Genome and evolution of the arbuscular mycorrhizal fungus Diversispora epigaea (formerly Glomus versiforme ) and its bacterial endosymbionts

The genome of Rhizophagus clarus HR1 reveals a common genetic basis for auxotrophy among arbuscular mycorrhizal fungi

(2018) Yuuki Kobayashi et al.   BMC GENOMICS

Conserved Proteins of the RNA Interference System in the Arbuscular Mycorrhizal Fungus Rhizoglomus irregulare Provide New Insight into the Evolutionary History of Glomeromycota

(2018) Soon-Jae Lee et al.   Genome Biology and Evolution

Impact of spatial organization on a novel auxotrophic interaction among soil microbes

(2018) Xue Jiang et al.   ISME Journal

Mycoplasma-related endobacteria within Mortierellomycotina fungi: diversity, distribution and functional insights into their lifestyle

(2018) Alessandro Desirò et al.   ISME Journal

Arbuscular mycorrhizal fungi: intraspecific diversity and pangenomes

(2018) Stephanie Mathieu et al.   NEW PHYTOLOGIST

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

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

Host- and stage-dependent secretome of the arbuscular mycorrhizal fungus Rhizophagus irregularis

(2018) Tian Zeng et al.   PLANT JOURNAL

‘Candidatus Moeniiplasma glomeromycotorum’, an endobacterium of arbuscular mycorrhizal fungi

(2017)   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Who lives in a fungus? The diversity, origins and functions of fungal endobacteria living in Mucoromycota

(2017) Paola Bonfante et al.   ISME Journal

Widespread adenine N6-methylation of active genes in fungi

(2017) Stephen J Mondo et al.   NATURE GENETICS

Arbuscular mycorrhiza-specific enzymes FatM and RAM2 fine-tune lipid biosynthesis to promote development of arbuscular mycorrhiza

(2017) Armando Bravo et al.   NEW PHYTOLOGIST

Plant Signaling and Metabolic Pathways Enabling Arbuscular Mycorrhizal Symbiosis

(2017) Allyson M. MacLean et al.   PLANT CELL

Plants transfer lipids to sustain colonization by mutualistic mycorrhizal and parasitic fungi

(2017) Yina Jiang et al.   SCIENCE

Genome-wide analyses of chitin synthases identify horizontal gene transfers towards bacteria and allow a robust and unifying classification into fungi

(2016) Isabelle R. Gonçalves et al.   BMC EVOLUTIONARY BIOLOGY

Expansion of Signal Transduction Pathways in Fungi by Extensive Genome Duplication

(2016) Luis M. Corrochano et al.   CURRENT BIOLOGY

Uniting species- and community-oriented approaches to understand arbuscular mycorrhizal fungal diversity

(2016) Maarja Öpik et al.   Fungal Ecology

Defying Muller’s Ratchet: Ancient Heritable Endobacteria Escape Extinction through Retention of Recombination and Genome Plasticity

(2016) Mizue Naito et al.   mBio

The Epigenomic Landscape of Prokaryotes

(2016) Matthew J. Blow et al.   PLoS Genetics

Evidence for the sexual origin of heterokaryosis in arbuscular mycorrhizal fungi

(2016) Jeanne Ropars et al.   Nature Microbiology

Fungal Effectors and Plant Susceptibility

(2015) Libera Lo Presti et al.   Annual Review of Plant Biology

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

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

(2015) Annegret Kohler et al.   NATURE GENETICS

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

(2015) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS 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

Minimal genomes of mycoplasma-related endobacteria are plastic and contain host-derived genes for sustained life within Glomeromycota

(2015) Mizue Naito et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global assessment of arbuscular mycorrhizal fungus diversity reveals very low endemism

(2015) J. Davison et al.   SCIENCE

Beyond the Whole-Genome Duplication: Phylogenetic Evidence for an Ancient Interspecies Hybridization in the Baker's Yeast Lineage

(2015) Marina Marcet-Houben et al.   PLOS BIOLOGY

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

(2015) Braham Dhillon et al.   BMC GENOMICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

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

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

Fatty acid synthesis and lipid metabolism in the obligate biotrophic fungusRhizophagus irregularisduring mycorrhization ofLotus japonicus

(2014) Vera Wewer et al.   PLANT JOURNAL

Single Nucleus Genome Sequencing Reveals High Similarity among Nuclei of an Endomycorrhizal Fungus

(2014) Kui Lin et al.   PLoS Genetics

NextClip: an analysis and read preparation tool for Nextera Long Mate Pair libraries

(2013) Richard M. Leggett et al.   BIOINFORMATICS

Shared Signatures of Parasitism and Phylogenomics Unite Cryptomycota and Microsporidia

(2013) Timothy Y. James et al.   CURRENT BIOLOGY

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

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

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

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

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

(2012) Ruibang Luo et al.   GigaScience

RNA Interference in Fungi: Pathways, Functions, and Applications

(2011) Yunkun Dang et al.   EUKARYOTIC CELL

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

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

The genome of the obligate endobacterium of an AM fungus reveals an interphylum network of nutritional interactions

(2011) Stefano Ghignone et al.   ISME Journal

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

Revealing Natural Relationships among Arbuscular Mycorrhizal Fungi: Culture Line BEG47 Represents Diversispora epigaea, Not Glomus versiforme

(2011) Arthur Schüßler et al.   PLoS One

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

A glimpse into the basis of vision in the kingdom Mycota

(2010) Alexander Idnurm et al.   FUNGAL GENETICS AND BIOLOGY

Photobiology in the Zygomycota: Multiple photoreceptor genes for complex responses to light

(2010) Luis M. Corrochano et al.   FUNGAL GENETICS AND BIOLOGY

The obligate endobacteria of arbuscular mycorrhizal fungi are ancient heritable components related to the Mollicutes

(2010) Maria Naumann et al.   ISME Journal

Fungal lipochitooligosaccharide symbiotic signals in arbuscular mycorrhiza

(2010) Fabienne Maillet et al.   NATURE

Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation

(2010) A. Zemach et al.   SCIENCE

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

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

A CRY-DASH-type photolyase/cryptochrome from Sclerotinia sclerotiorum mediates minor UV-A-specific effects on development

(2008) Selvakumar Veluchamy et al.   FUNGAL GENETICS AND BIOLOGY