Towards a plant model for enigmatic U‐to‐C RNA editing: the organelle genomes, transcriptomes, editomes and candidate RNA editing factors in the hornwort Anthoceros agrestis

Delineation of pentatricopeptide repeat codes for target RNA prediction

(2019) Junjie Yan et al.   NUCLEIC ACIDS RESEARCH

Multifarious Evolutionary Pathways of a Nuclear RNA Editing Factor: Disjunctions in Coevolution of DOT4 and Its Chloroplast Target rpoC1eU488SL

(2019) Anke Hein et al.   Genome Biology and Evolution

Stable native RIP9 complexes associate with C‐to‐U RNA editing activity, PPRs, RIPs, OZ1, ORRM1, and ISE2

(2019) Rafael Sandoval et al.   PLANT JOURNAL

Unparalleled variation in RNA editing among Selaginella plastomes

(2019) David Roy Smith   PLANT PHYSIOLOGY

Plant organelle RNA editing and its specificity factors: enhancements of analyses and new database features in PREPACT 3.0

(2018) Henning Lenz et al.   BMC BIOINFORMATICS

Complete mitochondrial genome sequence of Anthoceros angustus: conservative evolution of the mitogenomes in hornworts

(2018) Shanshan Dong et al.   BRYOLOGIST

Plant Evolution: Phylogenetic Relationships between the Earliest Land Plants

(2018) Stefan A. Rensing   CURRENT BIOLOGY

The Interrelationships of Land Plants and the Nature of the Ancestral Embryophyte

(2018) Mark N. Puttick et al.   CURRENT BIOLOGY

Great moments in evolution: the conquest of land by plants

(2018) Stefan A Rensing   CURRENT OPINION IN PLANT BIOLOGY

The DYW Domains of Pentatricopeptide Repeat RNA Editing Factors Contribute to Discriminate Target and Non-Target Editing Sites

(2018) Mizuho Ichinose et al.   PLANT AND CELL PHYSIOLOGY

Towards a comprehensive picture of C-to-U RNA editing sites in angiosperm mitochondria

(2018) Alejandro A. Edera et al.   PLANT MOLECULAR BIOLOGY

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

Genome-wide organellar analyses from the hornwort Leiosporoceros dussii show low frequency of RNA editing

(2018) Juan Carlos Villarreal A. et al.   PLoS One

Land Plant Molecular Phylogenetics: A Review with Comments on Evaluating Incongruence Among Phylogenies

(2018) Cymon J. Cox   CRITICAL REVIEWS IN PLANT SCIENCES

Nuclear protein phylogenies support the monophyly of the three bryophyte groups (Bryophyta Schimp.)

(2018) Filipe Sousa et al.   NEW PHYTOLOGIST

Comprehensive prediction of target RNA editing sites for PLS-class PPR proteins in Arabidopsis thaliana

(2018) Takehito Kobayashi et al.   PLANT AND CELL PHYSIOLOGY

Contemporaneous radiations of fungi and plants linked to symbiosis

(2018) François Lutzoni et al.   Nature Communications

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

Crystal structures of the Arabidopsis thaliana organellar RNA editing factors MORF1 and MORF9

(2017) Sascha Haag et al.   NUCLEIC ACIDS RESEARCH

Bilaterally symmetric axes with rhizoids composed the rooting structure of the common ancestor of vascular plants

(2017) Alexander J. Hetherington et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A protein with an unusually short PPR domain, MEF8, affects editing at over 60 Arabidopsis mitochondrial C targets of RNA editing

(2017) Michael F. Diaz et al.   PLANT JOURNAL

Two interacting PPR proteins are major Arabidopsis editing factors in plastid and mitochondria

(2017) Damien Guillaumot et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multiple PPR protein interactions are involved in the RNA editing system inArabidopsismitochondria and plastids

(2017) Nuria Andrés-Colás et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reverse U-to-C editing exceeds C-to-U RNA editing in some ferns – a monilophyte-wide comparison of chloroplast and mitochondrial RNA editing suggests independent evolution of the two processes in both organelles

