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

Merfin: improved variant filtering, assembly evaluation and polishing via k-mer validation

(2022) Giulio Formenti et al.   NATURE METHODS

Whole genome analyses based on single, field collected spores of the arbuscular mycorrhizal fungus Funneliformis geosporum

(2022) Shadi Eshghi Sahraei et al.   MYCORRHIZA

Divergent genomic trajectories predate the origin of animals and fungi

(2022) Eduard Ocaña-Pallarès et al.   NATURE

Genome Assembly and Transcriptome Analysis of the Fungus Coniella diplodiella During Infection on Grapevine (Vitis vinifera L.)

(2021) Ruitao Liu et al.   Frontiers in Microbiology

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

(2021) Mathu Malar C et al.   CURRENT BIOLOGY

A genome-scale phylogeny of the kingdom Fungi

(2021) Yuanning Li et al.   CURRENT BIOLOGY

Towards complete and error-free genome assemblies of all vertebrate species

(2021) Arang Rhie et al.   NATURE

Sensitive protein alignments at tree-of-life scale using DIAMOND

(2021) Benjamin Buchfink et al.   NATURE METHODS

antiSMASH 6.0: improving cluster detection and comparison capabilities

(2021) Kai Blin et al.   NUCLEIC ACIDS RESEARCH

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

Global view on the metabolism of RNA poly(A) tails in yeast Saccharomyces cerevisiae

(2021) Agnieszka Tudek et al.   Nature Communications

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

Rhizophagus proliferus genome sequence reiterates conservation of genetic traits in AM fungi, but predicts higher saprotrophic activity

(2021) Pushplata Prasad Singh et al.   ARCHIVES OF MICROBIOLOGY

Telomere-to-telomere genome assembly of asparaginase-producing Trichoderma simmonsii

(2021) Dawoon Chung et al.   BMC GENOMICS

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

(2021) Alexandra Dallaire et al.   GENOME RESEARCH

Haplotype-aware variant calling with PEPPER-Margin-DeepVariant enables high accuracy in nanopore long-reads

(2021) Kishwar Shafin et al.   NATURE METHODS

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

Analysis of the co-translational assembly of the fungal fatty acid synthase (FAS)

(2020) Manuel Fischer et al.   Scientific Reports

MitoFinder: Efficient automated large‐scale extraction of mitogenomic data in target enrichment phylogenomics

(2020) Rémi Allio et al.   Molecular Ecology Resources

Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes

(2020) Kishwar Shafin et al.   NATURE BIOTECHNOLOGY

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

Large-scale genome sequencing of mycorrhizal fungi provides insights into the early evolution of symbiotic traits

(2020) Shingo Miyauchi et al.   Nature Communications

Genome evolution in fungal plant pathogens: looking beyond the two-speed genome model

(2020) David E. Torres et al.   Fungal Biology Reviews

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

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

(2019) Peng Ni et al.   BIOINFORMATICS

RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference

(2019) Alexey M Kozlov 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

Tracing the origin and evolution of pseudokinases across the tree of life

(2019) Annie Kwon et al.   Science Signaling

Effector proteins of Rhizophagus proliferus: conserved protein domains may play a role in host-specific interaction with different plant species

(2019) Pushplata Prasad Singh et al.   BRAZILIAN JOURNAL OF MICROBIOLOGY

Small RNAs from the plant pathogenic fungus Sclerotinia sclerotiorum highlight host candidate genes associated with quantitative disease resistance

(2019) Mark Derbyshire et al.   MOLECULAR PLANT PATHOLOGY

ModelTest-NG: A New and Scalable Tool for the Selection of DNA and Protein Evolutionary Models

(2019) Diego Darriba et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

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

(2018) Yuuki Kobayashi et al.   BMC GENOMICS

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

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

Earth BioGenome Project: Sequencing life for the future of life

(2018) Harris A. Lewin 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

Rapid divergence of genome architectures following the origin of an ectomycorrhizal symbiosis in the genus Amanita

(2018) Jaqueline Hess et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2018) Stefanie Voß et al.   Frontiers in Microbiology

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

(2018) Xuepeng Sun et al.   NEW PHYTOLOGIST

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

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

(2017) Armando Bravo et al.   NEW PHYTOLOGIST

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

(2017) Leonie H. Luginbuehl et al.   SCIENCE

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

(2017) Yina Jiang et al.   SCIENCE

Lipid transfer from plants to arbuscular mycorrhiza fungi

(2017) Andreas Keymer et al.   eLife

Mitochondrial comparative genomics and phylogenetic signal assessment of mtDNA among arbuscular mycorrhizal fungi

(2016) Maryam Nadimi et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Bandage: interactive visualization ofde novogenome assemblies: Fig. 1.

(2015) Ryan R. Wick et al.   BIOINFORMATICS

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Up-regulation of genes involved in N-acetylglucosamine uptake and metabolism suggests a recycling mode of chitin in intraradical mycelium of arbuscular mycorrhizal fungi

(2015) Yoshihiro Kobae et al.   MYCORRHIZA

Cryo-EM structure of fatty acid synthase (FAS) fromRhodosporidium toruloidesprovides insights into the evolutionary development of fungal FAS

(2015) Manuel Fischer et al.   PROTEIN SCIENCE

Global assessment of arbuscular mycorrhizal fungus diversity reveals very low endemism

(2015) J. Davison et al.   SCIENCE

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

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

(2014) Vera Wewer et al.   PLANT JOURNAL

Evolutionary Origins of the Multienzyme Architecture of Giant Fungal Fatty Acid Synthase

(2014) Habib S.T. Bukhari et al.   STRUCTURE

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

(2014) Kui Lin et al.   PLoS Genetics

Protein Complexes Are under Evolutionary Selection to Assemble via Ordered Pathways

(2013) Joseph A. Marsh et al.   CELL

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

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

In silico Analysis of 3'-End-Processing Signals in Aspergillus oryzae Using Expressed Sequence Tags and Genomic Sequencing Data

(2011) M. Tanaka et al.   DNA RESEARCH

Evolution of 5' Untranslated Region Length and Gene Expression Reprogramming in Yeasts

(2011) Z. Lin et al.   MOLECULAR BIOLOGY AND EVOLUTION

Modernizing Reference Genome Assemblies

(2011) Deanna M. Church et al.   PLOS BIOLOGY

Comprehensive annotation of the transcriptome of the human fungal pathogen Candida albicans using RNA-seq

(2010) V. M. Bruno et al.   GENOME RESEARCH

Mechanisms underlying beneficial plant–fungus interactions in mycorrhizal symbiosis

(2010) Paola Bonfante et al.   Nature Communications

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

The mitochondrial genome sequence of the arbuscular mycorrhizal fungusGlomus intraradicesisolate 494 and implications for the phylogenetic placement ofGlomus

(2009) Jaikoo Lee et al.   NEW PHYTOLOGIST

Arbuscular mycorrhiza: the mother of plant root endosymbioses

(2008) Martin Parniske   NATURE REVIEWS MICROBIOLOGY

Genome level analysis of rice mRNA 3′-end processing signals and alternative polyadenylation

(2008) Yingjia Shen et al.   NUCLEIC ACIDS RESEARCH

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

(2008) Brian J Haas et al.   GENOME BIOLOGY