Transcriptional activity and epigenetic regulation of transposable elements in the symbiotic fungus Rhizophagus irregularis

Evolutionary dynamics of transposable elements in bdelloid rotifers

(2021) Reuben W Nowell et al.   eLife

The methylome of the model arbuscular mycorrhizal fungus, Rhizophagus irregularis, shares characteristics with early diverging fungi and Dikarya

(2021) Anurag Chaturvedi et al.   Communications Biology

Long reads and Hi‐C sequencing illuminate the two‐compartment genome of the model arbuscular mycorrhizal symbiont Rhizophagus irregularis

(2021) Gökalp Yildirir et al.   NEW PHYTOLOGIST

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

Parasexual and Sexual Reproduction in Arbuscular Mycorrhizal Fungi: Room for Both

(2020) Gökalp Yildirir et al.   TRENDS IN MICROBIOLOGY

Different Genetic Sources Contribute to the Small RNA Population in the Arbuscular Mycorrhizal Fungus Gigaspora margarita

(2020) Alessandro Silvestri et al.   Frontiers in Microbiology

A universal method for the rapid isolation of all known classes of functional silencing small RNAs

(2020) Thomas Grentzinger et al.   NUCLEIC ACIDS RESEARCH

Nuclear Dynamics in the Arbuscular Mycorrhizal Fungi

(2020) Vasilis Kokkoris et al.   TRENDS IN PLANT SCIENCE

Lineage-Specific Genes and Cryptic Sex: Parallels and Differences between Arbuscular Mycorrhizal Fungi and Fungal Pathogens

(2020) Didier Reinhardt et al.   TRENDS IN PLANT SCIENCE

Comparative genomics of Rhizophagus irregularis , R. cerebriforme , R. diaphanus and Gigaspora rosea highlights specific genetic features in Glomeromycotina

(2019) Emmanuelle Morin et al.   NEW PHYTOLOGIST

Decoding the 5′ nucleotide bias of PIWI-interacting RNAs

(2019) Chad B. Stein et al.   Nature Communications

In silico analysis of fungal small RNA accumulation reveals putative plant mRNA targets in the symbiosis between an arbuscular mycorrhizal fungus and its host plant

(2019) Alessandro Silvestri et al.   BMC GENOMICS

Diversity of cytosine methylation across the fungal tree of life

(2019) Adam J. Bewick et al.   Nature Ecology & Evolution

DeepSignal: detecting DNA methylation state from Nanopore sequencing reads using deep-learning

(2019) Peng Ni et al.   BIOINFORMATICS

g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update)

(2019) Uku Raudvere et al.   NUCLEIC ACIDS RESEARCH

At the nexus of three kingdoms: the genome of the mycorrhizal fungus Gigaspora margarita provides insights into plant, endobacterial and fungal interactions

(2019) Francesco Venice et al.   ENVIRONMENTAL MICROBIOLOGY

The birth and death of effectors in rapidly evolving filamentous pathogen genomes

(2018) Simone Fouché et al.   CURRENT OPINION IN MICROBIOLOGY

High intraspecific genome diversity in the model arbuscular mycorrhizal symbiont Rhizophagus irregularis

(2018) Eric C. H. Chen et al.   NEW PHYTOLOGIST

Horizontal Gene Transfer From Bacteria and Plants to the Arbuscular Mycorrhizal Fungus Rhizophagus irregularis

(2018) Meng Li et al.   Frontiers in Plant Science

RiCRN1, a Crinkler Effector From the Arbuscular Mycorrhizal Fungus Rhizophagus irregularis, Functions in Arbuscule Development

(2018) Stefanie Voß et al.   Frontiers in Microbiology

Contemporaneous radiations of fungi and plants linked to symbiosis

(2018) François Lutzoni et al.   Nature Communications

Single nucleus sequencing reveals evidence of inter-nucleus recombination in arbuscular mycorrhizal fungi

(2018) Eric CH Chen et al.   eLife

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

(2017) Shujun Ou et al.   PLANT PHYSIOLOGY

Fungal Mating in the Most Widespread Plant Symbionts?

