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

Non-coding RNA may be associated with cytoplasmic male sterility in Silene vulgaris

(2017) James D. Stone et al.   JOURNAL OF EXPERIMENTAL BOTANY

Mitochondrial Retroprocessing Promoted Functional Transfers of rpl5 to the Nucleus in Grasses

(2017) Zhiqiang Wu et al.   MOLECULAR BIOLOGY AND EVOLUTION

Molecular Approaches for Manipulating Male Sterility and Strategies for Fertility Restoration in Plants

(2017) Pawan Shukla et al.   MOLECULAR BIOTECHNOLOGY

Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis

(2017) Sayed Mohammad Ebrahim Sahraeian et al.   Nature Communications

Assembly and comparative analysis of complete mitochondrial genome sequence of an economic plantSalix suchowensis

(2017) Ning Ye et al.   PeerJ

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

Completion of the mitochondrial genome sequence of onion (Allium cepa L.) containing the CMS-S male-sterile cytoplasm and identification of an independent event of the ccmF N gene split

(2016) Bongju Kim et al.   CURRENT GENETICS

Localized Retroprocessing as a Model of Intron Loss in the Plant Mitochondrial Genome

(2016) Argelia Cuenca et al.   Genome Biology and Evolution

The Roles of Mutation, Selection, and Expression in Determining Relative Rates of Evolution in Mitochondrial versus Nuclear Genomes

(2016) Justin C. Havird et al.   MOLECULAR BIOLOGY AND EVOLUTION

Complete mitochondrial genomes from the ferns Ophioglossum californicum and Psilotum nudum are highly repetitive with the largest organellar introns

(2016) Wenhu Guo et al.   NEW PHYTOLOGIST

The Unexpected Diversity of Plant Organelle RNA Editosomes

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

Uncovering the novel characteristics of Asian honey bee, Apis cerana, by whole genome sequencing

(2015) Doori Park et al.   BMC GENOMICS

Retention of functional genes for S19 ribosomal protein in both the mitochondrion and nucleus for over 60 million years

(2015) Sruthi Atluri et al.   MOLECULAR GENETICS AND GENOMICS

Predictable Alteration of Sequence Recognition by RNA Editing Factors from Arabidopsis

(2015) Peter Kindgren et al.   PLANT CELL

Empty pericarp7encodes a mitochondrial E-subgroup pentatricopeptide repeat protein that is required forccmFNediting, mitochondrial function and seed development in maize

(2015) Feng Sun et al.   PLANT JOURNAL

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

AliView: a fast and lightweight alignment viewer and editor for large datasets

(2014) Anders Larsson   BIOINFORMATICS

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

A genome-wide association study of seed protein and oil content in soybean

(2014) Eun-Young Hwang et al.   BMC GENOMICS

Assembly and analysis of a male sterile rubber tree mitochondrial genome reveals DNA rearrangement events and a novel transcript

(2014) Jeremy R Shearman et al.   BMC PLANT BIOLOGY

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

(2014) Felix Grewe et al.   MITOCHONDRION

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

The application of RNA-seq to the comprehensive analysis of plant mitochondrial transcriptomes

(2014) James D. Stone et al.   MOLECULAR GENETICS AND GENOMICS

RNA metabolism in plant mitochondria

(2014) Kamel Hammani et al.   TRENDS IN PLANT SCIENCE

RNA Editing in Plants and Its Evolution

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

The “fossilized” mitochondrial genome of Liriodendron tulipifera: ancestral gene content and order, ancestral editing sites, and extraordinarily low mutation rate

(2013) Aaron O Richardson et al.   BMC BIOLOGY

The genome and transcriptome of perennial ryegrass mitochondria

(2013) Md Islam et al.   BMC GENOMICS

Reverse Transcription of Spliced psbA mRNA in Chlamydomonas spp. and Its Possible Role in Evolutionary Intron Loss

(2013) Obed W. Odom et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Differential regulation of Arabidopsis plastid gene expression and RNA editing in non-photosynthetic tissues

(2013) Ching-Chih Tseng et al.   PLANT MOLECULAR BIOLOGY

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

Pentatricopeptide repeat proteins involved in plant organellar RNA editing

(2013) Yusuke Yagi et al.   RNA Biology

Horizontal Transfer of Entire Genomes via Mitochondrial Fusion in the Angiosperm Amborella

(2013) D. W. Rice et al.   SCIENCE

Comprehensive High-Resolution Analysis of the Role of an Arabidopsis Gene Family in RNA Editing

(2013) Stéphane Bentolila et al.   PLoS Genetics

A Complete Sequence and Transcriptomic Analyses of Date Palm (Phoenix dactylifera L.) Mitochondrial Genome

(2012) Yongjun Fang et al.   PLoS One

Capturing the Biofuel Wellhead and Powerhouse: The Chloroplast and Mitochondrial Genomes of the Leguminous Feedstock Tree Pongamia pinnata

(2012) Stephen H. Kazakoff et al.   PLoS One

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

Accurate identification of A-to-I RNA editing in human by transcriptome sequencing

(2011) J. H. Bahn et al.   GENOME RESEARCH

The nucleocytoplasmic conflict, a driving force for the emergence of plant organellar RNA editing

(2011) Benoît Castandet et al.   IUBMB LIFE

De novo transcriptome assembly and polymorphism detection in the flowering plant Silene vulgaris (Caryophyllaceae)

(2011) DANIEL B. SLOAN et al.   Molecular Ecology Resources

The evolution of RNA editing and pentatricopeptide repeat genes

(2011) Sota Fujii et al.   NEW PHYTOLOGIST

Genome size differentiates co-occurring populations of the planktonic diatom Ditylum brightwellii (Bacillariophyta)

(2010) Julie A Koester et al.   BMC EVOLUTIONARY BIOLOGY

When you can’t trust the DNA: RNA editing changes transcript sequences

(2010) Volker Knoop   CELLULAR AND MOLECULAR LIFE SCIENCES

Editing site analysis in a gymnosperm mitochondrial genome reveals similarities with angiosperm mitochondrial genomes

(2010) Michael Lee Salmans et al.   CURRENT GENETICS

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

Testing for Selection on Synonymous Sites in Plant Mitochondrial DNA: The Role of Codon Bias and RNA Editing

(2010) Daniel B. Sloan et al.   JOURNAL OF MOLECULAR EVOLUTION

Evaluation of Models of the Mechanisms Underlying Intron Loss and Gain in Aspergillus Fungi

(2010) Lei-Ying Zhang et al.   JOURNAL OF MOLECULAR EVOLUTION

Insights into the Evolution of Mitochondrial Genome Size from Complete Sequences of Citrullus lanatus and Cucurbita pepo (Cucurbitaceae)

(2010) A. J. Alverson et al.   MOLECULAR BIOLOGY AND EVOLUTION

Mammalian recombination hot spots: properties, control and evolution

(2010) Kenneth Paigen et al.   NATURE REVIEWS 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

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 Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast evolution of the retroprocessed mitochondrial rps3 gene in Conifer II and further evidence for the phylogeny of gymnosperms

(2009) Jin-Hua Ran et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

A trans -splicing group I intron and tRNA-hyperediting in the mitochondrial genome of the lycophyte Isoetes engelmannii

(2009) Felix Grewe et al.   NUCLEIC ACIDS RESEARCH

The PREP suite: predictive RNA editors for plant mitochondrial genes, chloroplast genes and user-defined alignments

(2009) J. P. Mower   NUCLEIC ACIDS RESEARCH

RESOPS: A Database for Analyzing the Correspondence of RNA Editing Sites to Protein Three-Dimensional Structures

(2009) Kei Yura et al.   PLANT AND CELL PHYSIOLOGY

Fine-scale mergers of chloroplast and mitochondrial genes create functional, transcompartmentally chimeric mitochondrial genes

(2009) W. Hao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Did RNA editing in plant organellar genomes originate under natural selection or through genetic drift?

(2008) Richard W Jobson et al.   Biology Direct

Correlation between amino acid residues converted by RNA editing and functional residues in protein three-dimensional structures in plant organelles

(2008) Kei Yura et al.   BMC PLANT BIOLOGY

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

(2008) Anja Zehrmann et al.   MITOCHONDRION

Genetic Architecture of Mitochondrial Editing in Arabidopsis thaliana

(2007) S. Bentolila et al.   GENETICS