Population genomics reveals that within-fungus polymorphism is common and maintained in populations of the mycorrhizal fungus Rhizophagus irregularis

Denoising DNA deep sequencing data—high-throughput sequencing errors and their correction

(2015) David Laehnemann et al.   BRIEFINGS IN BIOINFORMATICS

Analysis of mixtures using next generation sequencing of mitochondrial DNA hypervariable regions

(2015) Hanna Kim et al.   CROATIAN MEDICAL JOURNAL

Studying Genome Heterogeneity within the Arbuscular Mycorrhizal Fungal Cytoplasm

(2015) Eva Boon et al.   Genome Biology and Evolution

Homokaryotic vs heterokaryotic mycelium in arbuscular mycorrhizal fungi: different techniques, different results?

(2015) Jeanne Ropars et al.   NEW PHYTOLOGIST

Cost-efficient high-throughput HLA typing by MiSeq amplicon sequencing

(2014) Vinzenz Lange et al.   BMC GENOMICS

High-throughput sequencing reveals inbreeding depression in a natural population

(2014) J. I. Hoffman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome Sequencing and Comparative Genomics of the Broad Host-Range Pathogen Rhizoctonia solani AG8

(2014) James K. Hane et al.   PLoS Genetics

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

(2014) Kui Lin et al.   PLoS Genetics

The complex transcriptional landscape of the anucleate human platelet

(2013) Paul F Bray et al.   BMC GENOMICS

Rapid genotypic change and plasticity in arbuscular mycorrhizal fungi is caused by a host shift and enhanced by segregation

(2013) Caroline Angelard et al.   ISME Journal

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Going where traditional markers have not gone before: utility of and promise for RAD sequencing in marine invertebrate phylogeography and population genomics

(2013) A. M. Reitzel et al.   MOLECULAR ECOLOGY

Stacks: an analysis tool set for population genomics

(2013) Julian Catchen et al.   MOLECULAR ECOLOGY

Global sampling of plant roots expands the described molecular diversity of arbuscular mycorrhizal fungi

(2013) Maarja Öpik et al.   MYCORRHIZA

The In Vitro Mass-Produced Model Mycorrhizal Fungus, Rhizophagus irregularis, Significantly Increases Yields of the Globally Important Food Security Crop Cassava

(2013) Isabel Ceballos et al.   PLoS One

Improved Detection of Rare HIV-1 Variants using 454 Pyrosequencing

(2013) Brendan B. Larsen et al.   PLoS One

Allelic Differences within and among Sister Spores of the Arbuscular Mycorrhizal Fungus Glomus etunicatum Suggest Segregation at Sporulation

(2013) Eva Boon et al.   PLoS One

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

RAD tag sequencing as a source of SNP markers in Cynara cardunculus L

(2012) Davide Scaglione et al.   BMC GENOMICS

Establishment and interpretation of the genome sequence of the phytopathogenic fungus Rhizoctonia solani AG1-IB isolate 7/3/14

(2012) Daniel Wibberg et al.   JOURNAL OF BIOTECHNOLOGY

Genome sequence of dwarf birch (Betula nana) and cross-species RAD markers

(2012) Nian Wang et al.   MOLECULAR ECOLOGY

Genome-wide association genetics of an adaptive trait in lodgepole pine

(2012) THOMAS L. PARCHMAN et al.   MOLECULAR ECOLOGY

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

Significant genetic and phenotypic changes arising from clonal growth of a single spore of an arbuscular mycorrhizal fungus over multiple generations

(2012) Martine O. Ehinger et al.   NEW PHYTOLOGIST

Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species

(2012) Brant K. Peterson et al.   PLoS One

Genetic Exchange in an Arbuscular Mycorrhizal Fungus Results in Increased Rice Growth and Altered Mycorrhiza-Specific Gene Transcription

(2011) Alexandre Colard et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Genotype and SNP calling from next-generation sequencing data

(2011) Rasmus Nielsen et al.   NATURE REVIEWS GENETICS

Estimation of the Glomus intraradices nuclear DNA content

(2011) Kinga A. Sędzielewska et al.   NEW PHYTOLOGIST

Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems

(2011) André E Minoche et al.   GENOME BIOLOGY

Arbuscular Mycorrhiza: The Challenge to Understand the Genetics of the Fungal Partner

(2010) Ian R. Sanders et al.   Annual Review of Genetics

Segregation in a Mycorrhizal Fungus Alters Rice Growth and Symbiosis-Specific Gene Transcription

(2010) Caroline Angelard et al.   CURRENT BIOLOGY

Diversity of mitochondrial large subunit rDNA haplotypes ofGlomus intraradicesin two agricultural field experiments and two semi-natural grasslands

(2010) BORIS BÖRSTLER et al.   MOLECULAR ECOLOGY

Effect of segregation and genetic exchange on arbuscular mycorrhizal fungi in colonization of roots

(2010) Caroline Angelard et al.   NEW PHYTOLOGIST

Resolving postglacial phylogeography using high-throughput sequencing

(2010) K. J. Emerson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags

(2010) Paul A. Hohenlohe et al.   PLoS Genetics

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

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

(2009) Martine Ehinger et al.   NEW PHYTOLOGIST

The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems

(2008) Marcel G. A. van der Heijden et al.   ECOLOGY LETTERS

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

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

Genetic diversity of the arbuscular mycorrhizal fungusGlomus intraradicesas determined by mitochondrial large subunit rRNA gene sequences is considerably higher than previously expected

(2008) Boris Börstler et al.   NEW PHYTOLOGIST

Genetic diversity and host plant preferences revealed by simple sequence repeat and mitochondrial markers in a population of the arbuscular mycorrhizal fungusGlomus intraradices

(2008) Daniel Croll et al.   NEW PHYTOLOGIST

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

(2008) Nathan A. Baird et al.   PLoS One