(2016) Nils Knie et al.   BMC EVOLUTIONARY BIOLOGY

Convergent Evolution of Fern-Specific Mitochondrial Group II Intron atp1i361g2 and Its Ancient Source Paralogue rps3i249g2 and Independent Losses of Intron and RNA Editing among Pteridaceae

(2016) Simon Maria Zumkeller et al.   Genome Biology and Evolution

MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices

(2016) Dinghua Li et al.   METHODS

W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis

(2016) Jana Trifinopoulos et al.   NUCLEIC ACIDS RESEARCH

Redefining the structural motifs that determine RNA binding and RNA editing by pentatricopeptide repeat proteins in land plants

(2016) Shifeng Cheng et al.   PLANT JOURNAL

The Unexpected Diversity of Plant Organelle RNA Editosomes

(2016) Tao Sun et al.   TRENDS IN PLANT SCIENCE

Establishment of Anthoceros agrestis as a model species for studying the biology of hornworts

(2015) Péter Szövényi et al.   BMC PLANT BIOLOGY

Selective Homo- and Heteromer Interactions between the Multiple Organellar RNA Editing Factor (MORF) Proteins inArabidopsis thaliana

(2015) Anja Zehrmann et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A Conserved Glutamate Residue in the C-terminal Deaminase Domain of Pentatricopeptide Repeat Proteins Is Required for RNA Editing Activity

(2015) Michael L. Hayes et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A Zinc Finger Motif-Containing Protein Is Essential for Chloroplast RNA Editing

(2015) Tao Sun et al.   PLoS Genetics

Variable Frequency of Plastid RNA Editing among Ferns and Repeated Loss of Uridine-to-Cytidine Editing from Vascular Plants

(2015) Wenhu Guo et al.   PLoS One

Pentatricopeptide Repeat Proteins in Plants

(2014) Alice Barkan et al.   Annual Review of Plant Biology

A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data

(2014) David Coil et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Identification of a pentatricopeptide repeat RNA editing factor inPhyscomitrella patenschloroplasts

(2014) Mizuho Ichinose et al.   FEBS LETTERS

Cytidine Deaminase Motifs within the DYW Domain of Two Pentatricopeptide Repeat-containing Proteins Are Required for Site-specific Chloroplast RNA Editing

(2014) Jessica A. Wagoner et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The cytidine deaminase signature HxE(x)nCxxC of DYW1 binds zinc and is necessary for RNA editing ofndhD-1

(2014) Clément Boussardon et al.   NEW PHYTOLOGIST

Phylotranscriptomic analysis of the origin and early diversification of land plants

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

Chloroplast RNA editing going extreme: more than 3400 events of C-to-U editing in the chloroplast transcriptome of the lycophyteSelaginella uncinata

(2014) Bastian Oldenkott et al.   RNA

The plastid genome of the hornwort Nothoceros aenigmaticus (Dendrocerotaceae): Phylogenetic signal in inverted repeat expansion, pseudogenization, and intron gain

(2013) Juan Carlos Villarreal et al.   AMERICAN JOURNAL OF BOTANY

Identification of Two Pentatricopeptide Repeat Genes Required for RNA Editing and Zinc Binding by C-terminal Cytidine Deaminase-like Domains

(2013) Michael L. Hayes et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Evolution of Plant Mitochondrial Intron-Encoded Maturases: Frequent Lineage-Specific Loss and Recurrent Intracellular Transfer to the Nucleus

(2013) Wenhu Guo et al.   JOURNAL OF MOLECULAR EVOLUTION

aLeaves facilitates on-demand exploration of metazoan gene family trees on MAFFT sequence alignment server with enhanced interactivity

(2013) Shigehiro Kuraku et al.   NUCLEIC ACIDS RESEARCH

OrganellarGenomeDRAW—a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets

(2013) Marc Lohse et al.   NUCLEIC ACIDS RESEARCH

Two DYW Subclass PPR Proteins are Involved in RNA Editing of ccmFc and atp9 Transcripts in the Moss Physcomitrella patens: First Complete Set of PPR Editing Factors in Plant Mitochondria

