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Transposable Elements: From DNA Parasites to Architects of Metazoan Evolution

https://doi.org/10.3390/genes3030409
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Outgoing claims: the papers this work cites, builds on, or argues with.

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SINE insertions: powerful tools for molecular systematics
inferredcites →https://doi.org/10.1002/bies.20452openalex-snapshot
Turning junk into gold: domestication of transposable elements and the creation of new genes in eukaryotes
inferredcites →https://doi.org/10.1007/978-1-61779-603-6_6openalex-snapshot
Methods and Software in NGS for TE Analysis
inferredcites →https://doi.org/10.1007/978-94-011-4156-7_22openalex-snapshot
Molecular domestication — more than a sporadic episode in evolution
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Sauria SINEs: Novel Short Interspersed Retroposable Elements That Are Widespread in Reptile Genomes
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Exonization of transposed elements: A challenge and opportunity for evolution
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Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages
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Phylogenomics Revives Traditional Views on Deep Animal Relationships
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Mobile elements and mammalian genome evolution
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Genomic alterations upon integration of zebrafish L1 elements revealed by the TANT method
inferredcites →https://doi.org/10.1016/j.gene.2008.11.030openalex-snapshot
The evolution of two partner LINE/SINE families and a full-length chromodomain-containing Ty3/Gypsy LTR element in the first reptilian genome of Anolis carolinensis
inferredcites →https://doi.org/10.1016/j.gene.2009.11.005openalex-snapshot
Characterization of a novel SINE superfamily from invertebrates: “Ceph-SINEs” from the genomes of squids and cuttlefish
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From “Junk” to Gene: Curriculum vitae of a Primate Receptor Isoform Gene
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Beyond DNA: RNA Editing and Steps Toward Alu Exonization in Primates
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Helitrons on a roll: eukaryotic rolling-circle transposons
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190. First Draft of the Genomic Organization of a PIII-SVMP Gene
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First draft of the genomic organization of a PIII-SVMP gene
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SINEs of speciation: tracking lineages with retroposons
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Promiscuous DNA: horizontal transfer of transposable elements and why it matters for eukaryotic evolution
inferredcites →https://doi.org/10.1016/j.ympev.2006.08.005openalex-snapshot
Toothed whale monophyly reassessed by SINE insertion analysis: The absence of lineage sorting effects suggests a small population of a common ancestral species
inferredcites →https://doi.org/10.1016/s0092-8674(02)01041-3openalex-snapshot
LINEs Mobilize SINEs in the Eel through a Shared 3′ Sequence
inferredcites →https://doi.org/10.1016/s0168-9525(01)02445-3openalex-snapshot
Transposable elements are found in a large number of human protein-coding genes
inferredcites →https://doi.org/10.1016/s0168-9525(02)00006-9openalex-snapshot
Origin of a substantial fraction of human regulatory sequences from transposable elements
inferredcites →https://doi.org/10.1016/s0378-1119(97)00409-5openalex-snapshot
SINEs and LINEs share common 3′ sequences: a review
inferredcites →https://doi.org/10.1017/s0094837300004310openalex-snapshot
Exaptation—a Missing Term in the Science of Form
inferredcites →https://doi.org/10.1023/a:1004070603792openalex-snapshot
Molecular domestication – more than a sporadic episode in evolution
inferredcites →https://doi.org/10.1038/284601a0openalex-snapshot
Selfish genes, the phenotype paradigm and genome evolution
inferredcites →https://doi.org/10.1038/284604a0openalex-snapshot
Selfish DNA: the ultimate parasite
inferredcites →https://doi.org/10.1038/35057062openalex-snapshot
Initial sequencing and analysis of the human genome
inferredcites →https://doi.org/10.1038/362241a0openalex-snapshot
The mariner transposable element is widespread in insects
inferredcites →https://doi.org/10.1038/hdy.2009.165openalex-snapshot
Identifying repeats and transposable elements in sequenced genomes: how to find your way through the dense forest of programs
inferredcites →https://doi.org/10.1038/nature04696openalex-snapshot
A distal enhancer and an ultraconserved exon are derived from a novel retroposon
inferredcites →https://doi.org/10.1038/nature05805openalex-snapshot
Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences
inferredcites →https://doi.org/10.1038/nature06614openalex-snapshot
Broad phylogenomic sampling improves resolution of the animal tree of life
inferredcites →https://doi.org/10.1038/nature07191openalex-snapshot
The Trichoplax genome and the nature of placozoans
inferredcites →https://doi.org/10.1038/nature08830openalex-snapshot
The dynamic genome of Hydra
inferredcites →https://doi.org/10.1038/nature08939openalex-snapshot
A role for host–parasite interactions in the horizontal transfer of transposons across phyla
inferredcites →https://doi.org/10.1038/nature09201openalex-snapshot
The Amphimedon queenslandica genome and the evolution of animal complexity
inferredcites →https://doi.org/10.1038/nature10390openalex-snapshot
The genome of the green anole lizard and a comparative analysis with birds and mammals
inferredcites →https://doi.org/10.1038/ncomms1448openalex-snapshot
Mesozoic retroposons reveal parrots as the closest living relatives of passerine birds
inferredcites →https://doi.org/10.1038/ng.917openalex-snapshot
Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals
inferredcites →https://doi.org/10.1038/nrg2165openalex-snapshot
A unified classification system for eukaryotic transposable elements
inferredcites →https://doi.org/10.1038/nrg2165-c1openalex-snapshot
A universal classification of eukaryotic transposable elements implemented in Repbase
inferredcites →https://doi.org/10.1038/nrg2337openalex-snapshot
Transposable elements and the evolution of regulatory networks
inferredcites →https://doi.org/10.1038/nrg793openalex-snapshot
Plant transposable elements: where genetics meets genomics
inferredcites →https://doi.org/10.1038/nrg798openalex-snapshot
Alu repeats and human genomic diversity
inferredcites →https://doi.org/10.1038/sj.hdy.6801094openalex-snapshot
Revisiting horizontal transfer of transposable elements in Drosophila
inferredcites →https://doi.org/10.1073/pnas.0600833103openalex-snapshot
Self-synthesizing DNA transposons in eukaryotes
inferredcites →https://doi.org/10.1073/pnas.0606204104openalex-snapshot
Phylogenomics of nonavian reptiles and the structure of the ancestral amniote genome
inferredcites →https://doi.org/10.1073/pnas.0700531104openalex-snapshot
Poxviruses as possible vectors for horizontal transfer of retroposons from reptiles to mammals
inferredcites →https://doi.org/10.1073/pnas.0709398105openalex-snapshot
Possible involvement of SINEs in mammalian-specific brain formation
inferredcites →https://doi.org/10.1073/pnas.0806548105openalex-snapshot
Repeated horizontal transfer of a DNA transposon in mammals and other tetrapods
inferredcites →https://doi.org/10.1073/pnas.0809297106openalex-snapshot
Retroposon analysis and recent geological data suggest near-simultaneous divergence of the three superorders of mammals
inferredcites →https://doi.org/10.1073/pnas.1104997108openalex-snapshot
Convergent evolution of two mammalian neuronal enhancers by sequential exaptation of unrelated retroposons
inferredcites →https://doi.org/10.1073/pnas.17.8.485openalex-snapshot
The Order of the Genes C, Sh and Wx in Zea Mays with Reference to a Cytologically Known Point in the Chromosome
inferredcites →https://doi.org/10.1073/pnas.36.6.344openalex-snapshot
The origin and behavior of mutable loci in maize
inferredcites →https://doi.org/10.1073/pnas.89.22.10706openalex-snapshot
On "genomenclature": a comprehensive (and respectful) taxonomy for pseudogenes and other "junk DNA".
inferredcites →https://doi.org/10.1073/pnas.90.15.6995openalex-snapshot
Determination of the phylogenetic relationships among Pacific salmonids by using short interspersed elements (SINEs) as temporal landmarks of evolution.
inferredcites →https://doi.org/10.1073/pnas.95.18.10704openalex-snapshot
Unusual horizontal transfer of a long interspersed nuclear element between distant vertebrate classes
inferredcites →https://doi.org/10.1073/pnas.96.18.10261openalex-snapshot
Phylogenetic relationships among cetartiodactyls based on insertions of short and long interpersed elements: Hippopotamuses are the closest extant relatives of whales
inferredcites →https://doi.org/10.1073/pnas.96.6.2869openalex-snapshot
CORE-SINEs: Eukaryotic short interspersed retroposing elements with common sequence motifs
inferredcites →https://doi.org/10.1080/10635150601052637openalex-snapshot
Phylogenomic Analysis of the L1 Retrotransposons in Deuterostomia
inferredcites →https://doi.org/10.1080/10635150601058014openalex-snapshot
Extensive Morphological Convergence and Rapid Radiation in the Evolutionary History of the Family Geoemydidae (Old World Pond Turtles) Revealed by SINE Insertion Analysis
inferredcites →https://doi.org/10.1080/10635150601077683openalex-snapshot
Distribution and Phylogeny of Penelope-Like Elements in Eukaryotes
inferredcites →https://doi.org/10.1093/bfgp/els010openalex-snapshot
Transposon diversity is higher in amphioxus than in vertebrates: functional and evolutionary inferences
inferredcites →https://doi.org/10.1093/bib/bbm048openalex-snapshot
Discovering and detecting transposable elements in genome sequences
inferredcites →https://doi.org/10.1093/bioinformatics/bti1003openalex-snapshot
PILER: identification and classification of genomic repeats
inferredcites →https://doi.org/10.1093/bioinformatics/bti1018openalex-snapshot
De novo identification of repeat families in large genomes
inferredcites →https://doi.org/10.1093/gbe/evp023openalex-snapshot
Exploring Repetitive DNA Landscapes Using REPCLASS, a Tool That Automates the Classification of Transposable Elements in Eukaryotic Genomes
inferredcites →https://doi.org/10.1093/genetics/124.2.339openalex-snapshot
Evidence for horizontal transmission of the P transposable element between Drosophila species.
inferredcites →https://doi.org/10.1093/genetics/14.2.180openalex-snapshot
A CYTOLOGICAL AND GENETICAL STUDY OF TRIPLOID MAIZE
inferredcites →https://doi.org/10.1093/genetics/157.2.777openalex-snapshot
SINE Insertions in Cladistic Analyses and the Phylogenetic Affiliations of Tarsius bancanus to Other Primates
inferredcites →https://doi.org/10.1093/genetics/38.6.579openalex-snapshot
INDUCTION OF INSTABILITY AT SELECTED LOCI IN MAIZE
inferredcites →https://doi.org/10.1093/molbev/msh057openalex-snapshot
Evolutionary Genomics of Chromoviruses in Eukaryotes
inferredcites →https://doi.org/10.1093/molbev/msm014openalex-snapshot
Causes of Insertion Sequences Abundance in Prokaryotic Genomes
inferredcites →https://doi.org/10.1093/molbev/msp104openalex-snapshot
A Single-Copy IS5-Like Transposon in the Genome of a Bdelloid Rotifer
inferredcites →https://doi.org/10.1093/molbev/msq089openalex-snapshot
Improved Phylogenomic Taxon Sampling Noticeably Affects Nonbilaterian Relationships
inferredcites →https://doi.org/10.1093/molbev/msq337openalex-snapshot
Population Genomics of Transposable Elements in Drosophila melanogaster
inferredcites →https://doi.org/10.1093/molbev/msr115openalex-snapshot
Tracking the Ancestry of a Deeply Conserved Eumetazoan SINE Domain
inferredcites →https://doi.org/10.1093/molbev/msr319openalex-snapshot
Retroposon Insertion Patterns of Neoavian Birds: Strong Evidence for an Extensive Incomplete Lineage Sorting Era
inferredcites →https://doi.org/10.1093/nar/gkq1291openalex-snapshot
T-lex: a program for fast and accurate assessment of transposable element presence using next-generation sequencing data
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a003727openalex-snapshot
Evolutionary Dynamics and Evolutionary History in the RTE Clade of Non-LTR Retrotransposons
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a003768openalex-snapshot
Evolutionary Dynamics in a Novel L2 Clade of Non-LTR Retrotransposons in Deuterostomia
inferredcites →https://doi.org/10.1101/gr.087932.108openalex-snapshot
Atypical relaxation of structural constraints in Hox gene clusters of the green anole lizard
inferredcites →https://doi.org/10.1101/gr.090647.108openalex-snapshot
Mosaic retroposon insertion patterns in placental mammals
inferredcites →https://doi.org/10.1101/gr.106419.110openalex-snapshot
High-throughput sequencing reveals extensive variation in human-specific L1 content in individual human genomes
inferredcites →https://doi.org/10.1101/gr.212302openalex-snapshot
V-SINEs: A New Superfamily of Vertebrate SINEs That Are Widespread in Vertebrate Genomes and Retain a Strongly Conserved Segment within Each Repetitive Unit
inferredcites →https://doi.org/10.1101/gr.5255506openalex-snapshot
Functional noncoding sequences derived from SINEs in the mammalian genome
inferredcites →https://doi.org/10.1101/gr.6320607openalex-snapshot
Functional persistence of exonized mammalian-wide interspersed repeat elements (MIRs)
inferredcites →https://doi.org/10.1101/gr.88502openalex-snapshot
Automated De Novo Identification of Repeat Sequence Families in Sequenced Genomes
inferredcites →https://doi.org/10.1111/j.0014-3820.2001.tb01268.xopenalex-snapshot
PERSPECTIVE: TRANSPOSABLE ELEMENTS, PARASITIC DNA, AND GENOME EVOLUTION
inferredcites →https://doi.org/10.1111/j.1365-2443.2010.01429.xopenalex-snapshot
Emergence of mammals by emergency: exaptation
inferredcites →https://doi.org/10.1111/j.1432-1033.1997.00772.xopenalex-snapshot
Bov‐B Long Interspersed Repeated DNA (LINE) Sequences are Present in Vipera Ammodytes Phospholipase A2 Genes and in Genomes of Viperidae Snakes
inferredcites →https://doi.org/10.1126/science.1089670openalex-snapshot
Mobile Elements: Drivers of Genome Evolution
inferredcites →https://doi.org/10.1126/science.1098119openalex-snapshot
Ultraconserved Elements in the Human Genome
inferredcites →https://doi.org/10.1126/science.1140871openalex-snapshot
Developmentally Regulated Activation of a SINE B2 Repeat as a Domain Boundary in Organogenesis
inferredcites →https://doi.org/10.1126/science.1156407openalex-snapshot
Massive Horizontal Gene Transfer in Bdelloid Rotifers
inferredcites →https://doi.org/10.1126/science.1178534openalex-snapshot
The B73 Maize Genome: Complexity, Diversity, and Dynamics
inferredcites →https://doi.org/10.1126/science.1653453openalex-snapshot
Possible Horizontal Transfer of Drosophila Genes by the Mite Proctolaelaps regalis
inferredcites →https://doi.org/10.1126/science.1990437openalex-snapshot
Retroposons—Seeds of Evolution
inferredcites →https://doi.org/10.1126/science.282.5396.2012openalex-snapshot
Genome Sequence of the Nematode C. elegans : A Platform for Investigating Biology
inferredcites →https://doi.org/10.1128/mcb.16.7.3756openalex-snapshot
The 3′ Ends of tRNA-Derived Short Interspersed Repetitive Elements Are Derived from the 3′ Ends of Long Interspersed Repetitive Elements
inferredcites →https://doi.org/10.1146/annurev.genet.40.110405.090448openalex-snapshot
DNA Transposons and the Evolution of Eukaryotic Genomes
inferredcites →https://doi.org/10.1159/000084984openalex-snapshot
Penelope-like elements – a new class of retroelements: distribution, function and possible evolutionary significance
inferredcites →https://doi.org/10.1159/000092503openalex-snapshot
Retrotransposable Elements and Human Disease
inferredcites →https://doi.org/10.1159/000294999openalex-snapshot
Transposable Elements in Reptilian and Avian (Sauropsida) Genomes
inferredcites →https://doi.org/10.1159/000452856openalex-snapshot
Cellular Scaling Rules for the Brains of Marsupials: Not as “Primitive” as Expected
inferredcites →https://doi.org/10.1186/1471-2148-10-376openalex-snapshot
A novel web-based TinT application and the chronology of the Primate Alu retroposon activity
inferredcites →https://doi.org/10.1186/1471-2148-11-154openalex-snapshot
BEL/Pao retrotransposons in metazoan genomes
inferredcites →https://doi.org/10.1186/1471-2148-11-258openalex-snapshot
Molecular evolution under increasing transposable element burden in Drosophila: A speed limit on the evolutionary arms race
inferredcites →https://doi.org/10.1186/1471-2148-7-190openalex-snapshot
