Cytonuclear Interactions and Relaxed Selection Accelerate Sequence Evolution in Organelle Ribosomes

Tuning a ménage à trois: Co-evolution and co-adaptation of nuclear and organellar genomes in plants

(2013) Stephan Greiner et al.   BIOESSAYS

Optimizing de novo assembly of short-read RNA-seq data for phylogenomics

(2013) Ya Yang et al.   BMC GENOMICS

Succinate dehydrogenase: the complex roles of a simple enzyme

(2013) Shaobai Huang et al.   CURRENT OPINION IN PLANT BIOLOGY

Mitochondrial–Nuclear Interactions: Compensatory Evolution or Variable Functional Constraint among Vertebrate Oxidative Phosphorylation Genes?

(2013) Feifei Zhang et al.   Genome Biology and Evolution

An Incompatibility between a Mitochondrial tRNA and Its Nuclear-Encoded tRNA Synthetase Compromises Development and Fitness in Drosophila

(2013) Colin D. Meiklejohn et al.   PLoS Genetics

Recent Acceleration of Plastid Sequence and Structural Evolution Coincides with Extreme Mitochondrial Divergence in the Angiosperm Genus Silene

(2012) Daniel B. Sloan et al.   Genome Biology and Evolution

Quantifying the Elevation of Mitochondrial DNA Evolutionary Substitution Rates Over Nuclear Rates in the Intertidal Copepod Tigriopus californicus

(2012) Christopher S. Willett   JOURNAL OF MOLECULAR EVOLUTION

Comparative Genomics Reveals Adaptive Protein Evolution and a Possible Cytonuclear Incompatibility between European and American Eels

(2012) Pierre-Alexandre Gagnaire et al.   MOLECULAR BIOLOGY AND EVOLUTION

High Levels of Gene Expression Explain the Strong Evolutionary Constraint of Mitochondrial Protein-Coding Genes

(2012) B. Nabholz et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evidence for Compensatory Evolution of Ribosomal Proteins in Response to Rapid Divergence of Mitochondrial rRNA

(2012) F. S. Barreto et al.   MOLECULAR BIOLOGY AND EVOLUTION

A disproportionate role for mtDNA in Dobzhansky-Muller incompatibilities?

(2012) Ronald S. Burton et al.   MOLECULAR ECOLOGY

Intraspecific variation in mitochondrial genome sequence, structure, and gene content inSilene vulgaris, an angiosperm with pervasive cytoplasmic male sterility

(2012) Daniel B. Sloan et al.   NEW PHYTOLOGIST

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

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

Mitochondrial–Nuclear Interactions and Accelerated Compensatory Evolution: Evidence from the Primate Cytochrome c Oxidase Complex

(2011) Naoki Osada et al.   MOLECULAR BIOLOGY AND EVOLUTION

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

The Arabidopsis lyrata genome sequence and the basis of rapid genome size change

(2011) Tina T Hu et al.   NATURE GENETICS

Whole-genome sequencing of multiple Arabidopsis thaliana populations

(2011) Jun Cao et al.   NATURE GENETICS

Phytozome: a comparative platform for green plant genomics

(2011) David M. Goodstein et al.   NUCLEIC ACIDS RESEARCH

Extensive loss of translational genes in the structurally dynamic mitochondrial genome of the angiosperm Silene latifolia

(2010) Daniel B Sloan et al.   BMC EVOLUTIONARY BIOLOGY

Estimation of the Neutrality Index

(2010) N. Stoletzki et al.   MOLECULAR BIOLOGY AND EVOLUTION

The energetics of genome complexity

(2010) Nick Lane et al.   NATURE

Cytoplasmic phylogeny and evidence of cyto-nuclear co-adaptation in Arabidopsis thaliana

(2010) Michaël Moison et al.   PLANT JOURNAL

Functional and Evolutionary Insights from the Genomes of Three Parasitoid Nasonia Species

(2010) J. H. Werren et al.   SCIENCE

SOAP2: an improved ultrafast tool for short read alignment

(2009) R. Li et al.   BIOINFORMATICS

Ribosomal protein L10 is encoded in the mitochondrial genome of many land plants and green algae

(2009) Jeffrey P Mower et al.   BMC EVOLUTIONARY BIOLOGY

The erratic mitochondrial clock: variations of mutation rate, not population size, affect mtDNA diversity across birds and mammals

(2009) Benoit Nabholz et al.   BMC EVOLUTIONARY BIOLOGY

Phylogenetic analysis of mitochondrial substitution rate variation in the angiosperm tribe Sileneae

(2009) Daniel B Sloan et al.   BMC EVOLUTIONARY BIOLOGY

Discovery of the rpl10 Gene in Diverse Plant Mitochondrial Genomes and Its Probable Replacement by the Nuclear Gene for Chloroplast RPL10 in Two Lineages of Angiosperms

(2009) N. Kubo et al.   DNA RESEARCH

The Functional Transfer of Genes From the Mitochondria to the Nucleus: The Effects of Selection, Mutation, Population Size and Rate of Self-Fertilization

(2009) Yaniv Brandvain et al.   GENETICS

Comparative Analysis of Structural Diversity and Sequence Evolution in Plant Mitochondrial Genes Transferred to the Nucleus

(2009) S.-L. Liu et al.   MOLECULAR BIOLOGY AND EVOLUTION

The causes of mutation accumulation in mitochondrial genomes

(2009) M. Neiman et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Plastid Evolution

(2008) Sven B. Gould et al.   Annual Review of Plant Biology

Incompatibility of Nuclear and Mitochondrial Genomes Causes Hybrid Sterility between Two Yeast Species

(2008) Hsin-Yi Lee et al.   CELL

Rapidly Evolving Mitochondrial Genome and Directional Selection in Mitochondrial Genes in the Parasitic Wasp Nasonia (Hymenoptera: Pteromalidae)

(2008) D. C. S. G. Oliveira et al.   MOLECULAR BIOLOGY AND EVOLUTION

Relative rates of synonymous substitutions in the mitochondrial, chloroplast and nuclear genomes of seed plants

(2008) G DROUIN et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

PPDB, the Plant Proteomics Database at Cornell

(2008) Qi Sun et al.   NUCLEIC ACIDS RESEARCH

A genome-wide view of the spectrum of spontaneous mutations in yeast

(2008) M. Lynch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Direct Estimation of the Mitochondrial DNA Mutation Rate in Drosophila melanogaster

(2008) Cathy Haag-Liautard et al.   PLOS BIOLOGY