High transcript abundance, RNA editing, and small RNAs in intergenic regions within the massive mitochondrial genome of the angiosperm Silene noctiflora

Organellar non-coding RNAs: Emerging regulation mechanisms

(2015) André Dietrich et al.   BIOCHIMIE

Surveillance and Cleavage of Eukaryotic tRNAs

(2015) Cyrille Megel et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Dynamic evolution ofGeraniummitochondrial genomes through multiple horizontal and intracellular gene transfers

(2015) Seongjun Park et al.   NEW PHYTOLOGIST

Miniaturized mitogenome of the parasitic plantViscum scurruloideumis extremely divergent and dynamic and has lost allnadgenes

(2015) Elizabeth Skippington et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mosaic nature of the mitochondrial proteome: Implications for the origin and evolution of mitochondria

(2015) Michael W. Gray   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The massive mitochondrial genome of the angiospermSilene noctiflorais evolving by gain or loss of entire chromosomes

(2015) Zhiqiang Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   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

Paternally Transmitted Mitochondria Express a New Gene of Potential Viral Origin

(2014) Liliana Milani et al.   Genome Biology and Evolution

History of Plastid DNA Insertions Reveals Weak Deletion and AT Mutation Biases in Angiosperm Mitochondrial Genomes

(2014) Daniel B. Sloan et al.   Genome Biology and Evolution

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

(2014) Felix Grewe et al.   MITOCHONDRION

DNA-binding proteins in plant mitochondria: Implications for transcription

(2014) José M. Gualberto et al.   MITOCHONDRION

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

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

Homologous recombination and retention of a single form of most genes shape the highly chimeric mitochondrial genome of a cybrid plant

(2014) M. Virginia Sanchez-Puerta et al.   NEW PHYTOLOGIST

Defining functional DNA elements in the human genome

(2014) M. Kellis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA Editing in Plants and Its Evolution

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

The mitochondrial genome encodes abundant small noncoding RNAs

(2013) Seungil Ro et al.   CELL RESEARCH

On the Immortality of Television Sets: "Function" in the Human Genome According to the Evolution-Free Gospel of ENCODE

(2013) D. Graur et al.   Genome Biology and Evolution

A Comparative Analysis of Mitochondrial ORFans: New Clues on Their Origin and Role in Species with Doubly Uniparental Inheritance of Mitochondria

(2013) Liliana Milani et al.   Genome Biology and Evolution

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

Transcription of atp1 is influenced by both genomic configuration and nuclear background in the highly rearranged mitochondrial genomes of Silene vulgaris

(2013) Karel Müller et al.   PLANT MOLECULAR BIOLOGY

Is junk DNA bunk? A critique of ENCODE

(2013) W. F. Doolittle   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2013) D. W. Rice et al.   SCIENCE

Mitochondria: One of the destinations of miRNAs

(2012) Lakshmi Sripada et al.   MITOCHONDRION

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The mitochondrial genome of Malus domestica and the import-driven hypothesis of mitochondrial genome expansion in seed plants

(2012) Vadim V. Goremykin et al.   PLANT JOURNAL

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

(2012) Yongjun Fang et al.   PLoS One

Rapid Evolution of Enormous, Multichromosomal Genomes in Flowering Plant Mitochondria with Exceptionally High Mutation Rates

(2012) Daniel B. Sloan et al.   PLOS BIOLOGY

A unique horizontal gene transfer event has provided the octocoral mitochondrial genome with an active mismatch repair gene that has potential for an unusual self-contained function

(2011) Jaret P Bilewitch et al.   BMC EVOLUTIONARY BIOLOGY

Transcriptome map of plant mitochondria reveals islands of unexpected transcribed regions

(2011) Sota Fujii et al.   BMC GENOMICS

A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa)

(2011) Lu Wang et al.   BMC GENOMICS

The Human Mitochondrial Transcriptome

(2011) Tim R. Mercer et al.   CELL

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Origins and Recombination of the Bacterial-Sized Multichromosomal Mitochondrial Genome of Cucumber

(2011) A. J. Alverson et al.   PLANT CELL

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

Low Nucleotide Diversity for the Expanded Organelle and Nuclear Genomes of Volvox carteri Supports the Mutational-Hazard Hypothesis

(2010) D. R. Smith et al.   MOLECULAR BIOLOGY AND 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

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

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

Coping with cryptic and defective transcripts in plant mitochondria

(2008) S HOLEC et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms