resource of genome assemblies for 101 lines of 93 drosophilid species has been built, providing highly contiguous and complete genomes with high accuracy in coding regions.

ELIFE (2021)

Review Genetics & Heredity

The Structural, Functional and Evolutionary Impact of Transposable Elements in Eukaryotes

Dareen Almojil et al.

Summary: Transposable elements (TEs) are widespread in eukaryotes and have had a significant impact on genome organization and evolution, playing roles in regulating genes and providing a source for genetic novelties. This impact is now being more fully appreciated and their role in various biological processes, such as speciation and adaptation, is still being deciphered.

GENES (2021)

Article Multidisciplinary Sciences

Horizontal transfer and evolution of transposable elements in vertebrates

Hua-Hao Zhang et al.

NATURE COMMUNICATIONS (2020)

Review Genetics & Heredity

Measuring and interpreting transposable element expression

Sophie Lanciano et al.

NATURE REVIEWS GENETICS (2020)

Article Biochemical Research Methods

Global analysis of repetitive DNA from unassembled sequence reads using RepeatExplorer2

Petr Novak et al.

NATURE PROTOCOLS (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)

Article Multidisciplinary Sciences

Evolutionary history and classification of Micropia retroelements in Drosophilidae species

Juliana Cordeiro et al.

PLOS ONE (2019)

Article Evolutionary Biology

An Improved Genome Assembly for Drosophila navojoa, the Basal Species in the mojavensis Cluster

Thyago Vanderlinde et al.

JOURNAL OF HEREDITY (2019)

Article Multidisciplinary Sciences

A transposable element insertion is associated with an alternative life history strategy

Alyssa Woronik et al.

NATURE COMMUNICATIONS (2019)

Article Biochemical Research Methods

Versatile genome assembly evaluation with QUAST-LG

Alla Mikheenko et al.

BIOINFORMATICS (2018)

Article Cell Biology

Horizontal acquisition of transposable elements and viral sequences: patterns and consequences

Clement Gilbert et al.

CURRENT OPINION IN GENETICS & DEVELOPMENT (2018)

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 Biotechnology & Applied Microbiology

Ten things you should know about transposable elements

Guillaume Bourque et al.

GENOME BIOLOGY (2018)

Article Genetics & Heredity

Canalization by Selection of de Novo Induced Mutations

Laura Fanti et al.

GENETICS (2017)

Article Biochemistry & Molecular Biology

Copy number increases of transposable elements and protein-coding genes in an invasive fish of hybrid origin

Stefan Dennenmoser et al.

MOLECULAR ECOLOGY (2017)

Article Multidisciplinary Sciences

Massive horizontal transfer of transposable elements in insects

Jean Peccoud et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)

Article Biochemistry & Molecular Biology

Ecological networks to unravel the routes to horizontal transposon transfers

Samuel Venner et al.

PLOS BIOLOGY (2017)

Article Genetics & Heredity

Canalization by Selection of de Novo Induced Mutations

Laura Fanti et al.

GENETICS (2017)

Article Evolutionary Biology

Cryptic diversity and speciation in the Zygothrica genus group (Diptera, Drosophilidae): the case of Z-vittimaculosa Wiedemann

Pedro Mesquita Fonseca et al.

INSECT SYSTEMATICS & EVOLUTION (2017)

Article Biochemistry & Molecular Biology

VHICA, a New Method to Discriminate between Vertical and Horizontal Transposon Transfer: Application to the Mariner Family within Drosophila

Gabriel Luz Wallau et al.

MOLECULAR BIOLOGY AND EVOLUTION (2016)

Article Evolutionary Biology

Accurate Transposable Element Annotation Is Vital When Analyzing New Genome Assemblies

Roy N. Platt et al.

GENOME BIOLOGY AND EVOLUTION (2016)

Article Biochemistry & Molecular Biology

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update

Enis Afgan et al.

NUCLEIC ACIDS RESEARCH (2016)

Review Ecology

Adaptation to Global Change: A Transposable Element-Epigenetics Perspective

Olivier Rey et al.

TRENDS IN ECOLOGY & EVOLUTION (2016)

Article Multidisciplinary Sciences

Ancient horizontal transfers of retrotransposons between birds and ancestors of human pathogenic nematodes

Alexander Suh et al.

NATURE COMMUNICATIONS (2016)

Review Genetics & Heredity

Roles for retrotransposon insertions in human disease

Dustin C. Hancks et al.

MOBILE DNA (2016)

Article Biochemical Research Methods

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

Felipe A. Simao et al.

BIOINFORMATICS (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 Computer Science, Interdisciplinary Applications

Fitting Linear Mixed-Effects Models Using lme4

Douglas Bates et al.

JOURNAL OF STATISTICAL SOFTWARE (2015)

Review Biochemistry & Molecular Biology

Transposable elements as agents of rapid adaptation may explain the genetic paradox of invasive species

Jessica Stapley et al.

MOLECULAR ECOLOGY (2015)

Review Genetics & Heredity

Population Genomics of Transposable Elements in Drosophila

Maite G. Barron et al.

ANNUAL REVIEW OF GENETICS, VOL 48 (2014)

Article Biochemical Research Methods

Informed and automated k-mer size selection for genome assembly

Rayan Chikhi et al.