(2013) Mizuho Ichinose et al.   PLANT AND CELL PHYSIOLOGY

A DYW-protein knockout inPhyscomitrellaaffects two closely spaced mitochondrial editing sites and causes a severe developmental phenotype

(2013) Mareike Schallenberg-Rüdinger et al.   PLANT JOURNAL

Elucidation of the RNA Recognition Code for Pentatricopeptide Repeat Proteins Involved in Organelle RNA Editing in Plants

(2013) Yusuke Yagi et al.   PLoS One

Improved Computational Target Site Prediction for Pentatricopeptide Repeat RNA Editing Factors

(2013) Mizuki Takenaka et al.   PLoS One

An RNA recognition motif-containing protein is required for plastid RNA editing in Arabidopsis and maize

(2013) T. Sun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Architecture of the PPR gene family in the mossPhyscomitrella patens

(2013) Mamoru Sugita et al.   RNA Biology

Nuclear DYW-Type PPR Gene Families Diversify with Increasing RNA Editing Frequencies in Liverwort and Moss Mitochondria

(2012) Mareike Rüdinger et al.   JOURNAL OF MOLECULAR EVOLUTION

Two Interacting Proteins Are Necessary for the Editing of the NdhD-1 Site in Arabidopsis Plastids

(2012) C. Boussardon et al.   PLANT CELL

RIP1, a member of an Arabidopsis protein family, interacts with the protein RARE1 and broadly affects RNA editing

(2012) S. Bentolila et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multiple organellar RNA editing factor (MORF) family proteins are required for RNA editing in mitochondria and plastids of plants

(2012) M. Takenaka et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Combinatorial Amino Acid Code for RNA Recognition by Pentatricopeptide Repeat Proteins

(2012) Alice Barkan et al.   PLoS Genetics

Extreme RNA Editing in Coding Islands and Abundant Microsatellites in Repeat Sequences of Selaginella moellendorffii Mitochondria: The Root of Frequent Plant mtDNA Recombination in Early Tracheophytes

(2011) Julia Hecht et al.   Genome Biology and Evolution

Evolution of the deaminase fold and multiple origins of eukaryotic editing and mutagenic nucleic acid deaminases from bacterial toxin systems

(2011) Lakshminarayan M. Iyer et al.   NUCLEIC ACIDS RESEARCH

Extensive Loss of RNA Editing Sites in Rapidly Evolving Silene Mitochondrial Genomes: Selection vs. Retroprocessing as the Driving Force

(2010) D. B. Sloan et al.   GENETICS

A unique transcriptome: 1782 positions of RNA editing alter 1406 codon identities in mitochondrial mRNAs of the lycophyte Isoetes engelmannii

(2010) Felix Grewe et al.   NUCLEIC ACIDS RESEARCH

The complete mitochondrial genome sequence of the hornwort Phaeoceros laevis: retention of many ancient pseudogenes and conservative evolution of mitochondrial genomes in hornworts

(2009) Jia-Yu Xue et al.   CURRENT GENETICS

Introducing the plant RNA editing prediction and analysis computer tool PREPACT and an update on RNA editing site nomenclature

(2009) Henning Lenz et al.   CURRENT GENETICS

The Complete Mitochondrial Genome Sequence of the Hornwort Megaceros aenigmaticus Shows a Mixed Mode of Conservative Yet Dynamic Evolution in Early Land Plant Mitochondrial Genomes

(2009) Libo Li et al.   JOURNAL OF MOLECULAR EVOLUTION

RNA editing: only eleven sites are present in the Physcomitrella patens mitochondrial transcriptome and a universal nomenclature proposal

(2009) Mareike Rüdinger et al.   MOLECULAR GENETICS AND GENOMICS

Moss and liverwort xyloglucans contain galacturonic acid and are structurally distinct from the xyloglucans synthesized by hornworts and vascular plants*

(2008) Maria J Peña et al.   GLYCOBIOLOGY