Survival trade-offs in plant roots during colonization by closely related beneficial and pathogenic fungi

Root Endophyte Colletotrichum tofieldiae Confers Plant Fitness Benefits that Are Phosphate Status Dependent

(2016) Kei Hiruma et al.   CELL

Fungal Effectors and Plant Susceptibility

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

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

(2015) Annegret Kohler et al.   NATURE GENETICS

Mutualistic root endophytism is not associated with the reduction of saprotrophic traits and requires a noncompromised plant innate immunity

(2015) Urs Lahrmann et al.   NEW PHYTOLOGIST

What lies beneath: belowground defense strategies in plants

(2015) Barbara De Coninck et al.   TRENDS IN PLANT SCIENCE

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Broad compatibility in fungal root symbioses

(2014) Alga Zuccaro et al.   CURRENT OPINION IN PLANT BIOLOGY

Root-associated fungi of Arabidopsis thaliana and Microthlaspi perfoliatum

(2014) Jessica Keim et al.   FUNGAL DIVERSITY

Identification of primary and secondary metabolites with phosphorus status-dependent abundance inArabidopsis, and of the transcription factor PHR1 as a major regulator of metabolic changes during phosphorus limitation

(2014) BIKRAM-DATT PANT et al.   PLANT CELL AND ENVIRONMENT

The rice endophyte Harpophora oryzae genome reveals evolution from a pathogen to a mutualistic endophyte

(2014) Xi-Hui Xu et al.   Scientific Reports

Comparative Phylogenomics Uncovers the Impact of Symbiotic Associations on Host Genome Evolution

(2014) Pierre-Marc Delaux et al.   PLoS Genetics

The carbohydrate-active enzymes database (CAZy) in 2013

(2013) Vincent Lombard et al.   NUCLEIC ACIDS RESEARCH

eggNOG v4.0: nested orthology inference across 3686 organisms

(2013) Sean Powell et al.   NUCLEIC ACIDS RESEARCH

Transcriptome Responses to Combinations of Stresses in Arabidopsis

(2013) S. Rasmussen et al.   PLANT PHYSIOLOGY

Mosaic genome structure of the barley powdery mildew pathogen and conservation of transcriptional programs in divergent hosts

(2013) S. Hacquard et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

REAPR: a universal tool for genome assembly evaluation

(2013) Martin Hunt et al.   GENOME BIOLOGY

The endophytic mycobiota of Arabidopsis thaliana

(2012) Elena García et al.   FUNGAL DIVERSITY

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

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

Detecting Patches of Protein Sites of Influenza A Viruses under Positive Selection

(2012) C. Tusche et al.   MOLECULAR BIOLOGY AND EVOLUTION

Lifestyle transitions in plant pathogenic Colletotrichum fungi deciphered by genome and transcriptome analyses

(2012) Richard J O'Connell et al.   NATURE GENETICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Comparative genomic and transcriptomic analyses reveal the hemibiotrophic stage shift ofColletotrichumfungi

(2012) Pamela Gan et al.   NEW PHYTOLOGIST

Fusion of two divergent fungal individuals led to the recent emergence of a unique widespread pathogen species

(2012) E. H. Stukenbrock et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

(2011) Carson Holt et al.   BMC BIOINFORMATICS

Inference of Gain and Loss Events from Phyletic Patterns Using Stochastic Mapping and Maximum Parsimony—A Simulation Study

(2011) Ofir Cohen et al.   Genome Biology and Evolution

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Endophytic Life Strategies Decoded by Genome and Transcriptome Analyses of the Mutualistic Root Symbiont Piriformospora indica

(2011) Alga Zuccaro et al.   PLoS Pathogens

Périgord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis

(2010) Francis Martin et al.   NATURE

Mechanisms underlying beneficial plant–fungus interactions in mycorrhizal symbiosis

(2010) Paola Bonfante et al.   Nature Communications

ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks

(2009) Gabriela Bindea et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(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

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Fungal endophytes: diversity and functional roles

(2009) R. J. Rodriguez et al.   NEW PHYTOLOGIST

MEROPS: the peptidase database

(2009) Neil D. Rawlings et al.   NUCLEIC ACIDS RESEARCH

cis-Element- and Transcriptome-Based Screening of Root Hair-Specific Genes and Their Functional Characterization in Arabidopsis

(2009) S.-K. Won et al.   PLANT PHYSIOLOGY

The Role of WRKY Transcription Factors in Plant Immunity

(2009) S. P. Pandey et al.   PLANT PHYSIOLOGY

Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training

(2008) V. Ter-Hovhannisyan et al.   GENOME RESEARCH

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Glucosinolate Metabolites Required for an Arabidopsis Innate Immune Response

(2008) N. K. Clay et al.   SCIENCE

A Glucosinolate Metabolism Pathway in Living Plant Cells Mediates Broad-Spectrum Antifungal Defense

(2008) P. Bednarek et al.   SCIENCE