BIOINFORMATICS (2014)

Article Biochemical Research Methods

ASTRAL: genome-scale coalescent-based species tree estimation

S. Mirarab et al.

BIOINFORMATICS (2014)

Review Biochemistry & Molecular Biology

Transposons, environmental changes, and heritable induced phenotypic variability

Lucia Piacentini et al.

CHROMOSOMA (2014)

Article Multidisciplinary Sciences

Compact genome of the Antarctic midge is likely an adaptation to an extreme environment

Joanna L. Kelley et al.

NATURE COMMUNICATIONS (2014)

Article Multidisciplinary Sciences

Transposable element islands facilitate adaptation to novel environments in an invasive species

Lukas Schrader et al.

NATURE COMMUNICATIONS (2014)

Article Genetics & Heredity

Horizontal transfer of transposons between and within crustaceans and insects

Mathilde Dupeyron et al.

MOBILE DNA (2014)

Article Biochemistry & Molecular Biology

pamlX: A Graphical User Interface for PAML

Bo Xu et al.

MOLECULAR BIOLOGY AND EVOLUTION (2013)

Review Biochemistry & Molecular Biology

The impact of transposable elements in environmental adaptation

Elena Casacuberta et al.

MOLECULAR ECOLOGY (2013)

Article Multidisciplinary Sciences

Widespread horizontal transfer of retrotransposons

Ali Morton Walsh et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)

Review Genetics & Heredity

Genetics of Climate Change Adaptation

Steven J. Franks et al.

ANNUAL REVIEW OF GENETICS, VOL 46 (2012)

Article Biochemical Research Methods

CD-HIT: accelerated for clustering the next-generation sequencing data

Limin Fu et al.

BIOINFORMATICS (2012)

Review Evolutionary Biology

Horizontal Transposon Transfer in Eukarya: Detection, Bias, and Perspectives

Gabriel Luz Wallau et al.

GENOME BIOLOGY AND EVOLUTION (2012)

Article Evolutionary Biology

Horizontal Transfers of Tc1 Elements between Teleost Fishes and Their Vertebrate Parasites, Lampreys

Shigehiro Kuraku et al.

GENOME BIOLOGY AND EVOLUTION (2012)

Article Biochemical Research Methods

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

Anton Bankevich et al.

JOURNAL OF COMPUTATIONAL BIOLOGY (2012)

Article Biochemistry & Molecular Biology

PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses

Robert Lanfear et al.

MOLECULAR BIOLOGY AND EVOLUTION (2012)

Article Multidisciplinary Sciences

Landscape of Somatic Retrotransposition in Human Cancers

Eunjung Lee et al.

SCIENCE (2012)

Article Evolutionary Biology

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

Fredrik Ronquist et al.

SYSTEMATIC BIOLOGY (2012)

Article Multidisciplinary Sciences

Convergent evolution of two mammalian neuronal enhancers by sequential exaptation of unrelated retroposons

Lucia F. Franchini et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

Article Biochemistry & Molecular Biology

The Effect of Mobile Element IS10 on Experimental Regulatory Evolution in Escherichia coli

Daniel M. Stoebel et al.

MOLECULAR BIOLOGY AND EVOLUTION (2010)

Review Biochemistry & Molecular Biology

Transposable elements: powerful facilitators of evolution

Keith R. Oliver et al.

BIOESSAYS (2009)

Article Multidisciplinary Sciences

The B73 Maize Genome: Complexity, Diversity, and Dynamics

Patrick S. Schnable et al.

SCIENCE (2009)

Review Biochemistry & Molecular Biology

Transposable elements as drivers of genomic and biological diversity in vertebrates

Astrid Boehne et al.

CHROMOSOME RESEARCH (2008)

Article Biochemistry & Molecular Biology

Genome-wide screening and characterization of transposable elements and their distribution analysis in the silkworm, Bombyx mori

Mizuko Osanai-Futahashi et al.

INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY (2008)

Article Entomology

Biogeographical aspects of drosophilids (Diptera, Drosophilidae) of the Brazilian savanna

Natalia Barbi Chaves et al.

REVISTA BRASILEIRA DE ENTOMOLOGIA (2008)

Review Genetics & Heredity

A unified classification system for eukaryotic transposable elements

Thomas Wicker et al.

NATURE REVIEWS GENETICS (2007)

Article Multidisciplinary Sciences

Genome sequence of Aedes aegypti, a major arbovirus vector

Vishvanath Nene et al.

SCIENCE (2007)

Article Evolutionary Biology

Molecular phylogeny of the Drosophila obscura species group, with emphasis on the Old World species

Jian-jun Gao et al.

BMC EVOLUTIONARY BIOLOGY (2007)

Article Biochemistry & Molecular Biology

Distribution and conservation of the transposable element gypsy in Drosophilid species

Fabiana Heredia et al.

GENETICS AND MOLECULAR BIOLOGY (2007)

Article Multidisciplinary Sciences

Genetics -: Junk DNA as an evolutionary force

Christian Biemont et al.

NATURE (2006)

Article Ecology

Maximum entropy modeling of species geographic distributions

SJ Phillips et al.

ECOLOGICAL MODELLING (2006)

Article Multidisciplinary Sciences

Pesticide resistance via transposition-mediated adaptive gene truncation in Drosophila

YT Aminetzach et al.

SCIENCE (2005)

Article Biochemistry & Molecular Biology

Cytoscape: A software environment for integrated models of biomolecular interaction networks

P Shannon et al.

GENOME RESEARCH (2003)