Evolution and Diversity of Transposable Elements in Vertebrate Genomes

The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons

(2016) Ingo Braasch et al.   NATURE GENETICS

A copy-and-paste gene regulatory network

(2016) V. J. Lynch   SCIENCE

Long-read sequence assembly of the gorilla genome

(2016) D. Gordon et al.   SCIENCE

Regulatory evolution of innate immunity through co-option of endogenous retroviruses

(2016) E. B. Chuong et al.   SCIENCE

A Helitron transposon reconstructed from bats reveals a novel mechanism of genome shuffling in eukaryotes

(2016) Ivana Grabundzija et al.   Nature Communications

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

(2016) Alexander Suh et al.   Nature Communications

Evolution of heterogeneous genome differentiation across multiple contact zones in a crow species complex

(2016) Nagarjun Vijay et al.   Nature Communications

The contribution of transposable elements to size variations between four teleost genomes

(2016) Bo Gao et al.   Mobile DNA

Pinpointing the vesper bat transposon revolution using the Miniopterus natalensis genome

(2016) Roy N. Platt et al.   Mobile DNA

The Lungfish Transcriptome: A Glimpse into Molecular Evolution Events at the Transition from Water to Land

(2016) Maria Assunta Biscotti et al.   Scientific Reports

An Integrative Breakage Model of genome architecture, reshuffling and evolution

(2015) Marta Farré et al.   BIOESSAYS

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

(2015) Domitille Chalopin et al.   Genome Biology and Evolution

A New Class of SINEs with snRNA Gene-Derived Heads

(2015) Kenji K. Kojima   Genome Biology and Evolution

De Novo Assembly and Annotation of the Asian Tiger Mosquito (Aedes albopictus) Repeatome with dnaPipeTE from Raw Genomic Reads and Comparative Analysis with the Yellow Fever Mosquito (Aedes aegypti)

(2015) Clément Goubert et al.   Genome Biology and Evolution

The Specific Requirements for CR1 Retrotransposition Explain the Scarcity of Retrogenes in Birds

(2015) Alexander Suh   JOURNAL OF MOLECULAR EVOLUTION

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

(2015) Jessica Stapley et al.   MOLECULAR ECOLOGY

A survey of transposable element classification systems – A call for a fundamental update to meet the challenge of their diversity and complexity

(2015) Benoît Piégu et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Convergent evolution of the genomes of marine mammals

(2015) Andrew D Foote et al.   NATURE GENETICS

What's in a genome? The C-value enigma and the evolution of eukaryotic genome content

(2015) Tyler A. Elliott et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Rapid molecular evolution across amniotes of the IIS/TOR network

(2015) Suzanne E. McGaugh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Whole-genome sequence of the Tibetan frogNanorana parkeriand the comparative evolution of tetrapod genomes

(2015) Yan-Bo Sun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ancient Transposable Elements Transformed the Uterine Regulatory Landscape and Transcriptome during the Evolution of Mammalian Pregnancy

(2015) Vincent J. Lynch et al.   Cell Reports

The Dynamics of Incomplete Lineage Sorting across the Ancient Adaptive Radiation of Neoavian Birds

(2015) Alexander Suh et al.   PLOS BIOLOGY

The Genome 10K Project: A Way Forward

(2015) Klaus-Peter Koepfli et al.   Annual Review of Animal Biosciences

Programmed DNA elimination in multicellular organisms

(2014) Jianbin Wang et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Composition and evolutionary importance of transposable elements in humans and primates

(2014) Hee-Eun Lee et al.   Genes & Genomics

Spontaneous germline excision of Tol1, a DNA-based transposable element naturally occurring in the medaka fish genome

(2014) Kohei Watanabe et al.   GENOME

Rolling-Circle Transposons Catalyze Genomic Innovation in a Mammalian Lineage

(2014) Jainy Thomas et al.   Genome Biology and Evolution

Recurrent Horizontal Transfers of Chapaev Transposons in Diverse Invertebrate and Vertebrate Animals

(2014) Hua-Hao Zhang et al.   Genome Biology and Evolution

Large Numbers of Novel miRNAs Originate from DNA Transposons and Are Coincident with a Large Species Radiation in Bats

(2014) Roy N. Platt et al.   MOLECULAR BIOLOGY AND EVOLUTION

Elephant shark genome provides unique insights into gnathostome evolution

(2014) Byrappa Venkatesh et al.   NATURE

The genomic substrate for adaptive radiation in African cichlid fish

(2014) David Brawand et al.   NATURE

Gibbon genome and the fast karyotype evolution of small apes

(2014) Lucia Carbone et al.   NATURE

Genomicus update 2015: KaryoView and MatrixView provide a genome-wide perspective to multispecies comparative genomics

(2014) Alexandra Louis et al.   NUCLEIC ACIDS RESEARCH

Interspecies Insertion Polymorphism Analysis Reveals Recent Activity of Transposable Elements in Extant Coelacanths

(2014) Magali Naville et al.   PLoS One

Evolution and gene capture in ancient endogenous retroviruses - insights from the crocodilian genomes

(2014) Amanda Y Chong et al.   Retrovirology

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs

(2014) R. E. Green et al.   SCIENCE

Comparative genomics reveals insights into avian genome evolution and adaptation

(2014) G. Zhang et al.   SCIENCE

The genomic landscape underlying phenotypic integrity in the face of gene flow in crows

(2014) J. W. Poelstra et al.   SCIENCE

Early Mesozoic Coexistence of Amniotes and Hepadnaviridae

(2014) Alexander Suh et al.   PLoS Genetics

nhmmer: DNA homology search with profile HMMs

(2013) T. J. Wheeler et al.   BIOINFORMATICS

Horizontal transfer of OC1 transposons in the Tasmanian devil

(2013) Clement Gilbert et al.   BMC GENOMICS

Lizards and LINEs: Selection and Demography Affect the Fate of L1 Retrotransposons in the Genome of the Green Anole (Anolis carolinensis)

(2013) Marc Tollis et al.   Genome Biology and Evolution

Coelacanth genomes reveal signatures for evolutionary transition from water to land

(2013) M. Nikaido et al.   GENOME RESEARCH

Transcriptional activity of transposable elements in coelacanth

(2013) Mariko Forconi et al.   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

Evolutionary active transposable elements in the genome of the coelacanth

(2013) Domitille Chalopin et al.   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

Genesis and Regulatory Wiring of Retroelement-Derived Domesticated Genes: A Phylogenomic Perspective

(2013) Janez Kokošar et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Norway spruce genome sequence and conifer genome evolution

(2013) Björn Nystedt et al.   NATURE

The African coelacanth genome provides insights into tetrapod evolution

(2013) Chris T. Amemiya et al.   NATURE

The zebrafish reference genome sequence and its relationship to the human genome

(2013) Kerstin Howe et al.   NATURE

The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan

(2013) Zhuo Wang et al.   NATURE GENETICS

Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution

(2013) Jeramiah J Smith et al.   NATURE GENETICS

Widespread horizontal transfer of retrotransposons

(2013) A. M. Walsh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Burmese python genome reveals the molecular basis for extreme adaptation in snakes

(2013) T. A. Castoe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system

(2013) F. J. Vonk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Draft genome sequence of the Tibetan antelope

(2013) Ri-Li Ge et al.   Nature Communications

The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage

(2013) H Bradley Shaffer et al.   GENOME BIOLOGY

Transposable Elements: An Abundant and Natural Source of Regulatory Sequences for Host Genes

(2012) Rita Rebollo et al.   Annual Review of Genetics

Distinct groups of repetitive families preserved in mammals correspond to different periods of regulatory innovations in vertebrates

(2012) Jerzy Jurka et al.   Biology Direct

Expansion of CORE-SINEs in the genome of the Tasmanian devil

(2012) Maria A Nilsson et al.   BMC GENOMICS

Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages

(2012) Dominic Schmidt et al.   CELL

A non-LTR retroelement extinction in Spermophilus tridecemlineatus

(2012) Roy N. Platt II et al.   GENE

The impact of transposable elements on eukaryotic genomes: From genome size increase to genetic adaptation to stressful environments

(2012) Benoît Chénais et al.   GENE

Accumulation and Rapid Decay of Non-LTR Retrotransposons in the Genome of the Three-Spine Stickleback

(2012) Eryn Blass et al.   Genome Biology and Evolution

Survey Sequencing Reveals Elevated DNA Transposon Activity, Novel Elements, and Variation in Repetitive Landscapes among Vesper Bats

(2012) H. J. T. Pagan et al.   Genome Biology and Evolution

Slow DNA Loss in the Gigantic Genomes of Salamanders

(2012) Cheng Sun et al.   Genome Biology and Evolution

A Universal Method for the Study of CR1 Retroposons in Nonmodel Bird Genomes

(2012) A. Suh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolution of the Australian Lungfish (Neoceratodus forsteri) Genome: A Major Role for CR1 and L2 LINE Elements

(2012) C. J. Metcalfe et al.   MOLECULAR BIOLOGY AND EVOLUTION

Retroposon Insertion Patterns of Neoavian Birds: Strong Evidence for an Extensive Incomplete Lineage Sorting Era

(2012) A. Matzke et al.   MOLECULAR BIOLOGY AND EVOLUTION

SINEBase: a database and tool for SINE analysis

(2012) Nikita S. Vassetzky et al.   NUCLEIC ACIDS RESEARCH

Functional characterization of piggyBat from the bat Myotis lucifugus unveils an active mammalian DNA transposon

(2012) R. Mitra et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transposable elements and viruses as factors in adaptation and evolution: an expansion and strengthening of the TE-Thrust hypothesis

(2012) Keith R. Oliver et al.   Ecology and Evolution

The genomic landscape shaped by selection on transposable elements across 18 mouse strains

(2012) Christoffer Nellåker et al.   GENOME BIOLOGY

LTR Retrotransposons Contribute to Genomic Gigantism in Plethodontid Salamanders

(2011) Cheng Sun et al.   Genome Biology and Evolution

Gorilla genome structural variation reveals evolutionary parallelisms with chimpanzee

(2011) M. Ventura et al.   GENOME RESEARCH

Origin and evolution of SINEs in eukaryotic genomes

(2011) D A Kramerov et al.   HEREDITY

Retrofitting the Genome: L1 Extinction Follows Endogenous Retroviral Expansion in a Group of Muroid Rodents

(2011) I. K. Erickson et al.   JOURNAL OF VIROLOGY

Zisupton--A Novel Superfamily of DNA Transposable Elements Recently Active in Fish

(2011) A. Bohne et al.   MOLECULAR BIOLOGY AND EVOLUTION

Retroposon Insertions and the Chronology of Avian Sex Chromosome Evolution

(2011) Alexander Suh et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Living Fossil in the Genome of a Living Fossil: Harbinger Transposons in the Coelacanth Genome

(2011) J. J. Smith et al.   MOLECULAR BIOLOGY AND EVOLUTION

Comparative and demographic analysis of orang-utan genomes

(2011) Devin P. Locke et al.   NATURE

A high-resolution map of human evolutionary constraint using 29 mammals

(2011) Kerstin Lindblad-Toh et al.   NATURE

The genome of the green anole lizard and a comparative analysis with birds and mammals

(2011) Jessica Alföldi et al.   NATURE

Genome sequencing reveals insights into physiology and longevity of the naked mole rat

(2011) Eun Bae Kim et al.   NATURE

Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals

(2011) Vincent J Lynch et al.   NATURE GENETICS

Dynamic interactions between transposable elements and their hosts

(2011) Henry L. Levin et al.   NATURE REVIEWS GENETICS

Mesozoic retroposons reveal parrots as the closest living relatives of passerine birds

(2011) Alexander Suh et al.   Nature Communications

Repetitive Elements May Comprise Over Two-Thirds of the Human Genome

(2011) A. P. Jason de Koning et al.   PLoS Genetics

Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development

(2011) Marilyn B Renfree et al.   GENOME BIOLOGY

Mobile DNA and the TE-Thrust hypothesis: supporting evidence from the primates

(2011) Keith R Oliver et al.   Mobile DNA

Genomics of Long-Range Regulatory Elements

(2010) James P. Noonan et al.   Annual Review of Genomics and Human Genetics

Epigenetic Regulation of Pericentromeric Heterochromatin during Mammalian Meiosis

(2010) A.M. Khalil et al.   CYTOGENETIC AND GENOME RESEARCH

Distribution of complete and defective copies of the Tol1 transposable element in natural populations of the medaka fish Oryzias latipes

(2010) Akihiko Koga et al.   GENES & GENETIC SYSTEMS

PiggyBac-ing on a Primate Genome: Novel Elements, Recent Activity and Horizontal Transfer

(2010) Heidi J. T. Pagan et al.   Genome Biology and Evolution

Pervasive Horizontal Transfer of Rolling-Circle Transposons among Animals

(2010) Jainy Thomas et al.   Genome Biology and Evolution

Rodent Evolution: Back to the Root

(2010) Gennady Churakov et al.   MOLECULAR BIOLOGY AND EVOLUTION

A role for host–parasite interactions in the horizontal transfer of transposons across phyla

(2010) Clément Gilbert et al.   NATURE

The genome of a songbird

(2010) Wesley C. Warren et al.   NATURE

The Genome of the Western Clawed Frog Xenopus tropicalis

(2010) U. Hellsten et al.   SCIENCE

Promiscuous DNA: horizontal transfer of transposable elements and why it matters for eukaryotic evolution

(2010) Sarah Schaack et al.   TRENDS IN ECOLOGY & EVOLUTION

Transposable elements: powerful facilitators of evolution

(2009) Keith R. Oliver et al.   BIOESSAYS

Transposable elements and an epigenetic basis for punctuated equilibria

(2009) David W. Zeh et al.   BIOESSAYS

Genome assembly reborn: recent computational challenges

(2009) M. Pop   BRIEFINGS IN BIOINFORMATICS

Tracking the past: Interspersed repeats in an extinct Afrotherian mammal, Mammuthus primigenius

(2009) F. Zhao et al.   GENOME RESEARCH

5S rRNA-derived and tRNA-derived SINEs in fruit bats

(2009) Konstantin P. Gogolevsky et al.   GENOMICS

Identifying repeats and transposable elements in sequenced genomes: how to find your way through the dense forest of programs

(2009) E Lerat   HEREDITY

New Superfamilies of Eukaryotic DNA Transposons and Their Internal Divisions

(2009) W. Bao et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Evolutionary Dynamics of Autonomous Non-LTR Retrotransposons in the Lizard Anolis Carolinensis Shows More Similarity to Fish Than Mammals

(2009) P. A. Novick et al.   MOLECULAR BIOLOGY AND EVOLUTION

Characterization and distribution of retrotransposons and simple sequence repeats in the bovine genome

(2009) D. L. Adelson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Programmed loss of millions of base pairs from a vertebrate genome

(2009) J. J. Smith et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Lineage-Specific Biology Revealed by a Finished Genome Assembly of the Mouse

(2009) Deanna M. Church et al.   PLOS BIOLOGY

Analysis of the platypus genome suggests a transposon origin for mammalian imprinting

(2009) Andrew J Pask et al.   GENOME BIOLOGY

Retroelements (LINEs and SINEs) in vole genomes: Differential distribution in the constitutive heterochromatin

(2008) M. J. Acosta et al.   CHROMOSOME RESEARCH

Loss of LINE-1 Activity in the Megabats

(2008) Michael A. Cantrell et al.   GENETICS

Extensive variation between inbred mouse strains due to endogenous L1 retrotransposition

(2008) K. Akagi et al.   GENOME RESEARCH

Retroposed SNOfall--A mammalian-wide comparison of platypus snoRNAs

(2008) J. Schmitz et al.   GENOME RESEARCH

Multiple waves of recent DNA transposon activity in the bat, Myotis lucifugus

(2008) D. A. Ray et al.   GENOME RESEARCH

Epigenetic, transposon and small RNA determinants of hybrid dysfunctions

(2008) P Michalak   HEREDITY

Identification of novel CR1 subfamilies in an avian order with recently active elements

(2008) J JOHN et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Genome analysis of the platypus reveals unique signatures of evolution

(2008) Wesley C. Warren et al.   NATURE

A universal classification of eukaryotic transposable elements implemented in Repbase

(2008) Vladimir V. Kapitonov et al.   NATURE REVIEWS GENETICS

Possible involvement of SINEs in mammalian-specific brain formation

(2008) T. Sasaki et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE

The diversity of retrotransposons and the properties of their reverse transcriptases

(2008) Thomas H. Eickbush et al.   VIRUS RESEARCH