Arbuscular mycorrhizal fungi heterokaryons have two nuclear populations with distinct roles in host–plant interactions

A pathogen effector FOLD diversified in symbiotic fungi

(2023) Albin Teulet et al.   NEW PHYTOLOGIST

A highly contiguous genome assembly reveals sources of genomic novelty in the symbiotic fungus Rhizophagus irregularis

(2023) Bethan F Manley et al.   G3-Genes Genomes Genetics

Haplotype-resolved assembly of diploid genomes without parental data

(2022) Haoyu Cheng et al.   NATURE BIOTECHNOLOGY

Phylogenomic insights into the early diversification of fungi

(2022) Jürgen F.H. Strassert et al.   CURRENT BIOLOGY

Haplotype‐phased and chromosome‐level genome assembly of Puccinia polysora , a giga‐scale fungal pathogen causing southern corn rust

(2022) Junmin Liang et al.   Molecular Ecology Resources

Host identity influences nuclear dynamics in arbuscular mycorrhizal fungi

(2021) Vasilis Kokkoris et al.   CURRENT BIOLOGY

Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm

(2021) Haoyu Cheng et al.   NATURE METHODS

Rapid and accurate alignment of nucleotide conversion sequencing reads with HISAT-3N

(2021) Yun Zhang et al.   GENOME RESEARCH

Lipid exchanges drove the evolution of mutualism during plant terrestrialization

(2021) Mélanie K. Rich et al.   SCIENCE

Phylogenomics of a new fungal phylum reveals multiple waves of reductive evolution across Holomycota

(2021) Luis Javier Galindo et al.   Nature Communications

Homo- and Dikaryons of the Arbuscular Mycorrhizal Fungus Rhizophagus irregularis Differ in Life History Strategy

(2021) Edward Umberto Serghi et al.   Frontiers in Plant Science

The arbuscular mycorrhizal fungus Rhizophagus irregularis harmonizes nuclear dynamics in the presence of distinct abiotic factors

(2021) Calvin Cornell et al.   FUNGAL GENETICS AND BIOLOGY

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

(2021) Alexandra Dallaire et al.   GENOME RESEARCH

EffectorP 3.0: Prediction of Apoplastic and Cytoplasmic Effectors in Fungi and Oomycetes

(2021) Jana Sperschneider et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

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

A comparative genomics study of 23 Aspergillus species from section Flavi

(2020) Inge Kjærbølling et al.   Nature Communications

Standardized phylogenetic and molecular evolutionary analysis applied to species across the microbial tree of life

(2020) Migun Shakya et al.   Scientific Reports

Galaxy HiCExplorer 3: a web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization

(2020) Joachim Wolff et al.   NUCLEIC ACIDS RESEARCH

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

Nuclear Dynamics in the Arbuscular Mycorrhizal Fungi

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

EvolClust: automated inference of evolutionary conserved gene clusters in eukaryotes

(2019) Marina Marcet-Houben et al.   BIOINFORMATICS

Maintenance of High Genome Integrity over Vegetative Growth in the Fairy-Ring Mushroom Marasmius oreades

(2019) Markus Hiltunen et al.   CURRENT BIOLOGY

Emergence of the Ug99 lineage of the wheat stem rust pathogen through somatic hybridisation

(2019) Feng Li et al.   Nature Communications

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

OUP accepted manuscript

(2018)   BIOINFORMATICS

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

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

Nucleus-specific expression in the multinuclear mushroom-forming fungusAgaricus bisporusreveals different nuclear regulatory programs

(2018) Thies Gehrmann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MUMmer4: A fast and versatile genome alignment system

(2018) Guillaume Marçais et al.   PLoS Computational Biology

D-GENIES: dot plot large genomes in an interactive, efficient and simple way

(2018) Floréal Cabanettes et al.   PeerJ

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

(2018) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

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

(2018) Eric CH Chen et al.   eLife

A population genomics approach shows widespread geographical distribution of cryptic genomic forms of the symbiotic fungus Rhizophagus irregularis

(2017) Romain Savary et al.   ISME Journal

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

Ancestral alliances: Plant mutualistic symbioses with fungi and bacteria

(2017) Francis M. Martin et al.   SCIENCE

Fungal Mating in the Most Widespread Plant Symbionts?

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

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 Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Estimating Individual Admixture Proportions from Next Generation Sequencing Data

(2013) Line Skotte et al.   GENETICS

Stacks: an analysis tool set for population genomics

(2013) Julian Catchen et al.   MOLECULAR ECOLOGY

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

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

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

A comprehensive phylogeny of Neurospora reveals a link between reproductive mode and molecular evolution in fungi

(2011) Kristiina Nygren et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

TagCleaner: Identification and removal of tag sequences from genomic and metagenomic datasets

(2010) Robert Schmieder et al.   BMC BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Fast model-based estimation of ancestry in unrelated individuals

(2009) D. H. Alexander et al.   GENOME RESEARCH

Changes in arbuscular mycorrhizal fungal phenotypes and genotypes in response to plant species identity and phosphorus concentration

(2009) Martine Ehinger et al.   NEW PHYTOLOGIST

EVOLUTIONARY SIGNIFICANCE OF IMBALANCED NUCLEAR RATIOS WITHIN HETEROKARYONS OF THE BASIDIOMYCETE FUNGUSHETEROBASIDION PARVIPORUM

(2008) Timothy Y. James et al.   EVOLUTION

The effects of deleterious mutations on evolution in non-recombining genomes

(2008) Vera B. Kaiser et al.   TRENDS IN GENETICS