Evolutionary dynamics of transposable elements in bdelloid rotifers

RepeatModeler2 for automated genomic discovery of transposable element families

(2020) Jullien M. Flynn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparative Genomic and Proteomic Analyses of Three Widespread Phytophthora Species: Phytophthora chlamydospora, Phytophthora gonapodyides and Phytophthora pseudosyringae

(2020) Jamie McGowan et al.   Microorganisms

Evolutionary Dynamics and Consequences of Parthenogenesis in Vertebrates

(2020) Matthew K. Fujita et al.   Annual Review of Ecology Evolution and Systematics

The genome, transcriptome, and proteome of the fish parasite Pomphorhynchus laevis (Acanthocephala)

(2020) Katharina Mauer et al.   PLoS One

Genomic Features of Parthenogenetic Animals

(2020) Kamil S Jaron et al.   JOURNAL OF HEREDITY

Genomic signatures of recombination in a natural population of the bdelloid rotifer Adineta vaga

(2020) Olga A. Vakhrusheva et al.   Nature Communications

Diversity and evolution of the transposable element repertoire in arthropods with particular reference to insects

(2019) Malte Petersen et al.   BMC EVOLUTIONARY BIOLOGY

Functional lability of RNA-dependent RNA polymerases in animals

(2019) Natalia Pinzón et al.   PLoS Genetics

The AAA-ATPase MIDASIN 1 Functions in Ribosome Biogenesis and Is Essential for Embryo and Root Development

(2019) Peng-Cheng Li et al.   PLANT PHYSIOLOGY

Giant Transposons in Eukaryotes: Is Bigger Better?

(2019) Irina R Arkhipova et al.   Genome Biology and Evolution

Revisiting metazoan phylogeny with genomic sampling of all phyla

(2019) Christopher E. Laumer et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

On the Population Dynamics of Junk: A Review on the Population Genomics of Transposable Elements

(2019) Yann Bourgeois et al.   Genes

The genome of the marine monogonont rotifer Brachionus plicatilis: Genome-wide expression profiles of 28 cytochrome P450 genes in response to chlorpyrifos and 2-ethyl-phenanthrene

(2019) Jeonghoon Han et al.   AQUATIC TOXICOLOGY

Small, but surprisingly repetitive genomes: transposon expansion and not polyploidy has driven a doubling in genome size in a metazoan species complex

(2019) J. Blommaert et al.   BMC GENOMICS

Asexual reproduction reduces transposable element load in experimental yeast populations

(2019) Jens Bast et al.   eLife

Evolution and diversity of transposable elements in fish genomes

(2019) Feng Shao et al.   Scientific Reports

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

ARKS: chromosome-scale scaffolding of human genome drafts with linked read kmers

(2018) Lauren Coombe et al.   BMC BIOINFORMATICS

Differential Effect of Selection against LINE Retrotransposons among Vertebrates Inferred from Whole-Genome Data and Demographic Modeling

(2018) Alexander T Xue et al.   Genome Biology and Evolution

The genome of the freshwater monogonont rotifer Brachionus calyciflorus

(2018) Hui-Su Kim et al.   Molecular Ecology Resources

Comparative genomics of bdelloid rotifers: Insights from desiccating and nondesiccating species

(2018) Reuben W. Nowell et al.   PLOS BIOLOGY

The Pfam protein families database in 2019

(2018) Sara El-Gebali et al.   NUCLEIC ACIDS RESEARCH

Direct determination of diploid genome sequences

(2017) Neil I. Weisenfeld et al.   GENOME RESEARCH

UFBoot2: Improving the Ultrafast Bootstrap Approximation

(2017) Diep Thi Hoang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Giant Reverse Transcriptase-Encoding Transposable Elements at Telomeres

(2017) Irina R. Arkhipova et al.   MOLECULAR BIOLOGY AND EVOLUTION

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons

(2017) Shujun Ou et al.   PLANT PHYSIOLOGY

Massive horizontal transfer of transposable elements in insects

(2017) Jean Peccoud et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

LTR-Retrotransposons from Bdelloid Rotifers Capture Additional ORFs Shared between Highly Diverse Retroelement Types

(2017) Fernando Rodriguez et al.   Viruses-Basel

Whole genome analysis of a schistosomiasis-transmitting freshwater snail

(2017) Coen M. Adema et al.   Nature Communications

Comparative genomics of the tardigrades Hypsibius dujardini and Ramazzottius varieornatus

(2017) Yuki Yoshida et al.   PLOS BIOLOGY

Evolution of bird genomes-a transposon's-eye view

(2016) Aurélie Kapusta et al.   Annals of the New York Academy of Sciences

MultiQC: summarize analysis results for multiple tools and samples in a single report