(2017) Nicolas Corradi et al.   TRENDS IN PLANT SCIENCE

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

(2016) Fernando Rodriguez et al.   GENETICS

Transposons passively and actively contribute to evolution of the two-speed genome of a fungal pathogen

(2016) Luigi Faino et al.   GENOME RESEARCH

Regulatory activities of transposable elements: from conflicts to benefits

(2016) Edward B. Chuong et al.   NATURE REVIEWS GENETICS

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

Evidence for the sexual origin of heterokaryosis in arbuscular mycorrhizal fungi

(2016) Jeanne Ropars et al.   Nature Microbiology

TEtranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets

(2015) Ying Jin et al.   BIOINFORMATICS

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

A role for palindromic structures in the cis -region of maize Sirevirus LTRs in transposable element evolution and host epigenetic response

(2015) Alexandros Bousios et al.   GENOME RESEARCH

Mosaic genome of endobacteria in arbuscular mycorrhizal fungi: Transkingdom gene transfer in an ancient mycoplasma-fungus association

(2015) Gloria Torres-Cortés et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Cluster of Recently Inserted Transposable Elements Associated with siRNAs in

(2015) Lei Gong et al.   Plant Genome

Evolutionally dynamic L1 regulation in embryonic stem cells

(2014) N. Castro-Diaz et al.   GENES & DEVELOPMENT

Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ

(2014) Jürgen Cox et al.   MOLECULAR & CELLULAR PROTEOMICS

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Gene body methylation shows distinct patterns associated with different gene origins and duplication modes and has a heterogeneous relationship with gene expression inOryza sativa(rice)

(2013) Yupeng Wang et al.   NEW PHYTOLOGIST

Selective Acquisition and Retention of Genomic Sequences by Pack-Mutator-Like Elements Based on Guanine-Cytosine Content and the Breadth of Expression

(2013) A. A. Ferguson et al.   PLANT PHYSIOLOGY

Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis

(2013) E. Tisserant et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ShortStack: Comprehensive annotation and quantification of small RNA genes

(2013) M. J. Axtell   RNA

RNA Interference Pathways in Fungi: Mechanisms and Functions

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

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Regulation of small RNA stability: methylation and beyond

(2012) Lijuan Ji et al.   CELL RESEARCH

Recent Retrotransposon Insertions Are Methylated and Phylogenetically Clustered in Japonica Rice (Oryza sativa spp. japonica)

(2012) Bridgett M. vonHoldt et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Accessory Genome as a Cradle for Adaptive Evolution in Pathogens

(2012) Daniel Croll et al.   PLoS Pathogens

Conserved Meiotic Machinery in Glomus spp., a Putatively Ancient Asexual Fungal Lineage

(2011) Sébastien Halary et al.   Genome Biology and Evolution

Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata

(2011) J. D. Hollister et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of an Active New Mutator Transposable Element in Maize

(2011) Bao-Cai Tan et al.   G3-Genes Genomes Genetics

Stc1: A Critical Link between RNAi and Chromatin Modification Required for Heterochromatin Integrity

(2010) Elizabeth H. Bayne et al.   CELL

Clonality and Recombination in the Life History of an Asexual Arbuscular Mycorrhizal Fungus

(2010) H. C. den Bakker et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome Expansion and Gene Loss in Powdery Mildew Fungi Reveal Tradeoffs in Extreme Parasitism

(2010) P. D. Spanu et al.   SCIENCE

Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation

(2010) A. Zemach et al.   SCIENCE

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

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Coevolution between a Family of Parasite Virulence Effectors and a Class of LINE-1 Retrotransposons

(2009) Soledad Sacristán et al.   PLoS One

DNA methylation is widespread and associated with differential gene expression in castes of the honeybee, Apis mellifera

(2009) N. Elango et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Sorting of Small RNAs into Arabidopsis Argonaute Complexes Is Directed by the 5′ Terminal Nucleotide

(2008) Shijun Mi et al.   CELL

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY

Argonaute proteins: key players in RNA silencing

(2007) Gyorgy Hutvagner et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY