The genome of Geosiphon pyriformis reveals ancestral traits linked to the emergence of the arbuscular mycorrhizal symbiosis

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

Haplotype-phased genome assembly of virulent Phythophthora ramorum isolate ND886 facilitated by long-read sequencing reveals effector polymorphisms and copy number variation

(2019) Mathu Malar C et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

(2019) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

A Medicago truncatula SWEET transporter implicated in arbuscule maintenance during arbuscular mycorrhizal symbiosis

(2019) Jianyong An et al.   NEW PHYTOLOGIST

Diversification of the gut fungi Smittium and allies (Harpellales) co-occurred with the origin of complete metamorphosis of their symbiotic insect hosts (lower Diptera)

(2019) Yan Wang et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Great moments in evolution: the conquest of land by plants

(2018) Stefan A Rensing   CURRENT OPINION IN PLANT BIOLOGY

Improved prediction of fungal effector proteins from secretomes with EffectorP 2.0

(2018) Jana Sperschneider et al.   MOLECULAR PLANT PATHOLOGY

The origin and evolution of mycorrhizal symbioses: from palaeomycology to phylogenomics

(2018) Christine Strullu-Derrien et al.   NEW PHYTOLOGIST

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

The timescale of early land plant evolution

(2018) Jennifer L. Morris et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fatty Acids, Hydrocarbons and Terpenes of Nannochloropsis and Nannochloris Isolates with Potential for Biofuel Production

(2018) Alan López-Rosales et al.   Energies

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

(2018) Xuepeng Sun et al.   NEW PHYTOLOGIST

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

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

Fatty acids in arbuscular mycorrhizal fungi are synthesized by the host plant

(2017) Leonie H. Luginbuehl et al.   SCIENCE

Changes in arbuscular mycorrhizal fungal attributes along a chronosequence of black locust ( Robinia pseudoacacia ) plantations can be attributed to the plantation-induced variation in soil properties

(2017) Min Sheng et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Diet of Arbuscular Mycorrhizal Fungi: Bread and Butter?

(2017) Mélanie K. Rich et al.   TRENDS IN PLANT SCIENCE

Lipid transfer from plants to arbuscular mycorrhiza fungi

(2017) Andreas Keymer et al.   eLife

Plant Communities Rather than Soil Properties Structure Arbuscular Mycorrhizal Fungal Communities along Primary Succession on a Mine Spoil

(2017) Claudia Krüger et al.   Frontiers in Microbiology

The Comparison of Expressed Candidate Secreted Proteins from Two Arbuscular Mycorrhizal Fungi Unravels Common and Specific Molecular Tools to Invade Different Host Plants

(2017) Laurent Kamel et al.   Frontiers in Plant Science

Genome-Wide Survey of Gut Fungi (Harpellales) Reveals the First Horizontally Transferred Ubiquitin Gene from a Mosquito Host

(2016) Yan Wang et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2016) Joseph W. Spatafora et al.   MYCOLOGIA

Evidence for the sexual origin of heterokaryosis in arbuscular mycorrhizal fungi

(2016) Jeanne Ropars et al.   Nature Microbiology

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

The two-speed genomes of filamentous pathogens: waltz with plants

(2015) Suomeng Dong et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Phylogenomic Analyses Indicate that Early Fungi Evolved Digesting Cell Walls of Algal Ancestors of Land Plants

(2015) Ying Chang et al.   Genome Biology and Evolution

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

Algal ancestor of land plants was preadapted for symbiosis

(2015) Pierre-Marc Delaux et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparative Analysis of Secretomes from Ectomycorrhizal Fungi with an Emphasis on Small-Secreted Proteins

(2015) Clement Pellegrin et al.   Frontiers in Microbiology

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

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

Cyanobacteria in Scandinavian coastal waters — A potential source for biofuels and fatty acids?

(2014) Franciska S. Steinhoff et al.   Algal Research-Biomass Biofuels and Bioproducts

The MaSuRCA genome assembler

(2013) Aleksey V. Zimin et al.   BIOINFORMATICS

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

Short-chain chitin oligomers from arbuscular mycorrhizal fungi trigger nuclear Ca2+spiking inMedicago truncatularoots and their production is enhanced by strigolactone

(2013) Andrea Genre et al.   NEW PHYTOLOGIST

The carbohydrate-active enzymes database (CAZy) in 2013

(2013) Vincent Lombard et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

MycoCosm portal: gearing up for 1000 fungal genomes

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

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

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses

(2012) R. Lanfear et al.   MOLECULAR BIOLOGY AND EVOLUTION

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

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

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

Phylogenetic reference data for systematics and phylotaxonomy of arbuscular mycorrhizal fungi from phylum to species level

(2011) Manuela Krüger et al.   NEW PHYTOLOGIST

The Genome Portal of the Department of Energy Joint Genome Institute

(2011) I. V. Grigoriev et al.   NUCLEIC ACIDS RESEARCH

Arbuscule-containing and non-colonized cortical cells of mycorrhizal roots undergo extensive and specific reprogramming during arbuscular mycorrhizal development

(2011) Nicole Gaude et al.   PLANT JOURNAL

Estimating the timing of early eukaryotic diversification with multigene molecular clocks

(2011) L. W. Parfrey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fungal lipochitooligosaccharide symbiotic signals in arbuscular mycorrhiza

(2010) Fabienne Maillet et al.   NATURE

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

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

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

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

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Recombination in Glomus intraradices, a supposed ancient asexual arbuscular mycorrhizal fungus

(2009) Daniel Croll et al.   BMC EVOLUTIONARY BIOLOGY

Global and cell-type gene expression profiles in tomato plants colonized by an arbuscular mycorrhizal fungus

(2009) Valentina Fiorilli et al.   NEW PHYTOLOGIST

Mycorrhizal associations and other means of nutrition of vascular plants: understanding the global diversity of host plants by resolving conflicting information and developing reliable means of diagnosis

(2009) Mark C. Brundrett   PLANT AND SOIL

Identification of the sex genes in an early diverged fungus

(2008) Alexander Idnurm et al.   NATURE

Arbuscular mycorrhiza: the mother of plant root endosymbioses

(2008) Martin Parniske   NATURE REVIEWS MICROBIOLOGY