(2016) Philip Ewels et al.   BIOINFORMATICS

Non-genetic polymorphisms in rotifers: environmental and endogenous controls, development, and features for predictable or unpredictable environments

(2016) John J. Gilbert   BIOLOGICAL REVIEWS

The Genome of Intoshia linei Affirms Orthonectids as Highly Simplified Spiralians

(2016) Kirill V. Mikhailov et al.   CURRENT BIOLOGY

Multitasking of the piRNA Silencing Machinery: Targeting Transposable Elements and Foreign Genes in the Bdelloid Rotifer Adineta vaga

(2016) Fernando Rodriguez et al.   GENETICS

Genetic Drift, Not Life History or RNAi, Determine Long-Term Evolution of Transposable Elements

(2016) Amir Szitenberg et al.   Genome Biology and Evolution

Phylogeny of Syndermata (syn. Rotifera): Mitochondrial gene order verifies epizoic Seisonidea as sister to endoparasitic Acanthocephala within monophyletic Hemirotifera

(2016) Malte Sielaff et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Redundans: an assembly pipeline for highly heterozygous genomes

(2016) Leszek P. Pryszcz et al.   NUCLEIC ACIDS RESEARCH

Extremotolerant tardigrade genome and improved radiotolerance of human cultured cells by tardigrade-unique protein

(2016) Takuma Hashimoto et al.   Nature Communications

Transposable Elements versus the Fungal Genome: Impact on Whole-Genome Architecture and Transcriptional Profiles

(2016) Raúl Castanera et al.   PLoS Genetics

Multitasking of the piRNA Silencing Machinery: Targeting Transposable Elements and Foreign Genes in the Bdelloid Rotifer Adineta vaga

(2016) Fernando Rodriguez et al.   GENETICS

BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS: Table 1.

(2015) Katharina J. Hoff et al.   BIOINFORMATICS

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Horizontal gene transfer in bdelloid rotifers is ancient, ongoing and more frequent in species from desiccating habitats

(2015) Isobel Eyres et al.   BMC BIOLOGY

Allele Sharing and Evidence for Sexuality in a Mitochondrial Clade of Bdelloid Rotifers

(2015) Ana Signorovitch et al.   GENETICS

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

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

The octopus genome and the evolution of cephalopod neural and morphological novelties

(2015) Caroline B. Albertin et al.   NATURE

The Lingula genome provides insights into brachiopod evolution and the origin of phosphate biomineralization

(2015) Yi-Jyun Luo et al.   Nature Communications

Allele Sharing and Evidence for Sexuality in a Mitochondrial Clade of Bdelloid Rotifers

(2015) Ana Signorovitch et al.   GENETICS

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

MCMC Methods for Multi-Response Generalized Linear Mixed Models: TheMCMCglmmRPackage

(2015) Jarrod D. Hadfield   Journal of Statistical Software

The Contributions of Transposable Elements to the Structure, Function, and Evolution of Plant Genomes

(2014) Jeffrey L. Bennetzen et al.   Annual Review of Plant Biology

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Gateway to genetic exchange? DNA double-strand breaks in the bdelloid rotiferAdineta vagasubmitted to desiccation

(2014) B. Hespeels et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Transcriptome Data Reveal Syndermatan Relationships and Suggest the Evolution of Endoparasitism in Acanthocephala via an Epizoic Stage

(2014) Alexandra R. Wey-Fabrizius et al.   PLoS One

Comparative genome sequencing reveals genomic signature of extreme desiccation tolerance in the anhydrobiotic midge

(2014) Oleg Gusev et al.   Nature Communications

“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files

(2014) Marc Bailly-Bechet et al.   Mobile DNA

Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction

(2014) Zhian N. Kamvar et al.   PeerJ

Functional diversification of Argonautes in nematodes: an expanding universe: Figure 1

(2013) Amy H. Buck et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Comparative transcriptome analysis of obligately asexual and cyclically sexual rotifers reveals genes with putative functions in sexual reproduction, dormancy, and asexual egg production

(2013) Sara J Hanson et al.   BMC GENOMICS

High-throughput sequencing reveals extraordinary fluidity of miRNA, piRNA, and siRNA pathways in nematodes

(2013) Z. Shi et al.   GENOME RESEARCH

Estimating Gene Gain and Loss Rates in the Presence of Error in Genome Assembly and Annotation Using CAFE 3

(2013) Mira V. Han et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga

(2013) Jean-François Flot et al.   NATURE

Genomic parasites or symbionts? Modeling the effects of environmental pressure on transposition activity in asexual populations

