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

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

(2016) Ivana Grabundzija et al.   Nature Communications

Whole genome comparative analysis of transposable elements provides new insight into mechanisms of their inactivation in fungal genomes

(2015) Joëlle Amselem et al.   BMC GENOMICS

Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists

(2015) Annegret Kohler et al.   NATURE GENETICS

Genome-wide profiling of DNA methylation provides insights into epigenetic regulation of fungal development in a plant pathogenic fungus, Magnaporthe oryzae

(2015) Junhyun Jeon et al.   Scientific Reports

Endogenous Small RNA Mediates Meiotic Silencing of a Novel DNA Transposon

(2015) Yizhou Wang et al.   G3-Genes Genomes Genetics

The landscape of transposable elements in the finished genome of the fungal wheat pathogen Mycosphaerella graminicola

(2015) Braham Dhillon et al.   BMC GENOMICS

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Highly expressed captured genes and cross-kingdom domains present in Helitrons create novel diversity in Pleurotus ostreatus and other fungi

(2014) Raúl Castanera et al.   BMC GENOMICS

Transposable element-assisted evolution and adaptation to host plant within the Leptosphaeria maculans-Leptosphaeria biglobosa species complex of fungal pathogens

(2014) Jonathan Grandaubert et al.   BMC GENOMICS

Spy: A New Group of Eukaryotic DNA Transposons without Target Site Duplications

(2014) Min-Jin Han et al.   Genome Biology and Evolution

Transposable Element Dynamics among Asymbiotic and Ectomycorrhizal Amanita Fungi

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

Populus trichocarpa and Populus deltoides Exhibit Different Metabolomic Responses to Colonization by the Symbiotic Fungus Laccaria bicolor

(2014) Timothy J. Tschaplinski et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Illumina TruSeq Synthetic Long-Reads Empower De Novo Assembly and Resolve Complex, Highly-Repetitive Transposable Elements

(2014) Rajiv C. McCoy et al.   PLoS One

Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi

(2014) Robert Riley et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Domesticated retroviral GAG gene in Drosophila: New functions for an old gene

(2014) L.N. Nefedova et al.   VIROLOGY

Genome-wide transcriptional profiling of Botrytis cinerea genes targeting plant cell walls during infections of different hosts

(2014) Barbara Blanco-Ulate et al.   Frontiers in Plant Science

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

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

MycoCosm portal: gearing up for 1000 fungal genomes

(2013) Igor V. Grigoriev et al.   NUCLEIC ACIDS RESEARCH

DIRS and Ngaro Retrotransposons in Fungi

(2013) Anna Muszewska et al.   PLoS One

Transposon Variants and Their Effects on Gene Expression in Arabidopsis

(2013) Xi Wang et al.   PLoS Genetics

Transcriptome analyses during fruiting body formation in Fusarium graminearum and Fusarium verticillioides reflect species life history and ecology

(2012) Usha Rani Sikhakolli et al.   FUNGAL GENETICS AND BIOLOGY

Patterns of Repeat-Induced Point Mutation in Transposable Elements of Basidiomycete Fungi

(2012) Felix Horns et al.   Genome Biology and Evolution

A second-generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence

(2012) T. T. Hu et al.   GENOME RESEARCH

SINE Retrotransposons Cause Epigenetic Reprogramming of Adjacent Gene Promoters

(2012) M. R. H. Estecio et al.   MOLECULAR CANCER RESEARCH

Characterization of Transposable Elements in the Ectomycorrhizal Fungus Laccaria bicolor

(2012) Jessy Labbé et al.   PLoS One

The Paleozoic Origin of Enzymatic Lignin Decomposition Reconstructed from 31 Fungal Genomes

(2012) D. Floudas et al.   SCIENCE

Transposable element small RNAs as regulators of gene expression

(2012) Andrea D. McCue et al.   TRENDS IN GENETICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Gene Capture by Helitron Transposons Reshuffles the Transcriptome of Maize

(2011) A. M. Barbaglia et al.   GENETICS

FungiDB: an integrated functional genomics database for fungi

(2011) J. E. Stajich et al.   NUCLEIC ACIDS RESEARCH

Frequent Gene Movement and Pseudogene Evolution Is Common to the Large and Complex Genomes of Wheat, Barley, and Their Relatives

(2011) Thomas Wicker et al.   PLANT CELL

Considering Transposable Element Diversification in De Novo Annotation Approaches

(2011) Timothée Flutre et al.   PLoS One

LTR Retrotransposons in Fungi

(2011) Anna Muszewska et al.   PLoS One

Obligate biotrophy features unraveled by the genomic analysis of rust fungi

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

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Genomic evidence of repeat-induced point mutation (RIP) in filamentous ascomycetes

(2010) A. John Clutterbuck   FUNGAL GENETICS AND BIOLOGY

Transposable elements in the mammalian germline: a comfortable niche or a deadly trap?

(2010) N Zamudio et al.   HEREDITY

Périgord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis

(2010) Francis Martin et al.   NATURE

Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium

(2010) Li-Jun Ma et al.   NATURE

Limitations of next-generation genome sequence assembly

(2010) Can Alkan et al.   NATURE METHODS

Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation

(2010) A. Zemach 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

Control of Transcription by Cell Size

(2010) Chia-Yung Wu et al.   PLOS BIOLOGY

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

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

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Epigenetic silencing of transposable elements: A trade-off between reduced transposition and deleterious effects on neighboring gene expression

(2009) J. D. Hollister et al.   GENOME RESEARCH

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

(2009) E Lerat   HEREDITY

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

(2009) M. N. Price et al.   MOLECULAR BIOLOGY AND EVOLUTION

The B73 Maize Genome: Complexity, Diversity, and Dynamics

(2009) P. S. Schnable et al.   SCIENCE

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS

Horizontal gene transfer in eukaryotic evolution

(2008) Patrick J. Keeling et al.   NATURE REVIEWS GENETICS

Transposable elements and the evolution of regulatory networks

(2008) Cédric Feschotte   NATURE REVIEWS GENETICS