Waves of genomic hitchhikers shed light on the evolution of gamebirds (Aves: Galliformes)
inferredcites →https://doi.org/10.1186/1471-2164-12-621openalex-snapshot
Eukaryote DIRS1-like retrotransposons: an overview
inferredcites →https://doi.org/10.1186/1471-2164-8-470openalex-snapshot
Maintenance of transposon-free regions throughout vertebrate evolution
inferredcites →https://doi.org/10.1186/1745-6150-5-18openalex-snapshot
Genome-wide analysis of transposable elements and tandem repeats in the compact placozoan genome
inferredcites →https://doi.org/10.1186/1745-6150-6-19openalex-snapshot
The struggle for life of the genome's selfish architects
inferredcites →https://doi.org/10.1186/1745-6150-6-59openalex-snapshot
Extensive intron gain in the ancestor of placental mammals
inferredcites →https://doi.org/10.1186/gb-2009-10-2-r22openalex-snapshot
Widespread evidence for horizontal transfer of transposable elements across Drosophilagenomes
inferredcites →https://doi.org/10.1371/journal.pbio.1000436openalex-snapshot
Tracking Marsupial Evolution Using Archaic Genomic Retroposon Insertions
inferredcites →https://doi.org/10.1371/journal.pcbi.0010022openalex-snapshot
Combined Evidence Annotation of Transposable Elements in Genome Sequences
inferredcites →https://doi.org/10.1371/journal.pcbi.0010043openalex-snapshot
ReAS: Recovery of Ancestral Sequences for Transposable Elements from the Unassembled Reads of a Whole Genome Shotgun
inferredcites →https://doi.org/10.1371/journal.pgen.0030166openalex-snapshot
Ancient Exaptation of a CORE-SINE Retroposon into a Highly Conserved Mammalian Neuronal Enhancer of the Proopiomelanocortin Gene
inferredcites →https://doi.org/10.1371/journal.pgen.1002384openalex-snapshot
Repetitive Elements May Comprise Over Two-Thirds of the Human Genome
inferredcites →https://doi.org/10.1371/journal.pntd.0000035openalex-snapshot
The bandit, a New DNA Transposon from a Hookworm—Possible Horizontal Genetic Transfer between Host and Parasite
inferredcites →https://doi.org/10.1371/journal.pone.0016526openalex-snapshot
Considering Transposable Element Diversification in De Novo Annotation Approaches
inferredcites →https://doi.org/10.1371/journal.pone.0028497openalex-snapshot
A Mammalian Conserved Element Derived from SINE Displays Enhancer Properties Recapitulating Satb2 Expression in Early-Born Callosal Projection Neurons
inferredcites →https://doi.org/10.21775/cimb.006.057openalex-snapshot
Factors that Affect the Horizontal Transfer of Transposable Elements

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Evidence of venom factor-like in crocodilians
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Molecular Evolution of Parasitic Helminths
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Transposable element discovery and characterization of LTR-retrotransposon evolutionary lineages in the tropical fruit species Passiflora edulis
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Megaevolutionary dynamics and the timing of evolutionary innovation in reptiles
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Non-coding RNAs in virology: an RNA genomics approach
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Ancient Persistence and Newfound Diversity of CR1-Group Retrotransposons Across Vertebrates
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Transposable elements activity reveals punctuated patterns of speciation in mammals
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Re-evaluating inheritance in genome evolution: widespread transfer of LINEs between species
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The impact of transposable elements in adaptive evolution
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Origin and Early Evolution of Squamates and Their Kin: From Fossils to Genomes
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Cnidarian-Microbe Interactions and the Origin of Innate Immunity in Metazoans
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Deep landscape update of dispersed and tandem repeats in the genome model of the red jungle fowl, Gallus gallus, using a series of de novo investigating tools
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Diversity and evolution of transposable elements in the plant-parasitic nematodes
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DNA methylation changes facilitated evolution of genes derived from Mutator-like transposable elements
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Horizontal transfer of BovB and L1 retrotransposons in eukaryotes
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How the pan-genome is changing crop genomics and improvement
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Alu SINE analyses of 3,000-year-old human skeletal remains: a pilot study
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Drosophila parasitoid wasps bears a distinct DNA transposon profile
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Horizontal transfer of BovB and L1 retrotransposons in eukaryotes
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Regulatory Potential of Mobile Genetic Elements in the Human MGMT Gene
inferred← citeshttps://doi.org/10.3389/fgene.2022.863547openalex-snapshot
Intergeneric hybridization of two stickleback species leads to introgression of membrane-associated genes and invasive TE expansion
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Gene Expression Order Attributed to Genome Reduction and the Steady Cellular State in Escherichia coli
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Acquisition and Exaptation of Endogenous Retroviruses in Mammalian Placenta
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Duplex Alu Screening for Degraded DNA of Skeletal Human Remains
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Existence of Bov-B LINE Retrotransposons in Snake Lineages Reveals Recent Multiple Horizontal Gene Transfers with Copy Number Variation
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HSV-1 and Endogenous Retroviruses as Risk Factors in Demyelination
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Additional file 1 of How the pan-genome is changing crop genomics and improvement
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Additional file 1 of Diversity and evolution of transposable elements in the plant-parasitic nematodes
inferred← citeshttps://doi.org/10.6084/m9.figshare.25893899openalex-snapshot
Additional file 2 of Diversity and evolution of transposable elements in the plant-parasitic nematodes
inferred← citeshttps://doi.org/10.6084/m9.figshare.26724764openalex-snapshot
Additional file 3 of Diversity and evolution of transposable elements in the plant-parasitic nematodes
inferred← citeshttps://doi.org/10.6084/m9.figshare.26724767openalex-snapshot
Additional file 4 of Diversity and evolution of transposable elements in the plant-parasitic nematodes
inferred← citeshttps://doi.org/10.6084/m9.figshare.26724770openalex-snapshot
Additional file 5 of Diversity and evolution of transposable elements in the plant-parasitic nematodes
inferred← citeshttps://doi.org/10.6084/m9.figshare.26724773openalex-snapshot
Additional file 6 of Diversity and evolution of transposable elements in the plant-parasitic nematodes
inferred← citeshttps://doi.org/10.6084/m9.figshare.26724776openalex-snapshot
Additional file 7 of Diversity and evolution of transposable elements in the plant-parasitic nematodes
inferred← citeshttps://doi.org/10.6084/m9.figshare.26724779openalex-snapshot
Additional file 8 of Diversity and evolution of transposable elements in the plant-parasitic nematodes
inferred← citeshttps://doi.org/10.6084/m9.figshare.26724782openalex-snapshot
Additional file 9 of Diversity and evolution of transposable elements in the plant-parasitic nematodes
inferred← citeshttps://doi.org/10.64898/2026.01.13.699120openalex-snapshot
Ancient persistence and newfound diversity of CR1-group retrotransposons across chordates
inferred← citeshttps://doi.org/10.7551/mitpress/14642.003.0018openalex-snapshot
Evolutionary Change Is Naturally Biological and Purposeful
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