(2013) Michał Startek et al.   THEORETICAL POPULATION BIOLOGY

Endonuclease-containing Penelope retrotransposons in the bdelloid rotifer Adineta vaga exhibit unusual structural features and play a role in expansion of host gene families

(2013) Irina R Arkhipova et al.   Mobile DNA

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

Multiple functionally divergent and conserved copies of alpha tubulin in bdelloid rotifers

(2012) Isobel Eyres et al.   BMC EVOLUTIONARY BIOLOGY

piRNAs Initiate an Epigenetic Memory of Nonself RNA in the C. elegans Germline

(2012) Masaki Shirayama et al.   CELL

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

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

The oyster genome reveals stress adaptation and complexity of shell formation

(2012) Guofan Zhang et al.   NATURE

Insights into bilaterian evolution from three spiralian genomes

(2012) Oleg Simakov et al.   NATURE

Whole-genome sequence of Schistosoma haematobium

(2012) Neil D Young et al.   NATURE GENETICS

Biochemical Diversification through Foreign Gene Expression in Bdelloid Rotifers

(2012) Chiara Boschetti et al.   PLoS Genetics

How does selfing affect the dynamics of selfish transposable elements?

(2012) Thibaud S Boutin et al.   Mobile DNA

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

Uniting Germline and Stem Cells: The Function of Piwi Proteins and the piRNA Pathway in Diverse Organisms

(2011) Celina Juliano et al.   Annual Review of Genetics

BamTools: a C++ API and toolkit for analyzing and managing BAM files

(2011) D. W. Barnett et al.   BIOINFORMATICS

GAGE: A critical evaluation of genome assemblies and assembly algorithms

(2011) S. L. Salzberg et al.   GENOME RESEARCH

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

Considering Transposable Element Diversification in De Novo Annotation Approaches

(2011) Timothée Flutre et al.   PLoS One

Soil rotifer communities are extremely diverse globally but spatially autocorrelated locally

(2011) M. S. Robeson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MOTMOT: models of trait macroevolution on trees

(2011) Gavin H. Thomas et al.   Methods in Ecology and Evolution

phytools: an R package for phylogenetic comparative biology (and other things)

(2011) Liam J. Revell   Methods in Ecology and Evolution

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The effect of sex on the mean and variance of fitness in facultatively sexual rotifers

(2010) L. BECKS et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Genome Structure of Bdelloid Rotifers: Shaped by Asexuality or Desiccation?

(2010) E. A. Gladyshev et al.   JOURNAL OF HEREDITY

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

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

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

DNA transposons and the role of recombination in mutation accumulation in Daphnia pulex

(2010) Sarah Schaack et al.   GENOME BIOLOGY

A subtelomeric non-LTR retrotransposon Hebe in the bdelloid rotifer Adineta vaga is subject to inactivation by deletions but not 5' truncations

(2010) Eugene A Gladyshev et al.   Mobile DNA

What Can Asexual Lineage Age Tell Us about the Maintenance of Sex?

(2009) Maurine Neiman et al.   Annals of the New York Academy of Sciences

Rotifer rDNA-specific R9 retrotransposable elements generate an exceptionally long target site duplication upon insertion

(2009) Eugene A. Gladyshev et al.   GENE

Evolution of the RNA-dependent RNA polymerase (RdRP) genes: Duplications and possible losses before and after the divergence of major eukaryotic groups

(2009) Jie Zong et al.   GENE

Multiple Dicer Genes in the Early-Diverging Metazoa

(2009) D. de Jong et al.   MOLECULAR BIOLOGY AND EVOLUTION

Small silencing RNAs: an expanding universe

(2009) Megha Ghildiyal et al.   NATURE REVIEWS GENETICS

Using native and syntenically mapped cDNA alignments to improve de novo gene finding

(2008) Mario Stanke et al.   BIOINFORMATICS

Degenerate Tetraploidy Was Established Before Bdelloid Rotifer Families Diverged

(2008) J. H. Hur et al.   MOLECULAR BIOLOGY AND EVOLUTION

A universal classification of eukaryotic transposable elements implemented in Repbase

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

Evidence for degenerate tetraploidy in bdelloid rotifers

(2008) David B. Mark Welch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Extreme resistance of bdelloid rotifers to ionizing radiation

(2008) Eugene Gladyshev et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Massive Horizontal Gene Transfer in Bdelloid Rotifers

(2008) E. A. Gladyshev et al.   SCIENCE

The Argonaute protein family

(2008) Julia Höck et al.   GENOME BIOLOGY