Lipid exchanges drove the evolution of mutualism during plant terrestrialization

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

How Plants Conquered Land

(2020) Stefan A. Rensing   CELL

Gene expression in Rhizoglomus irregulare at two different time points of mycorrhiza establishment in Helianthus annuus roots, as revealed by RNA-seq analysis

(2020) Alberto Vangelisti et al.   MYCORRHIZA

A Phylogenetic Study of the ANT Family Points to a preANT Gene as the Ancestor of Basal and euANT Transcription Factors in Land Plants

(2019) Melissa Dipp-Álvarez et al.   Frontiers in Plant Science

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

(2019) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

One thousand plant transcriptomes and the phylogenomics of green plants

(2019)   NATURE

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

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

AP2 transcription factor CBX1 with a specific function in symbiotic exchange of nutrients in mycorrhizal Lotus japonicus

(2018) Li Xue et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Medicago AP2-Domain Transcription Factor WRI5a Is a Master Regulator of Lipid Biosynthesis and Transfer during Mycorrhizal Symbiosis

(2018) Yina Jiang et al.   Molecular Plant

Contemporaneous radiations of fungi and plants linked to symbiosis

(2018) François Lutzoni et al.   Nature Communications

Fast and accurate de novo genome assembly from long uncorrected reads

(2017) Robert Vaser et al.   GENOME RESEARCH

UFBoot2: Improving the Ultrafast Bootstrap Approximation

(2017) Diep Thi Hoang et al.   MOLECULAR BIOLOGY AND EVOLUTION

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

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

(2017) Armando Bravo et al.   NEW PHYTOLOGIST

Transcriptome analysis of the Populus trichocarpa–Rhizophagus irregularis Mycorrhizal Symbiosis: Regulation of Plant and Fungal Transportomes under Nitrogen Starvation

(2017) Silvia Calabrese et al.   PLANT AND CELL PHYSIOLOGY

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

Compacting and correcting Trinity and Oases RNA-Seq de novo assemblies

(2017) Cédric Cabau et al.   PeerJ

Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences

(2016) Heng Li   BIOINFORMATICS

Modified low-salt CTAB extraction of high-quality DNA from contaminant-rich tissues

(2016) Jean-René Arseneau et al.   Molecular Ecology Resources

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

(2016) Mihaela Pertea et al.   Nature Protocols

Standards for plant synthetic biology: a common syntax for exchange of DNA parts

(2015) Nicola J. Patron et al.   NEW PHYTOLOGIST

Network of GRAS Transcription Factors Involved in the Control of Arbuscule Development inLotus japonicus

(2015) Li Xue et al.   PLANT PHYSIOLOGY

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

Host and non-host roots in rice: cellular and molecular approaches reveal differential responses to arbuscular mycorrhizal fungi

(2015) Valentina Fiorilli et al.   Frontiers in Plant Science

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

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

(2014) S. Anders et al.   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones 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

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

(2014) Vera Wewer et al.   PLANT JOURNAL

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

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

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

Multiplex and homologous recombination–mediated genome editing in Arabidopsis and Nicotiana benthamiana using guide RNA and Cas9

(2013) Jian-Feng Li et al.   NATURE BIOTECHNOLOGY

Spatio-temporal analysis of cellulose synthesis during cell plate formation in Arabidopsis

(2013) Fabien Miart et al.   PLANT JOURNAL

Expression of the genes coding for plastidic acetyl-CoA carboxylase subunits is regulated by a location-sensitive transcription factor binding site

(2013) Natsumi Fukuda et al.   PLANT MOLECULAR BIOLOGY

Comparison of the MpEF1α and CaMV35 promoters for application in Marchantia polymorpha overexpression studies

(2013) Felix Althoff et al.   TRANSGENIC RESEARCH

Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels

(2012) Marcel H. Schulz et al.   BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

WRINKLED Transcription Factors Orchestrate Tissue-Specific Regulation of Fatty Acid Biosynthesis in Arabidopsis

(2012) A. To et al.   PLANT CELL

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

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

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools

(2011) Philippe Lamesch et al.   NUCLEIC ACIDS RESEARCH

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

The regulation of arbuscular mycorrhizal symbiosis by phosphate in pea involves early and systemic signalling events

(2010) Coline Balzergue et al.   JOURNAL OF EXPERIMENTAL BOTANY

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

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Mutualistic mycorrhiza-like symbiosis in the most ancient group of land plants

(2010) Claire P. Humphreys et al.   Nature Communications

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

(2009) S. Capella-Gutierrez 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

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Genome Annotation in Plants and Fungi: EuGene as a Model Platform

(2008) Sylvain Foissac et al.   Current Bioinformatics