Cut-and-Paste Transposons in Fungi with Diverse Lifestyles

Integration site selection by retroviruses and transposable elements in eukaryotes

(2017) Tania Sultana et al.   NATURE REVIEWS GENETICS

Transposition of Mutator–like transposable elements (MULEs) resembles hAT and Transib elements and V(D)J recombination

(2017) Kun Liu et al.   NUCLEIC ACIDS RESEARCH

Application of the MAFFT sequence alignment program to large data—reexamination of the usefulness of chained guide trees

(2016) Kazunori D. Yamada et al.   BIOINFORMATICS

A Tale of Genome Compartmentalization: The Evolution of Virulence Clusters in Smut Fungi

(2016) Julien Y. Dutheil et al.   Genome Biology and Evolution

A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data

(2016) Joseph W. Spatafora et al.   MYCOLOGIA

Unearthing the roots of ectomycorrhizal symbioses

(2016) Francis Martin et al.   NATURE REVIEWS MICROBIOLOGY

Adaptation to Global Change: A Transposable Element–Epigenetics Perspective

(2016) Olivier Rey et al.   TRENDS IN ECOLOGY & EVOLUTION

Genome-Wide Comparison of Magnaporthe Species Reveals a Host-Specific Pattern of Secretory Proteins and Transposable Elements

(2016) Meghana Deepak Shirke et al.   PLoS One

HTT-DB: Horizontally transferred transposable elements database: Fig. 1.

(2015) Bruno Reis Dotto et al.   BIOINFORMATICS

DNA transposons have colonized the genome of the giant virus Pandoravirus salinus

(2015) Cheng Sun et al.   BMC BIOLOGY

Do larger genomes contain more diverse transposable elements?

(2015) Tyler A Elliott et al.   BMC EVOLUTIONARY BIOLOGY

Intrinsic retroviral reactivation in human preimplantation embryos and pluripotent cells

(2015) Edward J. Grow et al.   NATURE

Mycorrhizal ecology and evolution: the past, the present, and the future

(2015) Marcel G. A. van der Heijden et al.   NEW PHYTOLOGIST

The Dfam database of repetitive DNA families

(2015) Robert Hubley et al.   NUCLEIC ACIDS RESEARCH

Transposable Elements Contribute to Activation of Maize Genes in Response to Abiotic Stress

(2015) Irina Makarevitch et al.   PLoS Genetics

Microsporidian Genomes Harbor a Diverse Array of Transposable Elements that Demonstrate an Ancestry of Horizontal Exchange with Metazoans

(2014) Nicolas Parisot et al.   Genome Biology and Evolution

Transposable Element Dynamics among Asymbiotic and Ectomycorrhizal Amanita Fungi

(2014) Jaqueline Hess et al.   Genome Biology and Evolution

Gibbon genome and the fast karyotype evolution of small apes

(2014) Lucia Carbone et al.   NATURE

Mobile DNA elements in the generation of diversity and complexity in the brain

(2014) Jennifer A. Erwin et al.   NATURE REVIEWS NEUROSCIENCE

The RNase H-like superfamily: new members, comparative structural analysis and evolutionary classification

(2014) Karolina A. Majorek et al.   NUCLEIC ACIDS RESEARCH

Lineage-specific expansions of TET/JBP genes and a new class of DNA transposons shape fungal genomic and epigenetic landscapes

(2014) Lakshminarayan M. Iyer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNAi function, diversity, and loss in the fungal kingdom

(2013) R. Blake Billmyre et al.   CHROMOSOME RESEARCH

Structure Prediction and Analysis of DNA Transposon and LINE Retrotransposon Proteins

(2013) György Abrusán et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Evolution of fungal sexual reproduction

(2013) Joseph Heitman et al.   MYCOLOGIA

Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions

(2013) Jaina Mistry et al.   NUCLEIC ACIDS RESEARCH

A Superfamily of DNA Transposons Targeting Multicopy Small RNA Genes

(2013) Kenji K. Kojima et al.   PLoS One

Comparative Genomics of a Plant-Pathogenic Fungus, Pyrenophora tritici-repentis , Reveals Transduplication and the Impact of Repeat Elements on Pathogenicity and Population Divergence

(2013) Viola A. Manning et al.   G3-Genes Genomes Genetics

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

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

RNA Interference Pathways in Fungi: Mechanisms and Functions

(2012) Shwu-Shin Chang et al.   Annual Review of Microbiology

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

(2012) Limin Fu et al.   BIOINFORMATICS

ProtTest 3: fast selection of best-fit models of protein evolution

(2011) Diego Darriba et al.   BIOINFORMATICS

Diverse and tissue-enriched small RNAs in the plant pathogenic fungus, Magnaporthe oryzae

(2011) Cristiano C Nunes et al.   BMC GENOMICS

The catalytic domain of all eukaryotic cut-and-paste transposase superfamilies

(2011) Y.-W. Yuan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations

(2011) Thierry Rouxel et al.   Nature Communications

Finished Genome of the Fungal Wheat Pathogen Mycosphaerella graminicola Reveals Dispensome Structure, Chromosome Plasticity, and Stealth Pathogenesis

(2011) Stephen B. Goodwin et al.   PLoS Genetics

Involvement of transposon-like elements in penicillin gene cluster regulation

(2010) Mona Shaaban et al.   FUNGAL GENETICS AND BIOLOGY

Sex-induced silencing defends the genome of Cryptococcus neoformans via RNAi

(2010) X. Wang et al.   GENES & DEVELOPMENT

Population genomic sequencing of Coccidioides fungi reveals recent hybridization and transposon control

(2010) D. E. Neafsey et al.   GENOME RESEARCH

DNA methylation and the formation of heterochromatin in Neurospora crassa

(2010) M R Rountree et al.   HEREDITY

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

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Ginger DNA transposons in eukaryotes and their evolutionary relationships with long terminal repeat retrotransposons

(2010) Weidong Bao et al.   Mobile DNA

Dating the molecular clock in fungi – how close are we?

(2010) Mary L. Berbee et al.   Fungal Biology Reviews

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

Transposable Elements and Factors Influencing their Success in Eukaryotes

(2009) E. J. Pritham   JOURNAL OF HEREDITY

New Superfamilies of Eukaryotic DNA Transposons and Their Internal Divisions

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

Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans

(2009) Brian J. Haas et al.   NATURE

RNAi in Budding Yeast

(2009) I. A. Drinnenberg et al.   SCIENCE

Genomic Analysis of the Basal Lineage Fungus Rhizopus oryzae Reveals a Whole-Genome Duplication

(2009) Li-Jun Ma et al.   PLoS Genetics

The Genome of Nectria haematococca: Contribution of Supernumerary Chromosomes to Gene Expansion

(2009) Jeffrey J. Coleman et al.   PLoS Genetics

A universal classification of eukaryotic transposable elements implemented in Repbase

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