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

From algae to angiosperms–inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes

(2014) Brad R Ruhfel et al.   BMC EVOLUTIONARY BIOLOGY

Deep sequencing of the tobacco mitochondrial transcriptome reveals expressed ORFs and numerous editing sites outside coding regions

(2014) Benjamin T Grimes et al.   BMC GENOMICS

Comparative analysis of 11 Brassicales mitochondrial genomes and the mitochondrial transcriptome of Brassica oleracea

(2014) Felix Grewe et al.   MITOCHONDRION

Genome-Wide Transcript Profiling Reveals the Coevolution of Plastid Gene Sequences and Transcript Processing Pathways in the Fucoxanthin Dinoflagellate Karlodinium veneficum

(2014) Elisabeth Richardson et al.   MOLECULAR BIOLOGY AND EVOLUTION

Chloroplast Genome Evolution in Early Diverged Leptosporangiate Ferns

(2014) Hyoung Tae Kim et al.   MOLECULES AND CELLS

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

RNA Editing in Plants and Its Evolution

(2013) Mizuki Takenaka et al.   Annual Review of Genetics

Complete plastid genomes from Ophioglossum californicum, Psilotum nudum, and Equisetum hyemale reveal an ancestral land plant genome structure and resolve the position of Equisetales among monilophytes

(2013) Felix Grewe et al.   BMC EVOLUTIONARY BIOLOGY

Arabidopsischloroplast quantitative editotype

(2013) Hannes Ruwe et al.   FEBS LETTERS

Consistent Errors in First Strand cDNA Due to Random Hexamer Mispriming

(2013) Thomas P. van Gurp et al.   PLoS One

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

(2013) Daehwan Kim et al.   GENOME BIOLOGY

The Chloroplast Genome of Pellia endiviifolia: Gene Content, RNA-Editing Pattern, and the Origin of Chloroplast Editing

(2012) Christopher Grosche et al.   Genome Biology and Evolution

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

Loss of Two Introns from the Magnolia tripetala Mitochondrial cox2 Gene Implicates Horizontal Gene Transfer and Gene Conversion as a Novel Mechanism of Intron Loss

(2012) N. J. Hepburn et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The Mitochondrial Genome of the Lycophyte Huperzia squarrosa: The Most Archaic Form in Vascular Plants

(2012) Yang Liu et al.   PLoS One

RNA Editing in Mitochondrial Trans-Introns Is Required for Splicing

(2012) Jean-Claude Farré et al.   PLoS One

RNA editing restores critical domains of a group I intron in fern mitochondria

(2011) Dominique Bégu et al.   CURRENT 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

Organellar RNA editing

(2011) Anne-Laure Chateigner-Boutin et al.   Wiley Interdisciplinary Reviews-RNA

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Complete plastome sequences of Equisetum arvense and Isoetes flaccida: implications for phylogeny and plastid genome evolution of early land plant lineages

(2010) Kenneth G Karol et al.   BMC EVOLUTIONARY BIOLOGY

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

Biases in Illumina transcriptome sequencing caused by random hexamer priming

(2010) Kasper D. Hansen et al.   NUCLEIC ACIDS RESEARCH

Intron RNA editing is essential for splicing in plant mitochondria

(2010) B. Castandet et al.   NUCLEIC ACIDS RESEARCH

Large-scale detection and analysis of RNA editing in grape mtDNA by RNA deep-sequencing

(2010) Ernesto Picardi et al.   NUCLEIC ACIDS RESEARCH

The evolution of chloroplast genes and genomes in ferns

(2010) Paul G. Wolf et al.   PLANT MOLECULAR BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

The horsetail Equisetum arvense mitochondria share two group I introns with the liverwort Marchantia, acquired a novel group II intron but lost intron-encoded ORFs

(2009) Dominique Bégu et al.   CURRENT GENETICS

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

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

Characteristics and Prediction of RNA Editing Sites in Transcripts of the Moss Takakia lepidozioides Chloroplast

(2008) K. Yura et al.   DNA RESEARCH

Seven large variations in the extent of RNA editing in plant mitochondria between three ecotypes of Arabidopsis thaliana

(2008) Anja Zehrmann et al.   MITOCHONDRION

The Mitochondrial Genome of the Gymnosperm Cycas taitungensis Contains a Novel Family of Short Interspersed Elements, Bpu Sequences, and Abundant RNA Editing Sites

(2008) S.-M. Chaw et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genetic Architecture of Mitochondrial Editing in Arabidopsis thaliana

(2007) S. Bentolila et al.   GENETICS